United States
     Environmental Protection           EPA/600/R-06/163
     Agency                      December 2006
  ANNOTATED BIBLIOGRAPHY
OF HISTORICAL CONDITIONS IN
    STREAMS AND RIVERS OF
 THE WESTERN  UNITED STATES
    OFFICE OF RESEARCH AND DEVELOPMENT
           WASHINGTON D.C.

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                                                   EPA/600/R-06/163
                                                       December 2006
              ANNOTATED BIBLIOGRAPHY
OF HISTORICAL CONDITIONS IN STREAMS AND RIVERS
           OF THE WESTERN UNITED STATES


                        Compiled by
                     Lynne S. McAllister
                       Sandra A. Bryce
                    Shannon S. Chapman
                       Peter D. Lattin

                     Dynamac Corporation
     National Health and Environmental Effects Research Laboratory
                    Western Ecology Division
                      200 SW 35th Street
                     Corvallis, OR, 97333
                     Contract EP-D-06-013

         Work Assignment Contracting Officer Representative
                        Paul Ringold
               U.S. Environmental Protection Agency
     National Health and Environmental Effects Research Laboratory
                    Western Ecology Division
                     Corvallis, OR 97333
    ENVIRONMENTAL MONITORING AND ASSESSMENT PROGRAM
  NATIONAL HEALTH AND ENVIRONMENTAL EFFECTS LABORATORY
           OFFICE OF RESEARCH AND DEVELOPOMENT
           U.S. ENVIRONMENTAL PROTECTION AGENCY

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Abstract

       Resource managers are often challenged by the lack of adequate benchmarks, or
reference conditions, for assessing the biological condition of streams. Increasing human
alteration of landscapes reduces the availability of minimally-disturbed stream sites that can be
used to represent a reference condition in regional assessments.  Historical data offer an
alternative point of reference for gauging the relative deviation of current conditions from an
established minimally-disturbed condition and can thereby contribute to better-informed
management decisions within the context of present-day land uses and range of attainable
conditions.  This collection of over 150 annotated references represents a significant portion of
the literature that reports historical conditions and changes due to human impacts that have
occurred since European settlement relevant to fish, aquatic insects, amphibians, and physical
habitat. Its intent is to  provide sources of information for those involved in historical
reconstructions of stream  conditions. Key references providing the most comprehensive
syntheses at basin or regional scales in the western United States were selected for the
bibliography.  Bibliographic subsections are tailored toward EPA's Environmental Monitoring
and Assessment Program (EMAP), although the information  should be useful in a wide range of
environmental assessments and restorations that address basin- or regional-scale stream
conditions.
Notice

The information in this document has been funded wholly or in part by the U.S.
Environmental Protection Agency under Contracts 68-D-01-005 and EP-D-06-013 to
Dynamac Corporation.  It has been subject to review by the National Health and
Environmental Effects Research Laboratory and approved for publication. Approval
does not signify that the contents reflect the views of the Agency, nor does mention
of trade names or commercial products constitute endorsement or recommendation
for use.
Preferred Citation:

McAllister, L.S., S.A. Bryce, S.S. Chapman, and P.O. Lattin. 2007. Annotated Bibliography of
Historical Conditions in Streams and Rivers of the Western United States. EPA/600/R-06/163.
U.S. Environmental Protection Agency, Office of Research and Development, National Health
and Environmental Effects Research Laboratory, Washington, D.C.
                                           11

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                                      PREFACE

       This collection of annotated references represents a significant portion of the literature
that reports historical conditions and changes due to human impacts that have occurred since
European settlement relevant to fish, aquatic insects, amphibians, and physical habitat
(including riparian vegetation). The geographic scope of the literature includes  12 western
states comprising the assessment area for the Environmental  Monitoring and Assessment
Program's Western Pilot Study (EMAP-West), encompassing  EPA Regions 8-10.
       This project grew out of the need for benchmarks, summaries, and ancillary information
about minimally disturbed conditions that could enhance EMAP-West assessments of current
stream condition.  However, the information should apply to a  variety of environmental
assessments and restorations that are conducted at a basin or regional scale. It is particularly
relevant in regions that have undergone extensive land-use alterations and where existing least-
disturbed  reference sites may set unrealistically low reference benchmarks, resulting in
inadequate protection of the resource.  Historical data can provide a model of regional
ecosystem bio-integrity that can be used to assess the relative deviation of present day stream
condition from a pre-settlement, or minimally disturbed, condition.  The data are not intended for
re-creating historical conditions and landscapes but, rather, they offer a point of reference for
making better-informed management decisions within the context of present-day land uses and
range of attainable conditions.

Content and Format
       The bibliography includes primary literature sources (e.g., results of historical fish
surveys conducted in the 19th century), as well as more current literature syntheses that report
changes from the historical condition (e.g., estimated declines in fish populations) and the
causes of the changes. References report conditions and changes over broad regions or river
basins. Publications reporting results of small-scale or site-specific studies (e.g., stream
segments in a single drainage) are not included. Instead of including every reference identified
for a specific topic (e.g., salmon losses in the Columbia River  basin), we attempted to select key
publications that provided the broadest and most thorough syntheses of historical data or
changes from the historical condition.  Cited publications include historical documents, journal
articles, books and book chapters, reports, web sites,  and gray literature.  Gray literature was
considered valuable since it comprises numerous syntheses of changes in historical ranges and
populations, which was precisely the topic of interest for this project. As in any  use of gray
literature,  therefore,  it should be applied accordingly.
       When possible,  bibliographic entries report a minimally disturbed condition, defined as
pre-settlement or early settlement (i.e., 19th century). Since much of the earliest documentation
of stream  conditions was not made until the 20th century, later publications are also included in
the bibliography. This is particularly true for the macroinvertebrate literature,  much of which did
not appear until the mid-1900s.  In addition,  literature that contrasts a perceived minimally
disturbed  condition with a changed condition is also included.  For example, dam construction in
the Colorado River basin beginning in the 1930s drastically changed native fish habitat and
populations, which were considered relatively unchanged prior to that time. To  a limited extent,
literature that contrasts before/after conditions in a more recent time period are  also included,
for example, large-scale studies of fish assemblages and stream habitat in logged vs. unlogged
watersheds within relatively undisturbed forests.
       References focus on stream  habitats, although a broader landscape perspective is often
found in the literature for the Plains aggregated ecoregion because of the intermittent nature of
most streams and a closer association between stream and non-stream habitats in that region.
Also, early (pre-settlement) stream surveys in the Plains ecoregion are rare or non-existent, so
                                           in

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historical stream conditions may have to be inferred from characteristics of the broader
landscape.
       The annotated portion of each reference contains five summary fields: abstract (when
available), geographic location (see below for descriptors), value of the reference, results
relevant to EMAP, and keywords.  The 'value of the reference' field describes the general topic
of the publication and why it is considered useful for EMAP applications. It also may include the
type of publication (e.g., historical survey results vs. current synthesis), the format in which
information is presented, the degree of data synthesis already done, and the prominence of the
work in the literature. The 'results relevant to EMAP field briefly summarizes the major points
or findings of the publication relevant to EMAP topics of interest. Its purpose is to help the user
determine whether the publication is worth  acquiring and reading in further detail. The
'geographic location' field includes state, river basin, EPA ecoregion level III, EPA administrative
region, and EPA aggregate ecoregion (mountains, xeric, plains). The  'keywords' field specifies
the affected attribute (physical habitat, fish, macroinvertebrates, etc.) and the human impacts
that caused the change to historical condition.
       References are listed alphabetically. Within each citation, a number of search variables
are included in the geographic location and keyword fields to allow a user to more easily find
references for specific geographic areas, human disturbances, and impacted biota using the
"Find" function in the edit menu. The following lists show, in italics, potential search variables in
each category.

    •  Geographic Location

       State: Arizona, California, Colorado, Idaho, Montana, Nevada, North Dakota, Oregon,
       South Dakota, Utah, Washington, Wyoming

       EPA administrative region: region 'x' (e.g., region 8)

       EPA level III ecoregion: Eco'xx' (e.g., eco20)

       EMAP aggregate ecoregion:  mountains, plains, xeric

       River basin:  'xxxxxx' basin (major basins such as the Columbia River basin, Colorado
       River basin, or river tributaries within major basins, e.g.,  Snake River basin, Gila River
       basin)
      Keywords

       Human disturbances—activities that have brought about changes in streams or biota:
             grazing
             agriculture
             mining
             roads
             dams
             fishing (commercial or sport)
             nonnative species
             recreation
             urban
             water diversion
             channelization
                                           IV

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             groundwater pumping
             general (referring to any human impact; non-specific)

       Impacted Attribute:
             fish
             macro! nvertebrates
             amphibians
             riparian vegetation
             phab (physical habitat)
Application
       Information in the publications cited in this bibliography can be applied in a variety of
basin- or regional-scale assessments and restorations. Two examples of using the bibliography
in the context of EMAP stream assessments are illustrated here.

Riparian Vegetation in the Missouri River Basin
       Historical documentation indicates that, with the exception of badlands, riparian habitats
in the Northwestern Great Plains (Ecoregion 43; Missouri River basin) were composed largely of
forest and shrub  habitats prior to settlement (Warren 1856, Evermann and Cox 1896, Johnson
1992, Rumble et al. 1998). Descriptions in these references note extensive forests dominated
by cottonwood and willow; "extensive native woodlands"; canyons filled with deciduous trees
including cottonwood, willow, ash, oak, and wild plum; heavily-forested floodplains; "abundance
of wood"; "swarms of beaver"; "excellent timber of ash, oak, elm, and box-elder". At least-
disturbed reference sites in Ecoregion 43 today, however, EMAP physical habitat
measurements show that riparian canopy averages only 4% of the riparian cover. Total riparian
woody cover (the sum of woody cover in each of three vegetation layers, with highest potential
value of 300% due to overlapping layers) averages just 41%, less than half of today's total
riparian  cover including herbaceous species. This comparison suggests that  canopy cover at
least-disturbed sites is much less than what would be expected based on historical
documentation, and that woody vegetation as a proportion of the total is likely under-
represented.

Fish Assemblage Biotic Integrity in the South Platte River basin.
      Another useful application of historical information is in the development of multimetric
indices of biotic integrity (IBIs), which translate biological indicator abundance data into a
numeric score to evaluate stream condition.  In a highly altered region, historical information can
be used to set expectations for the number of species that would have been found in minimally
disturbed ecosystems of the region (Hughes et al.  1998). For example, EMAP field crews
sampled 23 native species of fish at 19 sites on the upper South  Platte River  in the foothills of
the Rocky Mountains of Colorado.  In a paper that reviewed historical collections on the South
Platte River, Probst and Carlson (1986) determined that three fish species had been extirpated
from the South Platte basin and several others were now rare.  Seven of these historically
recorded species were not collected during the EMAP-West survey.  If we were to construct an
IBI for the South  Platte basin, we might increase the total number of species from 23 to 30 to
more closely represent a state of biointegrity. Since total number of species is the denominator
in species proportionate metrics (for example, % tolerant species or  % native vagile species), all
such metrics would be scored somewhat lower than  metrics based on present day field data
alone, and the lower IBI score would more accurately reflect the departure of  sites in developed
regions from a minimally disturbed condition.

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                        ANNOTATED BIBLIOGRAPHY
Author: Abruzzi, W., others
Year: 2002
Title: Riparian Area Loss and Degradation
Reference Type: Electronic Source
Access Year: 2005
Access Date: July 25

Value of reference: Web site addresses reduction in riparian areas, the causes, and
associations between losses and fish distribution.  It proposes a link between native fish
presence and intact riparian areas.  The focus of numerous other publications is on the
devastating effects of river regulation and introduced species on the Colorado River native
fishery; this overview proposes that the presence of healthy riparian areas seems related to the
survival of some of the only remaining populations of native fish.

Results relevant to EMAP: Overall, a 90% loss of pre-settlement riparian ecosystems has
occurred in Arizona and New Mexico, beginning in the early 19th century with the near
extirpation of the beaver.

As a result of various human-related impacts, water tables are lowered, surface sediments are
desiccated, channels are less complex and more static,  erosion increases, suitable habitat for
establishment of riparian vegetation such as cottonwood and willow is limited, and plant
community structure changes.

The few remaining fish stocks native to smaller riparian systems on the Plateau survive only in
those areas with intact riparian habitats, often in remote upper-elevation watersheds.

Geographic location: Colorado Plateau, xeric,  Arizona, New Mexico,  eco20, eco21, eco22,
eco23, EPA  Region 9

Keywords: phab, fish, riparian vegetation, beaver, dams, agriculture, channelization, grazing,
logging, nonnative species, roads, urban

URL: http://www.cpluhna.nau.edu/Biota/riparian degradation.htm

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Author: Adams, S. B.; Frissell C.A.; Rieman, B.E.
Year: 2001
Title: Geography of invasions in mountain streams: consequences of headwater lake fish
introductions
Reference Type: Journal Article
Journal: Ecosystems
Volume: 2001
Pages: 296-307

Value of reference: This paper reviews the potential consequences of fish introductions into
headwater streams and lakes in the western United States, and the nature of the impacts upon
downstream aquatic ecosystems. A review of the literature is provided describing the
consequences of nonnative fish species invasions  in higher elevation mountainous regions.

The authors suggest that knowledge of the differential effectiveness of barriers can be used  in
conjunction with stocking history to interpret where stocking activities may have had impacts
upon native ichthyofauna, macroinvertebrates, and amphibians. This information can be of
value for interpreting the quality of vertebrate faunal metrics, particularly for stream reference
sites.

Results relevant to EMAP: Headwater streams historically provided refuges for native fish,
amphibians and aquatic macroinvertebrates. Approximately 95% of all high-mountain lakes in
the western United States lie above Pleistocene-age barriers to fish dispersal (Bahls 1992).
Where native fish species existed, stream dispersal barriers have prevented influences of
downstream communities which have been impacted by intentional and unintentional fish
introductions. Downstream dispersal offish is more effective than upstream dispersal,
consequently upstream or isolated drainages represent refugia for both native fish and non-fish
fauna such as amphibians and  invertebrates.

Intentional and accidental introduction offish species such as brook trout (Salvalinus fontinalis)
have occurred at upper elevations throughout the west since the late 1800s. Such introductions
have impacted native fauna through a wide range of mechanisms, and have often led to
displacement. Brook trout (S. fontinalis), for example, have been implicated in the displacement
of both native bull trout (Salvalinus confluentus) and cutthroat trout (Oncorhynchus clarki).

Geographic location: Region 8, Region 9, Idaho,  Montana, Rocky Mountains, MOUNTAINS,
MT-NROCK, SF Salmon River, eco15, eco16, Northern Rockies,  Idaho Batholith

Keywords: fish; invasion; dispersal; landscape; demography; conservation; nonnative species;
salmonids; lake; stream;  Columbia River basin; Idaho, Montana

Abstract: The introduction offish into high-elevation lakes can provide a geographic
and demographic boost to their invasion of stream  networks,  thereby further endangering the
native stream fauna. Increasingly remaining populations of native salmonids are concentrated in
fragmented headwater refugia that are protected by physical or biological barriers from
introduced fishes that originate in the pervasive source populations established at lower
elevations. Although fish introduced near mainstem rivers frequently encounter obstacles to
upstream dispersal, such as steep slopes or falls, we found brook trout (Salvelinus fontinalis)
dispersed downstream through channel slopes of 80% and 18-m-high falls. Thus,  headwater
lake  stocking  provides source populations that may be capable of invading most downstream
habitats, including headwater refugia of native fishes. The extent of additional area invasible

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from lakes, beyond that invasible from downstream, depends on the geography of the stream
network, particularly the density and distribution of headwater lakes and their location relative to
barriers inhibiting upstream dispersal. In the thermal and trophic environments downstream of
lakes, fish commonly grow faster and thus mature earlier and have higher fecundity-at-age than
their counterparts in other high-elevation streams. The resulting higher rates of population
growth facilitate invasion. Larger body sizes also potentially aid the fish in overcoming barriers
to invasion. Trout introductions to high-elevation headwater lakes thus pose disproportionately
large risks to native fishes - even when the place of introduction may appear to be spatially
disassociated from populations of the native species. Mapping the potential invasible area can
help to establish priorities in stocking and eradication efforts.

Notes: Bahls, P. 1992. The status offish populations and management of high mountain lakes
in the western United States. Northwest Science 66:183-93

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Author: Arizona Game and Fish Department
Year: 1994
Title: Gila Chub (G/7a intermedia), unpublished abstract
Reference Type: Electronic Source
Producer: Heritage Data Management System, Arizona Game and Fish Department
Access Year: 2005
Access Date: October 6
Last Update Date: December 4, 2002

Value of reference:  This is a short synopsis of this species, which includes a short description
of its historical and current distribution. It is useful for defining the historical range of the species
and estimating the proportion of it that is no longer occupied.

Results relevant to  EMAP: Historically the Gila chub was found in headwater streams of the
Gila River in Arizona, New Mexico and likely in Sonora, Mexico.  It is currently considered
extirpated from New  Mexico and from 3 waterways in AZ: Cave Creek, Fish Creek, and Monkey
Spring.   This report lists a number of creeks in Arizona where it is still found. The Gila chub
was commonly found in  association with Gila topminnow, desert and Sonora sucker and longfin
and speckled dace.

Populations have slowly been disappearing but are expected to fluctuate with habitat changes
due to climatic events. Threats to this species  include aquifer pumping, stream diversion,
reduced flows, habitat alteration, competition by nonnative crayfishes and competition and
predation by nonnative fishes

Geographic location: Arizona, EPA Region 9, eco22, eco23, xeric, Gila River basin

Keywords: fish, water diversion, groundwater pumping, impoundment, nonnative species,
habitat degradation

URL: http://www.gf.state.az.us7w c/edits/documents/Gilainte.fo 001.pdf

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Author: Beechie, T.; Beamer, E.; Wasserman, L.
Year: 1994
Title: Estimating coho salmon rearing habitat and smolt production losses in a large river basin,
and implications for habitat restoration
Reference Type: Journal Article
Journal: North American Journal of Fisheries Management
Volume: 14
Pages: 797-811

Value of reference: An extremely valuable reference that uses the historical record to estimate
the loss of summer and winter coho salmon rearing habitats and the associated loss of coho
smolt production for the entire Skagit River basin. In addition, the amount of lost habitat was
apportioned to particular land use impacts, an analysis that is not often seen.

Results relevant to EMAP: See abstract for loss of coho smolt production.

Early hydromodifications on the Skagit River, such as diking, dredging, and damming, caused
comparatively larger losses of physical habitat areas than more recent modifications, which are
more incremental impacts from multiple activities such as timber harvest, flood protection, and
residential and urban development.

Prior to settlement the river wandered freely over its floodplain creating new side channels,
oxbows, sloughs, and wetlands. In the lower river valley over 25% of the floodplain and delta
area consisted of beaver ponds, sloughs,  and wetlands.(The authors were  not able to estimate
lost beaver pond area.)  Diking and reclaiming the land for agriculture began in the early 1860's.
The lower elevation uplands were logged  in the early 20th Century; reports as early as 1921
reported habitat degradation and loss due to logging and hydroelectric dams.

The largest estimated losses in habitat area and smolt production have occurred in the side-
channel and distributary sloughs. Over 115 km - nearly 700,000 m2 - of Skagit River side
channel and distributary sloughs have been eliminated in the past century.

Geographic location: mountains, eco2, eco77, Skagit River basin,  Puget Sound, EPA Region
10

Keywords: salmonids, rivers, fish habitat, fish losses, coho salmon, agriculture, urban,
channelization, dredging, logging, phab

Abstract: To develop a habitat restoration strategy for the 8270 km2 Skagit River basin, we
estimated changes in smolt production of coho salmon (Oncorhynchus kisutch) since European
settlement began in the basin, based on changes in summer and winter rearing habitat areas.
We assessed changes in coho salmon smolt production by habitat type and by cause of habitat
alteration. We estimated that the coho salmon smolt production capacity of summer habitats in
the Skagit River basin has been reduced from 1.28 million smolts to 0.98 million smolts (-24%)
and that the production  capacity of winter  habitats has been reduced from 1.77 million to 1.17
million smolts (-34%). The largest proportion of summer non-main-stem habitat losses has
occurred in side-channel sloughs (41%), followed by losses in  small tributaries (31%) and
distributary sloughs (29%). The largest loss of winter habitats has occurred in side-channel
sloughs (52%), followed by losses in distributary sloughs (37%) and small tributaries (11%). By
type  of impact, hydromodification (diking, ditching, dredging) associated with agricultural and
urban lands accounts for 73% of summer  habitat losses and 91% of winter habitat losses. [33]

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Blocking culverts on [37 km of] small tributaries account for 13% of the decrease in summer
habitat and 6% of the decrease in winter habitat. Forestry activities account for 9% of summer
habitat losses and 3% of winter habitat losses. Limitations of the analysis and implications for
developing a habitat restoration strategy are discussed.

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Author: Behnke, R.J.
Year: 1992
Title: Native Trout of Western North America
Reference Type: Book
City: Bethesda, MD
Publisher: American Fisheries Society, Monograph 6
Number of Pages: 275

Value of reference: Book presents baseline information about historical presence by basin of
native trout (given for most species in the Distribution subsection).  Information can be further
used to assist in reconstructing historical trout occurrence and distribution in basins throughout
the West.

This reference is frequently cited and used. For example, the Interior Columbia Basin
Ecosystem Management Project (ICBEMP) used it to help define the historical ranges offish
species in the Interior Columbia Basin (see Lee et al.  1997, in this bibliography). Availability of
historical information is inconsistent among species, and it takes some piecing together of text
to isolate portions that are relevant to pre-settlement distributions.  Nevertheless, this work
seems to be a significant synopsis of trout species in the West.

Results relevant to EMAP: This book gives species-by-species distributions, original native
ranges (in some cases, but presented with different details) and status of western trout species.
Summaries also include  trout occurrence in lakes. Text is somewhat laborious for EMAP
purposes,  but presents good information about historical presence by basin and whether native
or exotic (i.e., many trout species have been introduced into streams where they did not occur
historically). This information would be valuable if there was an interest or need to know the
historic occurrences of trout species in river basins of the West in order to determine whether
trout of a particular basin have been introduced or are native or to assist in reconstructing  pre-
settlement fish communities. Bulk of book is text, but also includes a few maps and illustrations.

Geographic location: westwide distributions of multiple species of trout

Keywords: fish, trout, historical distribution, status, xeric, mountain, westwide

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Author: Bilby, R. E.; Ward, J. W.
Year: 1991
Title: Characteristics and function of large woody debris in streams draining old-growth, clear-
cut, and second-growth forests in southwestern Washington
Reference Type: Journal Article
Journal: Canadian Journal of Fisheries and Aquatic Sciences
Volume: 48
Pages: 2499-2508

Value of reference: This article compares woody debris at present day minimally disturbed
sites with that at logged sites. By examining the characteristics of large woody debris in streams
bordered by forests of different age classes, the authors document the ways in which large
woody debris volume changes following timber removal from the riparian area. They also record
the influence of large woody debris on stream channel morphology. A companion article to
Bisson et al.  1987 which relates old growth large woody debris distribution to salmon biomass.

Results relevant to EMAP: Plunge pools formed by large woody debris were significantly more
common at old-growth  sites than at second-growth sites for all stream-size classes and at clear-
cut sites in streams < 7 m wide. The frequency of large woody debris associated pools
decreased with increasing stream size for all three stand age classes, but was significantly
greater at  old growth sites than at the other two stand age classes. Average pool surface  area
was significantly greater in streams > 10 m wide at old growth sites.

Geographic location: Pacific Northwest, Wllapa Hills, southwest Washington, western
Cascades, ecol, eco4, EPA Region 10, mountains

Keywords: phab,  large woody debris, sediments, logging,  fish, pools, salmonids

Abstract:  Amount of large woody debris (LWD) surveyed in 70 stream reaches flowing through
old-growth, clear-cut, and second-growth forests decreased with increasing stream size for all
stand types but was greatest at old-growth sites. Average piece volume was larger at old-growth
sites than  at other stand types in streams > 10 m wide, but no differences were seen in smaller
streams. Scour pools accounted for 90% of the wood-associated pools at second-growth  and
clear-cut sites but  only 50% at old-growth sites, which  contained more pools than other stand
types, particularly for larger streams. Pool size was similar for all stand types in smaller streams,
but averaged 10 m2 in streams > 10 m wide at old-growth sites and 4 m2 for other stand types.
Sediment and fine organic matter retained by woody debris decreased with increasing stream
size for all stand types, but old-growth sites contained  greater amounts of both materials than
other stand types.  The frequency of pool formation, the type of pool formed, and sediment
accumulation were influenced by the amount of fine debris associated with LWD. Changes in
LWD amount, characteristics, and function occurred very rapidly following removal of
streamside vegetation.

Notes: This reference is a companion article to Bisson et al. 1987 which relates old growth large
woody debris distribution to salmon biomass.

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Author: Birken, A.S.; Cooper, D.J.
Year: 2006
Title: Processes of Tamarix invasion and floodplain development along the lower Green River,
Utah
Reference Type: Journal Article
Journal: Ecological Applications
Volume: 16
Issue: 3
Pages:  1103-1120

Value of reference: The study attempted to determine the cause and role of the invasion of
Tamarix with the intent of 1) providing insights into when, how, and why recent fluvial
adjustments may have occurred and 2) assessing the influence of exotic plant invasions in
altering  geomorphic and ecological processes, which have implications for river restoration
efforts.  It is notable for its finding that Tamarix invasion did not start because of river regulation.

The paper gives background on how Tamarix has changed southwestern riparian areas and
altered hydrogeomorphological processes. It is also an example of how historical information
can be used to address current resource management issues.

Results relevant to EMAP: Throughout the Southwest, floodplain vegetation was historically
dominated by Fremont cottonwood (Populus deltoides), but Populus has declined during the
20th century, while Tamarix has invaded and now dominates most floodplain ecosystems,
displacing native vegetation and reducing diversity. The invasion of Tamarix has altered the
hydraulic characteristics of floodplain surfaces, causing many rivers in the southwest to accrete
and narrow.  The invasion coincided with reduced flows and sediment transport in the mid-20th
century  caused by climate fluctuation, so it is difficult to determine whether Tamarix drove the
fluvial adjustments or whether it benefited from climate-or dam-induced reductions in peak flows
and sediment transport.

An increase in Tamarix establishment is more likely when peak flow is substantially lower in the
year following recruitment.   Tamarix began invading long before river regulation. Other factors,
such as multiple years of low flows and changing precipitation patterns in the 1930s, allowed it
to invade a previously unoccupied niche with little competition from native vegetation.  By 1951,
Tamarix had already occupied nearly all the floodplain area it presently occupies. It decreased
flow velocities and stabilized floodplain  landforms long before construction of Flaming Gorge
Dam; the species established and proliferated in unregulated river conditions. The return of
larger floods in the 1950s did not result in the erosion of landforms that Tamarix then occupied
because of its dense growth and anchoring ability.

Geographic location: Utah, Green River basin, EPA region  8, eco20,  xeric

Keywords: phab,  riparian vegetation, climate fluctuation, invasion, channel narrowing, exotic
plants, floodplain development, river regulation, Populus deltoides, Tamarix ramosissima.

Abstract: Significant ecological, hydrologic, and geomorphic changes have occurred during the
20th century along many large floodplain rivers in the American Southwest. Native Populus
forests have declined, while the exotic Eurasian shrub, Tamarix, has proliferated and now
dominates most floodplain ecosystems. Photographs from late 19th and early 20th centuries
illustrate wide river channels with largely bare in-channel landforms and shrubby higher channel
margin floodplains. However, by the mid-20th century, floodplains supporting dense Tamarix

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stands had expanded, and river channels had narrowed. Along the lower Green River in eastern
Utah, the causal mechanism of channel and floodplain changes remains ambiguous due to the
confounding effects of climatically driven reductions in flood magnitude, river regulation by
Flaming Gorge Dam, and Tamarix invasion. This study addressed whether Tamarix
establishment and spread followed climate- or dam-induced reductions in annual peak flows or
whether Tamarix was potentially a driver of floodplain changes. We aged 235 Tamarix and  57
Populus individuals, determined the hydrologic and geomorphic processes that controlled
recruitment, identified the spatial relationships of germination sites within floodplain stratigraphic
transects, and mapped woody riparian vegetation cohorts along three segments of the lower
Green River. The oldest Tamarix established along several sampling reaches in 1938, and  1.50-
2.25 m of alluvium has accreted above their germination surfaces. Nearly 90% of the Tamarix
and Populus samples established during flood years that exceeded the 2.5-year recurrence
interval. Recruitment was most common when large floods were followed by years with smaller
peak flows. The majority of Tamarix establishment and Green River channel narrowing occurred
long before river regulation by Flaming Gorge Dam. Tamarix initially colonized bare instream
sand deposits (e.g., islands and bars), and  most channel and floodplain changes followed the
establishment of Tamarix. Our results suggest that Tamarix recruitment was triggered by large
annual floods that were followed by years with lower peak flows, not by periods of low flow
alone. Tamarix appears to have actively invaded floodplains, while Populus colonization has
been limited. Thus, Tamarix invasion may have greatly influenced floodplain development and
riparian vegetation composition along the lower Green River since the  early 20th century.
                                          10

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Author: Bisson, P. A.; Bilby, R. E.; Bryant, M. D.; Dolloff, C. A.; Grette, G. B.; House, R. A.;
Murphy, M. L; Koski, K. V.; Sedell, J. R.
Year: 1987
Title: Large woody debris in forested streams in the Pacific Northwest: Past, present, and future
Reference Type: Book Section
Editor: Salo, E. O.; Cundy, T. W.
Book Title: Streamside Management:  Forestry and Fishery Interactions
City: Seattle, Washington
Publisher: University of Washington
Pages: 143-190

Value of reference: The reference includes a very complete examination of the functions of
large woody debris, its frequency in old growth forests, the history of its decline as a result of
logging practices over the last  150 years, and how  its presence or absence affects salmon
densities. Companion article to Bilby and Ward 1991 that discusses how large woody debris
shapes stream channel morphology.

Results relevant to EMAP: "The combination of debris removal for fish passage in headwater
areas of watersheds, historical splash damming, and removal of snags and logjams from large
rivers has led to situations where whole drainage systems no longer possess the debris load
present in pristine, undisturbed river basins."

Graph, p. 156 shows increasing densities of coho salmon with increasing volumes of large
organic debris.

Table, p. 160 showing biomass of large woody debris (kg/m2) in streams flowing through
regional examples of unmanaged old-growth forests in the Pacific Northwest

Geographic location: Pacific  Northwest, Washington, Oregon, Alaska, British Columbia, ecol,
eco4, mountains, EPA Region  10

Keywords: phab,  large woody debris, sediments, temperature, dissolved oxygen, logging, fish,
pools, salmonids

Abstract: This paper reviews the form, function, and management of woody debris in streams,
and reaches three major conclusions: (1) Large woody debris enhances the quality offish
habitat in all sizes of streams. (2) Removal of most trees in the riparian zone during  logging,
combined with thorough stream cleaning and short-rotation timber harvest, has altered  the
sources,  delivery mechanisms, and redistribution of debris in drainage systems, leading to
changes  in fish population abundance and species composition. (3) There is an urgent  need for
controlled field experiments and long-term studies that focus on the protection of existing large
woody debris  in stream channels and the recruitment of new debris from the surrounding forest.

Woody debris has long been considered a potential source of logjams that could block  river
navigation, water-based log transport, and the  upstream passage of salmon and trout on their
way to spawning grounds, but  is now understood to play an  important role in the creation and
maintenance of fish habitat throughout entire rivers. Although wood itself eventually enters the
food web of the stream ecosystem as it gradually decays,  the major importance of debris lies in
its structural characteristics and the way these features influence channel hydraulics. Physical
processes associated with debris in streams include the formation of pools and other important
rearing areas, control of sediment and organic matter storage, and modification of water quality.
                                          11

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Biological properties of debris-created structures can include blockages to fish migration,
provision of cover from predators and from high stream flow, and maintenance of organic matter
processing sites within the benthic community. The locations and principal roles of woody debris
change throughout the river system. In steep headwater streams where logs span the channel,
debris creates a stepped longitudinal profile that governs the storage and release of sediment
and detritus, a function that facilitates the biological processing of organic inputs from the
surrounding forest.  When the stream channel becomes too wide for spanning by large logs,
debris is deposited  along the  channel margins, where it often forms the most productive fish
habitat in main stem rivers. In all but the smallest streams there is some degree of clumping,
although  the size and spacing of debris clumps generally increase in a downstream direction.
Debris related fish habitat can be found anywhere in small forested streams. In large rivers it is
primarily  associated with debris accumulations along the margins and secondary channel
systems of the floodplain, although it also occurs behind and under very large pieces (intact
boles and root wads) along main stem gravel bars.

Changes in tree species composition, abundance, and input rates to streams resulting from
forest management practices have differed according to location in the watershed, and many
physical and biological processes have been altered by these changes in the river system's
debris load. Several questions have not been fully explored, particularly with regard to the long-
term consequences of streamside management for debris  recruitment. Yet the majority of
studies of streams in second-growth forests have demonstrated that the input of large,
potentially stable debris from  second growth stands in which nearly all large merchantable trees
had been harvested was significantly reduced relative to debris inputs from old growth stands.
Other studies have shown that loss of large debris has led to a shift in stream habitat
composition that favored underyearling steelhead (Salmo gairdneri) and cutthroat trout (S.
clarki) at  the expense of the older trout age classes as well as both underyearling and yearling
coho salmon (Oncorhynchus  kisutch). Loss  of debris has also reduced overwinter survival of all
species. In order to develop procedures that will protect existing instream debris, as well as
provide a continues supply of the proper quantity and  quality of large woody debris for the
future,  it will be necessary to test scientifically a variety of management options over a wide
range of stream sizes. Many management procedures have been proposed, including
techniques for removing slash from stream channels after logging, determining the configuration
of buffer strips, selective harvesting within the streamside management zone, and deliberately
adding debris to streams for habitat enhancement. Evaluation of these proposals will require a
great deal of time and effort, as well as the cooperation of many resource management
organizations. However, long term research is essential  in view of the complexity of debris
management issues.

Notes: This reference is a companion article to Bilby and Ward 1991 that discusses  how large
woody debris shapes stream  channel morphology.
                                          12

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Author: Blinn, D.W.; Cole, G.A.
Year: 1991
Title: Algal and invertebrate biota in the Colorado River: Comparison of pre-and post-dam
conditions
Reference Type: Book Section
Editor: Committee on Glen Canyon Environmental Studies
Book Title: Colorado River Ecology and Dam Management.
City: Washington, D.C.
Publisher: National Academy Press
Pages: 102-122

Value of reference: This is one of very few summary documents about algal and invertebrate
biota in a basin and is thus worth noting even though the historical information it contains is from
the mid-1900s (pre-dam) and the focus is on the mainstem lower Colorado River. It presents a
broad overview of changes in the biota of the Colorado River between Glen Canyon Dam and
Lake Mead, including some documentation for backwater and tributary conditions, as a result of
the closure of Glen Canyon Dam in 1963.  It also gives several examples of invertebrate
introductions in the Colorado River  basin.  The authors present material in a general summary
format (i.e., no data are presented)  that synthesizes an extensive body of literature and includes
a useful bibliography.

Results relevant to EMAP: The average suspended sediment load in the lower Colorado  River
before impoundment was 3.5 times higher than after the construction of Glen Canyon Dam.
Substrata available for attachment were more numerous.  Flowers (1959) reported 53 taxa of
riverine algae including 28 chlorophytes and 20 diatom taxa in tributaries of the canyon.  The
authors note the lack of pre-impoundment data for macroinvertebrates in the main stem but cite
several studies pertaining to species in tributaries or springs, dating back to 1911 (see Notes
section).  The difficulty in reconstructing historical invertebrate communities is due to both the
lack of historical data and the changes in native communities as  a result of numerous
introductions of invertebrates from other parts of the continent.

Cell densities for diatom species in  the Colorado River after impoundment were over 1600-fold
lower than prior to the impoundment of the river. (Williams 1964).

The authors mention numerous invertebrate introductions, beginning  in the late 1800s.

The species diversity of macroinvertebrates in the Colorado River is much lower than in the
tributaries, despite numerous introductions.  General community  change in algal and
macroinvertebrate communities as a result of dams is also discussed.

Geographic location: Arizona, Colorado River basin, eco22, xeric, EPA region 9

Keywords: macroinvertebrates, algae, phab, dams, invertebrate introductions, nonnative
species

Abstract:  Few reports exist on the physicochemical conditions of the pre-impounded Colorado
River that relate to the growth and development of algal and aquatic invertebrate communities.
Post-impoundment studies indicate that Cladophora glomerata is the dominant attached
filamentous green algal species. Two hundred-thirty-five diatom taxa from the Colorado River
and tributaries and from springs in the Glen and Grand Canyon systems have been reported.
Ephemeropterans, snails, leeches, species from at least 10 insect families, and crayfish were
                                          13

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intentionally introduced into the Colorado River after the Glen Canyon dam was closed.
Zooplankters show a richness of faunas in backwaters along the borders of the river channel
and at the mouths of tributaries. The macroinvertebrates occurring in the Colorado River consist
of only a few species. The amphipod Gammarus lacustris constitutes an important food for most
of the fishes of the Colorado River. Exotic and unusual species such as Craspedacusta
sowerbyi, Branchiura sowerbyi, and the parasite Lernaea cyprinacea have also been reported in
the Colorado River. Damming of the river has caused stranding of some plant and animal
communities during periods of low flow. Some species have shown adaptations to fluctuating
flow regimens caused by dams. Regulated flow can increase the standing crops of both
attached algae and aquatic macrophytes, as well as aquatic mosses. Creation of reservoirs may
cause enrichment of some nutrients that affect algal  growth. The most common effect of
impounded rivers on the macroinvertebrate community is reduced species diversity
accompanied by high density and biomass. Modifications in thermal conditions also contribute
to the compositional changes in macroinvertebrates  below reservoirs. Research priorities
recommended  are: seasonal studies of Cladophora glomerata, studies on optimal flow rates for
Cladophora glomerata population growth, food web studies in tail waters of Glen Canyon Dam,
phenological studies of invertebrates in the Colorado River ecosystem, and model development
to study the effects of physicochemical parameters on plant and animal communities in
regulated rivers. (See also W93-02624) (Geiger-PTT)

Notes: See Musser,  1959 (in this bibliography) for a list of macroinvertebrate species found in
Glen Canyon in 1958 (before dam closure).

Flowers, S. 1959.  Algae collected in Glen Canyon.  Pages 203-205 IN C.E. Dibble (ed.),
Ecological Studies of the Flora and Fauna in Glen Canyon, Appendix D.  University of Utah
Anthropology Papers, Salt lake City. 226 p.
                                          14

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Author: Bogan, M.A.; Allen, C.D.; Muldavin, E.H.; Platania, S.P.; Stuart, J.N.; Farley, G.H.;
Mehlop, P.; Belnap, J.
Year: 1998
Title: Southwest
Reference Type: Electronic Source
Producer: United States Geological Survey, Biological Resources Division
Access Year: 2005
Access Date: June 15

Value of reference: Synthesis article addresses changes in fish occurrence and distribution in
a very large river basin (Colorado) as a whole and also mentions changes in specific tributaries.
General historical ranges and declines or extinctions are given for four significant native fish
species: Colorado squawfish, bonytail, razorback sucker, and humpback chub.  Web site brings
together a number of important references, including some from gray literature.

Results relevant to EMAP: The percentage of the native fish fauna in the Colorado River basin
that are threatened is 85% in AZ, 72% in CA, 30% in NM,  and 42% in UT.

The Colorado squawfish is now reduced to about 1/3 its original range, with natural populations
extinct in the lower basin; Humpback chubs, once found in most large-river habitats of the CO
River, now exists in only five canyon reaches in the upper basin; Bonytails, once one of the
most abundant fishes in the basin, is now considered functionally extinct; Razorback suckers
were once so numerous that they were commercially fished in southern AZ in the early 1900s,
but now inhabit only  1208 river km in the upper basin.

These conditions have been brought about by dams, impoundments, loss of physical habitat,
habitat degradation,  chemical pollution, overfishing, altered water flow regime, groundwater
pumping, and introduction of at least 72 nonnative species.

Geographic location: southwest, xeric, mountains, Colorado, Utah, New Mexico, Arizona,
Colorado River basin, eco 20, eco22, eco23, eco81, eco14, xeric, EPA Region 8, EPA Region 9

Keywords: fish, dams, nonnative species, fishing, habitat degradation, pollution, groundwater
pumping

URL: http://biology.usgs.gov/s+t/SNT/index.htm
                                          15

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Author: Bradford, D.F.; Graber, D.M.; Tabatabai, F.
Year: 1994
Title: Population declines of the native frog, Rana muscosa, in Sequoia and Kings Canyon
National Parks, California
Reference Type: Journal Article
Journal: The Southwestern Naturalist
Volume: 39
Issue: 4
Pages: 323-327

Value of reference: This article reports the dramatic decline of the mountain yellow-legged frog
since 1955 from relatively undisturbed areas of the Sierra Nevada. Few accurate historical
records are available prior to 1955; the "historical" period was thus defined as 1955-1979.
Areas both within and outside Kings Canyon and Sequoia National Parks were compared on the
basis of historical and current (1988-91) presence of the species. Historical geographic range is
shown in Figure 1 (Zweifel 1955).

Results relevant to EMAP: In the current survey, Rana muscosa remained at 11 of 21
historical sites within the parks but at only 3 out of 24 historical sites outside the parks. The
authors conclude that the species has disappeared from about half of its historical localities in
the two parks during the past three decades, and has been extirpated in some drainages. The
magnitude of decline seems greater outside the parks.  The causes for the declines are not
clear. Several possible factors contributing the decline are discussed; the authors appear to
favor the hypothesis that the cause is due to habitat fragmentation and isolation of populations
by nonnative fishes (Bradford et al. 1993).  The degree of isolation differs by about tenfold
compared  to the  period prior to fish introduction.

Geographic location: Sierra Nevada, Kings Canyon National Park, Sequoia National Park,
San Joaquin River, Kings River, Kaweah River, Kern River,  EPA region 9, eco5, California,
mountains

Keywords: amphibians, declining populations, isolation, habitat fragmentation, headwater
streams, high elevation

Abstract:  Rana muscosa (mountain yellow-legged frog) is one of a number of amphibians
around the world that reportedly have declined in numbers in recent years in seemingly well-
protected environments. In Sequoia and Kings Canyon National Parks, California, two study
areas comprising the headwaters of seven creek systems were surveyed for R. muscosa and
Pseudacris regilla (Pacific chorus frog) in 1978-79 and again in 1989.  R. muscosa was found at
27 sites greater than 200 m apart in 1978-79, but at only one site in 1989, and the population at
this site disappeared by 1991.  In contrast, P. regilla was found at 15 to 17 sites both times. A
comparison of 21 historical (1955-1979) and recent (1989-90) records scattered throughout the
parks showed that R. muscosa remained at only 11 of these sites in 1989-90.  A similar
comparison of 24 historical and recent records elsewhere in the Sierra Nevada showed that R.
muscosa remained at only three sites. We conclude that R. muscosa has disappeared from
about half  of the historical localities in Sequoia and Kings Canyon National Parks during the
past three  decades, and has been extirpated in some drainages.  The magnitude of decline
appears to be even more pronounced outside the parks. The causes for these declines are not
clear.

Notes: Zweifel, R.G. 1955. Ecology, distribution, and systematics of frogs of the Rana boylei
                                          16

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group. University of California Publ. Zool. 54:207-292.

Bradford, D.F. et al. 1993.  Isolation of remaining populations of the native frog, Rana muscosa,
by introduced fishes in Sequoia and Kings Canyon National Parks, California.  Conservation
Biology 7:882-888.
                                           17

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Author: Bradford, D.F.; Jaeger, J.R.; Jennings, R.D.
Year: 2004
Title: Population status and distribution of a decimated amphibian, the relict leopard frog (Rana
onca)
Reference Type: Journal Article
Journal: The Southwestern Naturalist
Volume: 49
Issue: 2
Pages: 218-228

Value of reference: Previous publications describing this species' historical range (Jaeger et al.
2001; Jennings 1988, Jennings and Hayes 1994) are questioned because of taxonomic
uncertainties regarding various leopard frog populations within the region. This article
synthesizes past (pre-1970) and recent information and reports the latest understanding of
distribution, size, structure, and dynamics of extant and recently extinct R. onca populations.
The authors also specifically define a minimum historical distribution of R. onca in light of recent
taxonomic clarification and describe observations of habitat changes that seem to be causally
associated with recent population extinctions.

Results relevant to EMAP: The historical range was identified by examining museum
specimens, using morphological characters to distinguish between  R. onca and R. pipiens.
Since not all areas of the basins were sampled in the past, the study establishes a minimum
historical distribution.

R. onca occurred in springs, streams, and wetlands within the Virgin River drainage
downstream from the vicinity of Hurricane and Gunlock, Utah; along the Muddy River, Nevada;
and along  the Colorado River from its confluence with the Virgin River downstream to Black
Canyon below Lake  Mead in Nevada and Arizona. All historical localities are within a few km of
these rivers, and many localities are at the river (Figure 1).  The five populations currently
remaining  are small and isolated and concentrated in two areas: near the Overton Arm of Lake
Mead and  in Black Canyon along the Colorado River below Lake Mead, Nevada.  All remaining
populations inhabit spring systems with unaltered hydrology.

Possible causes of disappearance  from the majority of its historical range include habitat
alteration due to agriculture, impoundments, water diversions, and introduction of nonnative
species such as bullfrogs, various fishes, and red swamp crayfish.

Geographic location: Arizona, Nevada, Colorado River basin, Virgin River basin, Black
Canyon, Lake Mead, EPA Region 9, eco14, eco22, eco20, xeric

Keywords: amphibians, agriculture, nonnative species, water diversion
Abstract: The relict leopard frog (Rana onca) was once thought to be extinct, but has recently
been shown to comprise a valid taxon with extant populations. We delineate the minimum
historical range of the species based on records from 24 localities, report the extinction of 2 of 7
populations extant in the 1990s, and estimate total population size. The 5 remaining populations
occurred in 2 areas:  near the  Overton Arm of Lake Mead and in Black Canyon along the
Colorado River below Lake Mead,  Nevada. These 2 areas are only 3.6 and 5.1  km long,
respectively. The 5 extant populations inhabited spring systems with largely unaltered hydrology
and no introduced American bullfrogs (Rana catesbeiana) or game fishes. In a mark-recapture
study conducted in the
Overton Arm area, the estimated number of adult frogs averaged 36 over 555 m of stream
                                          18

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habitat, and estimated annual survivorship of adults averaged 0.27. A single mark-recapture
estimate for the size of the largest population within Black Canyon, at a site approximately 450
m in length, was 637 adult frogs. An estimate for the total number of frogs at all sites, based on
mark-recapture data, visual encounter surveys, and extent of habitat, was approximately 1,100
adults (range 693-1,833). The 2 recent population extinctions occurred concomitantly with
encroachment of emergent
vegetation into pools. We speculate that this occurred as a result of natural  processes in one
case, and anthropogenic processes in the other.

Notes: Jaeger, J.R.  et al. 2001. Rediscovering Rana onca: evidence for phylogenetically distinct
leopard frogs from the border region of Nevada, Utah, and  Arizona. Copeia 2001:339-354.

Jennings, M.R.  1988. Rana onca Cope, relict leopard frog.  Catalogue of American Amphibians
and Reptiles 417:1-2.

Jennings and Hayes. 1994.  Decline of native ranid frogs in the Desert Southwest. Pages 183-
211 IN Brown, P.R. and J.W. Wright, eds. Herpetology of the North American deserts.
Southwestern Herpetologists Society, Special Publication Number 5.
                                          19

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Author: Bradford, D. F.; Tabatabai, F.; Graber, D.M.
Year: 1993
Title: Isolation of remaining populations of the native frog, Rana muscosa, by introduced fishes
in Sequoia and Kings Canyon National Parks
Reference Type: Journal Article
Journal: Conservation Biology
Volume: 7
Issue: 4
Pages:  882-888

Value of reference: This paper documents the decline of yellow-legged frogs (Rana muscosa)
from a minimally-disturbed area within the Sierra Nevada during the past century. The decline is
attributed to intentional fish introductions stocking of lakes and streams. This reference provides
an example of how fish introductions can  influence vertebrate assemblages, vertebrate metrics,
and derived diversity indices.

Results relevant to EMAP: The authors  propose that the introduction of fish  into previously
fishless  streams and lakes has resulted in increased isolation of populations of yellow-legged
frogs (Rana muscosa). This isolation, they suggest, has made subpopulations more vulnerable
to extinction through natural causes associated with fluctuations in the physical environment,
and subsequent re-colonization through streams more difficult.

Much of the water within Sequoia and  Kings Canyon National Parks were historically fishless
due to the steep gradients of connecting streams, with the exception of certain streams and
possibly lakes containing golden trout  (Oncorhynchus aguabonita), and some rainbow trout (O.
mykiss). During the past century four species of trout and char, including golden trout,  rainbow
trout, brook trout (Salvalinus fontinalis) and  brown trout (Salmo trutta) have been systematically
introduced above fish barriers throughout the region.

To assess the level of "connectivity" between sample sites, the number of potential dispersal
links between present and former fishless stream networks were evaluated. Contemporary
yellow-legged frog-bearing sites are much more isolated (approximately 10-fold) from one
another than prior to beginning of fish  introductions early in the twentieth century. This loss of
connectivity is suggested as one cause of the decline of the species, attributed to natural
extinction due to stochastic processes, in  combination with decreased probability of re-
colonization.

Geographic location: California, Sierra Nevada, mountains, eco5, EPA Region 10

Keywords: amphibians; nonnative species; predation; habitat fragmentation

Abstract: Rana muscosa (mountain yellow-legged frog) was eliminated by introduced fishes
early in  this century in many of the lakes and streams in Sequoia and Kings Canyon National
Parks, California. In waters not inhabited by fish, however, R.  muscosa has disappeared from
many sites within the past 30 years, and it appears to have gone extinct in some drainage
systems. Fragmentation of populations may have caused or contributed to these recent
extinctions, because R. muscosa populations are significantly more isolated from one another
by fish at present than in pre-stocking  conditions. A total of 312 lake-sites in 95 drainage basins
were surveyed for amphibians and fish in  1989-90. For the 109 sites containing R. muscosa, we
delineated networks of sites connected to one another via fishless streams, and we compared
these present fishless networks ("present networks") to those expected for the same sites
                                          20

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assuming that fish had not been introduced to the parks ("former networks"). Most present
networks consist of only one site (mean 1.4), whereas the former networks average 5.2 sites.
This difference represents approximately a 10-fold difference in connectivity of populations,
which is defined as the mean number of potential links (fishless streams) per network.
Connectivity averages only 0.43 in present networks, in contrast to 4.15 in former ones.
                                          21

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Author: Brothers, T. S.
Year: 1984
Title: Historical vegetation change in the Owens River riparian woodland
Reference Type: Book Section
Editor: Warner, R. E.; Hendrix, K. M.
Book Title: California riparian systems: Ecology, conservation, and productive management
City: Berkeley, California
Publisher: University of California Press
Pages: 75-84

Value of reference: The article attempts to reconstruct the pre-settlement riparian vegetation of
the Owens River valley and compare it to present day riparian vegetation. Though there is very
little information available from early explorers' journals, available references to original
vegetation are compared with the subsequent land use and water management history to make
inferences about changes in riparian vegetation since settlement.

Results relevant to EMAP: The author pieces together evidence of riparian vegetation from the
Walker, Fremont, von Schmidt, and Brewer expeditions that passed through the Owens Valley
between 1834 and 1864. Fremont mentions willow and cottonwood, but the others mention only
a few small cottonwoods and no other timber. The author lists species recorded in the present
day sample and discusses which species may have increased since pre-settlement times
(narrowleaf willow and rabbitbrush tend to increase with grazing pressure).

The diversion of Owens River water to Los Angeles may have affected regeneration of willows
and cottonwoods that are dependent on periodic flooding to reproduce. Below the diversion
aqueduct on the Owens River, the riverbed is dry and vegetated with the alien saltcedar,
Russian olive, and herbaceous weeds.

Geographic location: California, EPA Region 9, Owens River, xeric, eco13, central basin and
range

Keywords: phab, riparian vegetation, water diversion

Abstract: This study evaluates human-caused vegetation change in the riparian woodland of
Owens River (Inyo Co., California), the greatest change has occurred below the intake of the
Los Angeles aqueduct, where drying of the channel has eliminated most native  riparian cover
and allowed invasion by saltcedar (Tamarix ramosissima) and Russian olive (Elaeagnus
angustifolia). Fire, water management, and other factors may have reduced tree cover above
the aqueduct intake and encouraged proliferation of weedy native shrubs. The present scarcity
of tree seedlings suggests that one or more of these factors continues to inhibit tree
regeneration.
                                          22

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Author: Brown, L.A.; Moyle, P. B.
Year: 2005
Title: Native fishes of the Sacramento-San Joaquin drainage, California: A history of decline
Reference Type: Book Section
Editor: Rinne, J. N.; Hughes, R. M.; Calamusso, B.
Book Title: Historical changes in large river fish assemblages of the Americas
City: Bethesda, Maryland
Publisher: American Fisheries Society Symposium 45
Pages: 75-98

Value of reference: This paper is a companion to  other papers on the Sacramento-San
Joaquin rivers in this collection (Skinner 1962 (salmon catch data), Katibah 1984 (riparian
forest), Scott and Marquiss 1984 (sediment)) that covers the decline of a broad variety of fishes,
both commercial and non-commercial, and how they have been affected by a range of human
disturbances.

Results relevant to EMAP: The fish assemblages of the Sacramento and San Joaquin rivers
and tributary streams are separated into elevational regions for the discussion of their historical
distribution and  present day status: mountains over 1000  m, fishless; mountains 450-1000 m,
rainbow trout assemblage (5 species); foothills 30-450 m, pikeminnow/hardhead/sucker
assemblage (up to 11 species); valley <30 m, deep bodied fish assemblage (10 species).

The valley fish assemblage, that once occupied low elevation rivers, oxbows,  and sloughs, only
exists as remnant  populations. The thicktail chub is globally extinct; the bull trout and coho
salmon have been extirpated; the Sacramento perch was once common, but now exists mostly
as transplanted populations in reservoirs;  the splittail is commonly found in Native American
middens in the Tulare basin where it is now scarce.

The huge increases in  sediments after mining in the mid-1800's may have facilitated the
invasion by alien striped bass and American shad that are more likely to thrive in systems with
high loads of fine sediment. The rise of agriculture  and the loss of wetland habitats led to the
extinction and decline of the valley fishes. Flow regime is  a key factor in the reproductive
success of native and alien fishes. The streams and rivers of the Sacramento system have a
relatively higher representation of native species than the San Joaquin likely because there is
less flow alteration on the Sacramento and no canal systems in agricultural areas. In the San
Joaquin drainage the native species are restricted to the areas just below the  reservoirs. Those
above the reservoirs are threatened by alien species moving upstream from the lakes.

Geographic location: EPA Region  9, Sacramento River, San Joaquin River,  Central Valley,
eco6, eco7, xeric

Keywords: fish, nonnative species,  mining, sediment, agriculture, altered water flow regime,
dams

Abstract: In this paper, we review information regarding the status of the native fishes of the
combined Sacramento River and San Joaquin River drainages (hereinafter the "Sacramento-
San Joaquin drainage") and the factors associated with their declines. The Sacramento-San
Joaquin drainage is the center of fish evolution in California, giving rise to 17 endemic species
of a total native  fish fauna of 28 species.  Rapid changes in land use and water use beginning
with the Gold Rush in the 1850's and continuing to the present have resulted in the extinction,
extirpation, and reduction in range and abundance of the  native fishes. Multiple factors are
                                          23

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associated with the declines of native fishes, including habitat alteration and loss, water storage
and diversion, flow alteration, water quality, and invasions of alien species. Although native
fishes can be quite tolerant of stressful physical conditions, in some rivers of the drainage the
physical habitat has been altered to the extent that it is now more suited for alien species. This
interaction of environmental changes and invasions of alien species makes it difficult to predict
the benefits of restoration efforts to native fishes. Possible effects of climate change on
California's aquatic habitats add additional complexity to restoration of native fishes. Unless
protection and restoration of native fishes is explicitly considered in future water management
decisions, declines are likely to continue.
                                            24

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Author: Brown, L. R.; Moyle, P. B.; Yoshiyama, R. M.
Year: 1994
Title: Historical decline and current status of coho salmon in California
Reference Type: Journal Article
Journal: North American Journal of Fisheries Management
Volume: 14
Issue: 2
Pages: 237-261

Value of reference: The article gives an overview of the vulnerable status of coho salmon in
California. Historical information on coho salmon is limited; here it is given in terms of historical
and current presence/absence records in individual streams.

Results relevant to EMAP: Unfortunately, much of the "historic" information in this article is
from the 1930's, 50's, and 70's as abundance figures from gill net or sport fish catches.
Examples: Klamath River, lower river 1919-11,162 in gill  net fishery; 1955-1145 in sport
catch. Klamath River; 301 km from  mouth - Coho termed abundant in 1923. By 1956, none
counted. Table of historic and recent abundance data for adult coho salmon in some California
Rivers, p. 244.

There are 582 California streams known to have supported coho salmon at some time.
Information on the recent presence or absence of coho salmon was available for only 248 of
those streams. Of these 248 streams, 54% still contained coho salmon and 46% did not. By
1956, it was estimated that  over 1600 km of streams in California had been lost as important
fish habitat.

Juvenile coho salmon require deep, cold pool habitats for high survival. Their wide distribution
over many small coastal streams and their relatively  short life span  (3 years) make California
coho salmon more vulnerable to severe declines during drought years. Inadequate protection of
watersheds from the effects of logging, grazing, and  urbanization has resulted in increased
water temperatures, the loss of pools through sedimentation, and the removal of large woody
debris needed for cover and pool formation.

Geographic location: xeric, California, Central Valley, Klamath River, Smith River, Redwood
Creek, Eel River, eco6, eco7,  EPA  Region 9

Keywords: fish, coho salmon, dams, logging, genetic integrity, roads, grazing, urbanization

Abstract: The southernmost populations of coho salmon (Oncorhynchus kisutch) occur in
California where native coho stocks have declined or disappeared from all streams in which
they were historically recorded. Coho salmon previously occurred in as many as 582 streams,
from the Smith River near the Oregon border to the San Lorenzo River on the central coast.
Information on the recent presence or absence of coho salmon was available for only 248 (43%)
of those streams. Of these 248 streams, 54% still contained coho salmon and 46% did not. The
farther south a stream is located, the more likely it is to have lost its coho salmon population.
We estimate that the total number of adult coho salmon entering California streams in 1987-
1991 averaged around 31,000 fish per year, with hatchery populations making up 57% of this
total. Thus, about 13,000 non-hatchery coho salmon have been spawning in California streams
each year since 1987, an estimate that includes naturalized stocks  containing about 9,000 fish
of recent hatchery ancestry. There are now probably less than 5,000 native coho salmon (with
no known hatchery ancestry) spawning in California each year, many of them in populations of
                                         25

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less than 100 individuals. Coho populations today are probably less than 6% of what they were
in the 1940's, and there has been at least a 70% decline since the 1960's.  There is every
reason to believe that California coho populations, including hatchery stocks, will continue to
decline. The reasons for the decline of coho salmon in California include: stream alterations
brought about by poor land use practices (especially those related to logging and urbanization)
and by the effects of periodic floods and drought, the breakdown of genetic integrity of native
stocks, introduced diseases, over-harvest, and climatic change. We believe that  coho salmon in
California qualify for listing as a threatened species under state law, and certain populations
may qualify for listing as threatened or endangered under federal law.
                                           26

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Author: Burroughs, Raymond Darwin
Year: 1961
Title: The natural history of the Lewis and Clark Expedition
Reference Type: Book
City: East Lansing, Michigan
Publisher: Michigan State University Press
Number of Pages: 340

Value of reference: This book summarizes the journals from the Lewis and Clark Expedition
and groups the information into chapters by species observed.  The chapters include:
Introduction, bears and raccoons, weasel family, wild dogs and cats, rodents and rabbits, deer-
elk and antelope, bison, mountain goats and bighorn sheep, diving and wading birds, ducks -
geese and swans, birds of prey, marsh and shore birds, gulls and terns, pigeons - parroquets -
goatsuckers and hummingbirds, woodpeckers, passerine birds, fishes, reptiles and amphibians.

Results relevant to EMAP: The information listed in the journals helps reconstruct habitats and
landscape elements at the time of observation.  The presence of certain mammals, birds, fish,
and plant species can paint a picture of what the riparian and landscape habitat was like when
first encountered by early explorers. A summary of the many fish, mammals, and other natural
history data collected on the expedition is included in the chapters of this book.

The chapters require some sifting through to extract small pieces of anecdotal information or to
reconstruct stream related attributes, however; the information is quite valuable and may be the
only  source of pre-settlement conditions of the plains. This is a good broad reference and
inventory that includes specific information about pre-settlement conditions along the route of
the expedition.

Geographic location: Great Plains, plains, mountains, Lewis & Clark expedition route,
Kansas, Missouri, Nebraska, Iowa, North Dakota, South Dakota, Montana, Idaho, Oregon,
Missouri River Basin, EPA region 7, EPA region 8, eco47, eco42, eco43, eco46,

Keywords: Lewis & Clark expedition, pre-settlement, mammals, phab, fish, natural history
                                          27

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Author: Bury, R. B.; Corn, P. S.
Year: 1988
Title: Responses of aquatic and streamside amphibians to timber harvest: A review
Reference Type: Book Section
Editor: Raedeke, K. J.
Book Title: Streamside management: Riparian wildlife and forestry interactions
City: Seattle, Washington
Publisher: College of Forest Resources, University of Washington
Volume: 59
Pages: 165-181

Value of reference: This study compared density estimates of four salamander species in
uncut vs. cut riparian reaches on 43 streams in the Coast Range of Oregon. It is one of a limited
number of papers examining the effects of logging on amphibians. Mature and old growth
reference reaches are used in the absence of historical information on amphibians and their
habitats.

Results relevant to EMAP:  "There were marked differences in the occurrence, density, and
biomass of amphibians between control streams and streams in logged sites. All four species
(tailed frogs, Pacific giant salamanders,  Olympic salamanders, and Dunn's salamanders)
occurred significantly more often in the control streams than in the streams in logged stands"
(bar graph, Figure 2, p. 172). The species differed in their sensitivity to temperatures and their
ability to withstand some level of logging activity.

Control streams had a higher percentage of cobbles and boulders in the substrate, while logged
streams had significantly  more sediment.  Sediments can be attributed to logging in this case
because there were no road  crossings upstream from the sample reach in any of the streams in
logged stands.

Geographic location: mountains, Pacific Northwest, Oregon, Coast Range, ecol,  EPA Region
10

Keywords: amphibians, tailed frog, Olympic salamander, Pacific giant salamander, Dunn's
salamander, logging, temperature, sediments, phab

Abstract: Stream dwelling amphibians,  which can be the dominant vertebrates of small streams
and forests of the Pacific  Northwest, are prototypic riparian organisms. Larvae of several
species are totally aquatic, while adults  use the terrestrial streamside (riparian) habitat to
varying degrees. Impacts of timber harvest vary among species, physical habitats, and regions
of the Pacific Northwest. Populations of giant salamanders (Dicamptodon) increase following
clear cutting in the Oregon Cascades, while in the Oregon Coast Range, the long term effects of
logging were negative and severe for all species. Timber harvest is less disruptive in high
gradient streams and in streams where  there is uncut timber remaining upstream. Buffer strips
adjacent to headwater and small streams can provide shad and reduce ecological requirements
of amphibians in headwaters, assess the effects of logging on amphibians in different regions
and under varying climatic regimes, and determine what  sizes of buffer strips or uncut  patches
are most effective and cost-efficient for protecting stream amphibians.
                                         28

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Author: Carlson, C.A.; Muth, R.T.
Year: 1989
Title: The Colorado River: Lifeline of the American Southwest
Reference Type: Journal Article
Journal: Canadian Special Publication of Fisheries and Aquatic Sciences
Volume: 106
Pages: 220-239

Value of reference: Important synthesis paper that summarizes many of the historical and
current published and gray literature on status of CO river and its biota. This key reference
presents an excellent summary of conditions prior to 1935 (date of Hoover Dam closure),
including historic distributions of 54 species of fish in different sections of the basin (see Table
2), specific historic locations where fish were found (also in Table 2), and historic riparian
community composition.  Historical conditions are contrasted with current conditions, and
causes for the changes are presented.

Results relevant to EMAP: River regulation has lowered mainstream water temperatures 10-
15 degrees C, resulting in cooler summer and warmer winter water temperatures below dams
(Stanford and Ward 1986a); lower summer temperatures have adversely affected native fishes.
By 1957, salinity (about 250 mg/L) at Lee Ferry had doubled (reports of 600, 825, and 750 mg/L
have been reported in various locations); paper also describes historical aquatic conditions for
oxygen levels, algae, nutrient levels, and zoobenthos.

Seventeen of the 54 native fish  are either threatened, endangered, or extinct, and most have
experienced  drastic abundance and range reductions due to impacts including dams and
impoundments, poisoning with rotenone, introduction of exotic species,  and stocking of various
invertebrates carried out  in the mid 1900s.

At least 2023 ha of cottonwood  communities existed along 322 km of potentially suitable habitat
on the lower river in the 1600s;  due to water management, grazing, competition with tamarisk,
and phreatophyte  removal, only about 1130  ha of these communities remain, and less than 202
ha can be considered pure cottonwood communities.

Geographic location: Colorado River Basin, Wyoming, Utah, Colorado, Arizona, New  Mexico,
Nevada, California, xeric, eco13, eco81, eco23, eco79, eco22, eco20, eco21, eco19, eco18,
EPA Region  8, EPA  Region  9.

Keywords: dams, water  diversion, nonnative species, grazing, water temperature,  sediments,
fish,  macroinvertebrates,  riparian vegetation

Abstract: In  less than a century, the wild Colorado River has been drastically and irreversibly
transformed  into a tamed, man-made system of regulated segments. The pristine Colorado,
characterized by widely fluctuating flows and physico-chemical extremes, supported unique
assemblages of indigenous flora and fauna.  Closure of Hoover Dam in 1935 marked the end of
the free-flowing river. The system has since become one of the most altered and intensively
controlled in  the United States; many mainstem and tributary dams, water diversions, and
channelized  river sections now exist in the basin.  Despite having one of the most arid
drainages in  the world, the river supplies more water for consumptive use than any river in the
United States. Its biota is dominated by non-native organisms, and about one third  of its native
fishes are threatened, endangered, or extinct.  This paper treats the Colorado River holistically
as an ecosystem and summarizes current knowledge on its ecology and management.  Little
                                          29

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has been published on productivity and fisheries of the mainstream river.
                                           30

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Author: Chapman, D.W.
Year: 1986
Title: Salmon and steelhead abundance in the Columbia River in the nineteenth century
Reference Type: Journal Article
Journal: Transactions of the American Fisheries Society
Volume: 115
Pages: 662-670

Value of reference: This reference synthesizes harvest data, early fish literature, and optimum
exploitation rates to reconstruct peak-period run estimates for salmon (4 species) and steelhead
in the Columbia River basin in the late 1800s.  The estimation procedure is based on 5
consecutive years of greatest total harvest and therefore overestimates the average year but
better approximates what the basin was capable of supporting, i.e., potential historical
production.

Results relevant to EMAP: Peak-period runs for the entire Columbia River system estimated
from optimum harvest rates were 2,623,000 sockeye, 4,338,000 Chinook (Table 3 breaks down
into summer, fall, and spring runs), 618,000 coho, 554,000 steelhead, and 748,000 chum-
8,881,000 adults altogether. These are based on optimum exploitation  rates (rate at maximum
sustained yield) from the literature of 0.77 for coho, 0.73 for sockeye, 0.68 for spring and
summer Chinook, 0.88 for fall Chinook, 0.69 for steelhead, and 0.48 for chum. On the basis of
the more probable harvest rates that produced overfishing (0.80-0.88), total run size was  about
7,505,000 adults, a single best estimate of total predevelopment runs. This estimate falls within
the low range of previous run estimates (cited in this publication), which were partly speculative
and varied drastically.

Overfishing and environmental degradation caused numbers to rapidly decrease after catches
peaked in the late 1800s. Mining, grazing, irrigation, dams, water diversions, and logging
contributed habitat degradation.

Losses can be estimated by subtracting current run sizes from predevelopment estimates of
7.5-8.8 X 106.  This publication is dated, but it gives the 1977-1981 run data, with corrections for
ocean harvest, as 2.5 X 106.

Geographic location: Columbia River basin, Oregon, Washington, Idaho, ecolO, eco4, ecol,
eco11, eco12,  eco 15,  eco16. eco3, eco9, EPA Region 10, xeric, mountains

Keywords: fish, salmon, mining, grazing,  irrigation, dams, water diversions, logging

Abstract: I estimated peak runs of Pacific salmon Oncorhynchus sp. and steelhead Salmo
gairdneri in the Columbia River during the 40 years centered on  1900 on the basis of peak-
period commercial catches and probable optimum exploitation rates. Peak-period catches were
estimated from mean catch weights during the five consecutive years of greatest total harvest,
and from mean weights offish reported in the early literature.  These catches were 1,700,000
summer Chinook salmon Oncorhynchus tshawytschaC\881-1885), 382,000 steelhead (1892-
1896), 1,100,000 fall Chinook salmon  (1915-1919), 400,000 spring Chinook salmon
(approximately), 476,000 coho salmon O.  kisutch (1894-1898), 1,915,000 sockeye salmon O.
nerka (1883-1887), and 359,000 chum salmon O. keta (1915-1991).  Optimum harvest rates for
maximum sustained yield from non-hatchery stocks were obtained from literature: 0.77 for coho,
0.73 for sockeye, 0.68 for spring and summer Chinook, 0.88 for fall Chinook, 0.69 for steelhead,
and 0.48 for chum. Peak-period runs estimated from optimum harvest rates were 2,623,000

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sockeye, 4,338,000 Chinook, 618,000 coho, 554,000 steelhead, and 748,000 chum-8,881,000
adults altogether.  On the basis of the more probable harvest rates that produced over-fishing (-
.80-0.88), total run size was about 7,505,000 adults, a single best estimate of total pre-
development runs. I discuss aboriginal catch in relation to the theory that decimation of Indian
populations after 1800 permitted salmon and steelhead stocks to expand.  Using the shape of
stock-recruitment functions and appropriate commercial harvest rates, I support the alternative
hypothesis that salmon stocks actually decreased in the early 1800s with decreased Indian
harvest, then increased after 1850 as commercial fisheries developed, and finally decreased in
response to overfishing.  Environmental degradation exacerbated the latter decrease.
                                          32

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Author: Close, D. A.; Fitzpatrick, M.; Li, H.; Parker, B.; Hatch, D.; James, G.
Year: 1995
Title: Status report of the Pacific Lamprey (Lampetra tridentata) in the Columbia River Basin
Reference Type: Report
City: Portland, Oregon
Institution: U. S. Department of Energy, Bonneville Power Administration, Division of Fish and
Wildlife
Pages: 40
Report Number: BPA Report DOE/BP-39067-1

Value of reference: This document provides a good synthesis of what is known of Pacific
lamprey population changes in the Columbia River and Snake River Basins during the last
century and suggests causes leading to dramatic declines in recent years.

Results relevant to EMAP: Historically, Pacific lamprey were fairly common in the Columbia
and Snake River drainages and occurred wherever salmon occurred.  During the early part of
the twentieth century, adult lamprey were used as food during artificial propagation of young
salmon. Twenty seven tons were reported harvested for this purpose in 1913. A commercial
market developed for this species, and 816 tons (approximately 10-20% of the total run) were
reported harvested in the Willamette River drainage alone between 1943 and 1949. Dramatic
declines in recent years are attributed to (1) problems for both adult and juvenile passage
through dams; (2) loss of spawning and rearing habitat; (3) declines in marine prey species
resulting from commercial fishing; and (4) chemical poisoning of streams  to remove non-game
species.

Geographic location: EPA Region 10, mountains, xeric, Oregon, Washington, Columbia River
basin, Snake River basin, Idaho, ecol, eco3, eco4, ecolO, eco11, eco12, eco15, eco16, eco17

Keywords: fish, Pacific  lamprey (Lampetra tridentata), fishing,  dams

URL: http://www.efw.pba.gov/cgi-bin/efw/FW/publications.cgi
                                         33

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Author: Collins, B.D.; Montgomery, D.R.; Mass, A.D.
Year: 2002
Title: Historical changes in the distribution and functions of large wood in Puget Lowland rivers
Reference Type: Journal Article
Journal: Canadian Journal of Fish and Aquatic Sciences
Volume: 59
Pages: 66-76

Value of reference: The useful part of this reference, with respect to pre-settlement conditions,
is the reconstruction of wood abundance, size, and log jamming using archival sources.  The
reference also demonstrates the use of historical information to evaluate the suitability of
reference sites, and the integrated use of both historical information and current least-disturbed
sites to re-create pre-settlement conditions.  The link between wood and fish habitat value is
mentioned on page 75, where two studies are referenced as support for large wood and wood
jams in fish habitat sustainability.

Results relevant to EMAP: Early accounts document transport by rivers of vast amounts of
wood, for example a Skagit river jam was described as 9 m deep, consisting of 5-8 tiers of logs,
ranging from 3-8 feet in diameter and existed for at least a century, as its surface supported live
trees 0.6-1.2 m in diameter (Interstate Publishing Company  1906); individual jams of this size
could have stored several hundred thousand pieces of wood.

Current numbers of snags are estimated at 0.2-0.4 pieces per km, which is 2 orders of
magnitude less than possible snag recruitment rates suggested by data from 1881-1909.
Annual maximum diameters between 1889 and 1909 were 3.6 to 5.3 m,  based on snagboat
records.

A comparison of pool data from the Snohomish and Stillaguamish rivers with data from the
Nisqually suggests that the transition from a freely migrating or avulsing  river with mature
floodplain forest to a leveed  river with little riparian recruitment has reduced the number of pools
by two to three times. Field  studies in the Skagit River indicate that wood (particularly wood
jams) significantly increases the fish habitat value of riverbanks.

Geographic location: Puget Lowland, Washington, ecol, eco2, eco77,  mountains, Nisqually
River, Skykomish River, Snoqualmie River, EPA Region 10

Keywords: phab, fish, large wood, wood jams, pools

Abstract: We examined changes in wood abundance and functions in Puget Lowland rivers
from the last -150 years of land use by comparing field data from an 11-km-long protected
reach of the Nisqually River with field data from the Snohomish and  Stillaguamish rivers and
with archival data from several Puget Lowland rivers. Current wood abundance is one to two
orders of magnitude less than before European settlement in the Snohomish and Stillaguamish
basins.  Most importantly, wood jams are now rare because of a lack of very large wood that
can function as key pieces and low rates of wood recruitment. These changes in wood
abundance and size appear to have fundamentally changed the morphology, dynamics, and
habitat abundance and characteristics of lowland rivers across scales from channel unit to
valley bottom.  Based on our field studies, rivers had substantially more and deeper pools
historically. Archival data and field studies indicate that wood jams were integral to creating and
maintaining a dynamic,  anastomosing river pattern with numerous floodplain channels and
abundant edge habitat and routed floodwaters and sediment onto floodplains. Establishing the
                                          34

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condition of the riverine landscape before European settlement sets a reference against which
to evaluate contemporary conditions and develop restoration objectives.
                                          35

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Author: Collins, B.D.; Sheikh, A.J.
Year: 2002
Title: Mapping historical conditions in the Snoqualmie River valley (RM 0 - RM 40)
Reference Type: Report
City: Seattle, WA
Institution: King County Department of Natural Resources and Department of Earth and Space
Sciences,  University of Washington
Pages: 30

Value of reference: This study used a combination of maps and field notes from the General
Land Office (GLO) cadastral survey 1871-1873 and aerial photographs from 1936.  These data
were then  put in a GIS database and used to establish a baseline of "historic condition" by
mapping the channel, wetland, forest, and oxbow ponds in the Snoqualmie River valley prior to
Euro-American settlement, or about 1870. To evaluate subsequent change, conditions were
also mapped from 1936 and 2000 aerial photos.

The availability of pre-settlement accounts and inventories of an area varies by region, so the
implementation of a combination of resources to establish a baseline may be the only way to try
to determine what the conditions were like before Euro-American settlement.  This report is a
good example of this type of method and is a useful tool to identify changes in stream habitat
since settlement.

Results relevant to EMAP: This study provides a good baseline of historic condition and
documents the changes to the system since settlement.

Much of the forest present prior to Euro-American settlement had been cleared, and much of
the wetland cleared and drained by 1936. Riparian vegetation remained along river channels
and oxbows in some areas in 1936

Since -1870, only a few additional oxbows have been created, because the river migration rate
is generally low; most oxbows that now exist were created prior to the earliest mapping in
-1870. Valley wetlands, on the other hand, are substantially diminished in area, in 2000 being
less than one-fifth (19%) the pre-settlement wetland area. Forest cover in 2000 is about one-
sixth (16%) its mapped pre-settlement extent. The small rate of change to the river itself
contrasts with the extensive historical changes to wetlands and forests, which have been greatly
diminished.

Geographic location: Washington, Snoqualmie River Valley, EPA region 10, eco77, mountains

Keywords: phab, riparian wetlands,  forest cover, oxbow, river valley, historical change, pre-
settlement, Euro-American settlement

URL: http://dnr.metrokc.gov/wlr/waterres/streams/snoqhist.htm
                                         36

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Author: Confluence Consulting Inc.
Year: 2004
Title: Powder River biological survey and implications for coalbed methane development
Reference Type: Report
City: Bozeman, MT
Institution: Confluence Consulting, Inc
Pages: 179

Value of reference: Land use practices in the Great Plains dramatically affect stream health
and watershed habitat. This report outlines the changes to the greater watershed looking at pre-
settlement and current conditions. The study includes: physiochemical water quality
measurements; count summaries and listings for, macroinvertebrates, periphyton, fish, reptiles,
amphibians, and birds; and overall habitat health summaries.

In addition, "this study provides a limited  opportunity to evaluate the effects of coalbed methane
(CBM) development already occurring in the Powder River basin in Wyoming. Site selection
provided comparisons of biological, physical, and chemical condition above and below CBM
development along the Powder River. These results allow inference on the effects of current
CBM development on the biological, physical, and chemical integrity of waters in the Powder
River basin."

Results relevant to EMAP: This report contains extensive sampling and survey information on
the Powder River Basin.  The detailed species listings and water quality information highlight the
habitat diversity still present within this system.  This system has remained relatively
undisturbed and data from the early 1960's could be used to estimate pre-settlement conditions.

The Powder River also has importance in terms of Wyoming's natural heritage. In an evaluation
of Wyoming's fish fauna since the 1960s, Patton et al (1998) identified several declining native
species, including flathead chub, plains minnow, river carpsucker, and channel  catfish. The
Powder River drainage " due to its relatively pristine conditions, remains one of the few places in
Wyoming where these species are abundant."

One of the few Great Plains prairie rivers lacking a main stem dam, the Powder River
represents one of the last ecosystems of its kind (Hubert 1993). Moreover, it represents our last
chance to conserve a community of fish and invertebrates that was once widespread. This
community probably occurred throughout the northern Great Plains but dams and other water
developments have changed the ecology of these rivers. As a result, this community is now
relegated to the Powder River and short segments of the Yellowstone and  Milk rivers in
Montana.

This report is a good source that illustrates a relatively undisturbed watershed (very close to
historic condition) along with the changes and impacts the system is currently facing.

Geographic location: Wyoming, Montana, Powder River Basin, Powder River, Clear Creek,
Piney Creek,  eco43, EPA region 8

Keywords: Coalbed methane, stream flow, Great Plains streams, disturbance,  salinity, soil
waterlogging, EIS, phab, native species,  biological survey

URL:
http://www.powderriverbasin.org/cbm/confluence study/CCI%20Powder%20River%20Biological
                                          37

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%20Survev%2010%20March%202004.pdf
                                   38

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Author: Cross, Frank B.; Moss, Randle E.
Year: 1987
Title: Historic changes in fish communities and aquatic habitats in Plains stream of Kansas
Reference Type: Book Section
Editor: Matthews, W.J.; Heins, D.C.
Book Title: Community and evolutionary ecology of North American stream fishes.
City: Norman, Oklahoma
Publisher: University of Oklahoma Press
Pages: 155-165

Value of reference: Article reviews early accounts and collections (mid to late 1800's) to try to
establish pre-settlement conditions of plains streams in Kansas.  Using this information as a
baseline the article summarizes the changes in habitat and fish assemblages over time and
current conditions.  This reference also documents the drastic changes in water use and flows
due to land uses, such as irrigation, cropland agriculture, and impoundments. A good overview
of the changes and disturbances in plains riverine habitats since settlement.

Although study area is outside of current EMAP region, the plains streams in Kansas are similar
to ones found in the plains ecoregions within the EMAP area (e.g., eastern Colorado) and
inferences may be drawn from this study. It is an important, frequently-cited article addressing
historical fish communities in the Plains and is included here because of its prominence in the
literature.

Results relevant to EMAP: Modified flow regimes have greatly altered the composition of the
riverine community in the past decades. Species most highly adapted, morphologically and
behaviorally, to plains rivers have been decimated, whereas fishes less specifically adapted to
fluctuating, turbid rivers have increased.

Changes documented in this article are predominately related to changes in water use and
flows; most of the habitat changes are within the last two to three decades.

Chapter is a good overview of change to historical stream conditions due to water use impacts.
Includes an extensive bibliography.

Geographic location: Kansas, plains, Arkansas river, Smokey hill river, Solomon river,
Kansas river, Missouri River, eco25,  High Plains,  eco27, Central Irregular Plains, eco 47,
Western Corn Belt Plains, EPA region 7

Keywords: phab, fish, nonnative species, turbidity, fish communities, modified flow, historic
condition, plains  rivers, impoundments, agriculture, irrigation

Abstract: Most fishes native to Plains streams have wide distributions in eastern North
America.  Species richness declines from east to west as aridity increases; taxonomic diversity
also decreases, with a few minnow and fewer killifishes becoming increasingly dominant
westward. Subordinate to that trend, the fauna contains distinguishable communities
characteristic of (1) large streams with erratically variable flow, sandy substrate, and high levels
of turbidity and dissolved solids, (2) prairie ponds,  marshes, and  small streams that are clear
and relatively stable, sustained by high water tables, and (3) residual pools of highly intermittent
streams.

The first community is most distinctive, including several endemic species with sensory and
                                          39

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reproductive adaptations to extreme turbidity and widely fluctuating discharge. The second
community includes relic populations of species whose occurrence in the Great Plains is
traceable to glacial climates.  The third community consists of four or five exceedingly
widespread, nearly ubiquitous species. Historically the small-stream  community in Kansas was
extirpated or reduced in complexity soon after settlement of the western plains in the last
quarter of the nineteenth century. Dominant species of the turbid-river community persisted
longer, but many declined precipitously in 1950-80 coincident with receding water tables in the
west and regulated flows in the east (following  impoundment of nearly all rivers in the region).
The endemic riverine fauna was largely replaced by sight-feeding planktivores and  piscivores
adapted to lentic habitats and clear, moderate flow. Several plains species that were common
30 year ago are now seriously threatened.
                                           40

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Author: Cross, Frank B.; Moss, Randle E.; Collins, Joseph T.
Year: 1985
Title: Assessment of dewatering impacts on stream fisheries in the Arkansas and Cimarron
Rivers
Reference Type: Report
City: Lawrence, KS
Institution: Kansas  Fish and Game Commission and Museum of Natural History, University of
Kansas
Pages: 161

Value of reference: Report summarizes status of fishes in Arkansas River basin in Kansas.
The summary utilizes reports from 1853 to 1983 to establish baseline information on fish
communities and stream flow and discharge for the basin.  The report includes hydrologic data
and fish habitat information (historic and present). It is a good summary of what historic
conditions may have been like (based on the historic accounts available) and how the region
has changed post-settlement.

The results of this project are arranged under the following headings: 1) Hydrologic records; 2)
Fish faunas and habitat notes at sites (or stream reaches)  for which an historic record is
available; 3) Accounts of species of primary concern; 4) Accounts of other species captured in
1979-83; 5) Summary: and 6) Appendix- field notes on collections made in 1983.

Although study area is outside of current EMAP region; the plains streams in Kansas are similar
to ones found in the  plains ecoregions within  the EMAP area and inferences may be drawn from
this study. This study highlights similar conditions and issues found in other plains streams
farther west.

Results relevant to EMAP: The objectives of the study were to locate populations of several
species characteristic of the western Plains segment of the Arkansas River basin; to assess the
extent to which these fishes are threatened, by comparison of current and historical
distributional records; and to examine the relationship between changes in stream flows and
changes  in the status of each species.

The first impact of changes on native fishes was extirpation or reduction in range of species
characteristic of small spring-fed streams and marshes. For example, the blacknose shiner and
the Topeka shiner have been extirpated, probably early in this century, before 1950. The
blacknose shiner was listed as abundant (1891), but has not been  found anywhere in Kansas
since 1900.  The second major impact on the native fish fauna of the region was the decline or
disappearance of several species characteristic of shallow, sandy river channels. Fishes
affected adversely are the Flathead chub, Speckled chub, Arkansas river shiner, Emerald
shiner, River shiner,  Plains minnow, and Plains killifish. The lower numbers and distributional
change is indicative  of altered flow conditions.

Altered flows in the larger rivers have not affected all native fishes  in the same way.  For
example  Red shiners have increased, probably as a result of reduced fluctuation and turbidity,
increased lentic habitat, and reduced competition from native species that have declined.

The riverine species that have declined most precipitously  are those whose native ranges were
confined  to prairie streams. Species that have sustained or increased their abundance all range
eastward into trans-Mississippi, forested watersheds. The composite effects of habitat
alteration in streams of this region have "caught in a crunch" those species best adapted to
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highly unstable Plains rivers. The climatic and edaphic conditions which caused highly variable
flows, unstable streambeds, high turbidity and salinity, and rapidly fluctuating stream
temperatures were negated by "dewatering" of the western part of the basin. "Plains river"
habitats are no longer attenuated down stream, due to loss of the western drainage, coupled
with extensive impoundment of the eastern streams.

Geographic location: Kansas, Arkansas River basin, Cimarron River, eco25, High Plains,
eco27, Central Irregular Plains, plains, EPA region 7

Keywords: fish, native species,  fish communities, historic condition, plains rivers, dewatering,
discharge records, impoundments
                                          42

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Author: Dodds, Walter K.; Gido, Keith; Whiles, Matt R.; Fritz, Ken M.; Matthews, William J.
Year: 2004
Title: Life on the Edge: The ecology of Great Plains prairie streams
Reference Type: Journal Article
Journal: BioScience
Volume: 54
Issue: 3
Pages: 205-215

Value of reference: This article presents a good overview of the ecology of plains streams.
Humans have modified most prairie rivers and streams with dams, channelization, pollution,
water abstraction, vast increases of impermeable surfaces in urbanized areas, and other
watershed modifications. These alterations have had a substantial negative impact on a diverse
fish fauna; loss of abundance,  smaller or fragmented habitat range, and extirpation.  They
disrupt the connectivity of river systems, alter flooding regimes, increase or decrease sediment
loads, decrease connection with riparian flood zones, and alter the food webs of the  Great
Plains rivers.

Understanding the ecosystem  function of small streams in the Great  Plains region is essential,
because those streams represent a key interface between terrestrial  habitats and downstream
areas, and substantial in-stream nutrient processing may control downstream water quality.
Physical and biological factors that influence the ecosystem function  of native prairie streams,
including even small headwater reaches, must be studied to help assess current water quality
issues on both local and  continental scales.

This reference has some limited historical information; primarily it is a good overview of the
ecology and unique characteristics found in plains streams. It also highlights many of the
disturbance issues that have occurred since settlement of the region in the mid to late 1800's.

Results relevant to EMAP: Great Plains stream fishes are highly adapted to harsh conditions
and can migrate to areas of permanent water, reproduce quickly, or withstand poor water quality
in isolated pools. Nevertheless, water withdrawals in a number of semiarid regions including the
Great Plains, have exacerbated stream drying and eliminated many spring refugia, while
impoundments have restricted the movement of fishes and further fragmented population.
These alterations to plains streams have had profound effects on the otherwise tolerant fish
communities. Streams in prairies are even more endangered, because many of the remaining
fragments of prairie are not large enough to encompass a significant, functional watershed.

The most heavily affected guild of fishes consists of the large-river minnows. These fish have
historically defined Great Plains river vertebrate communities.  This article summarizes the
ecology of the Great Plains streams and documents the changes in habitat extent, abundance,
and assemblages in some fish communities due to land use practices.

Geographic location: South Dakota,  Wyoming, Nebraska, Platte River, Loup River, Little
Missouri River, White River, Upper Missouri River,  Big Sheyenne River, eco43,  eco44, eco42,
eco47, eco46, plains, EPA region 7, EPA region 8

Keywords: disturbance,  drying, flood, prairie,  Great plains,  streams,  phab, fish, fragmentation

Abstract: Great Plains streams are highly endangered and can serve as model systems for
studying disturbance ecology and related issues of resistance and resilience in temperate
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freshwaters. These streams exist in a precarious balance between flood and drying. In general,
microbial activity recovers in days to weeks after drying or flooding, and invertebrate and fish
species are quick to follow. In lower forested  reaches, floods may be more intense but drying
less common. Upstream reaches of prairie streams are characterized by frequent drying, little
canopy cover, and limited leaf input. Life history and adaptations alter the  ways in which stream
organisms respond to these linear patterns. Human modification has altered these patterns,
leading to large-scale loss of native grassland streams. The future for Great Plains streams is
bleak, given the land-use changes  and water-use patterns in the region and the large areas
required to preserve intact, ecologically functional watersheds.

URL: http://www.bioone.orq/bioone/?request=qet-abstract&issn=0006-
3568&volume=054&issue=3&page=0205
                                          44

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Author: Dose, J.J.; Roper, B.B.
Year: 1995
Title: Long-term changes in low-flow channel widths within the South Umpqua Watershed,
Oregon
Reference Type: Journal Article
Journal: Water Resources Bulletin
Volume: 30
Issue: 4
Pages: 993-1000

Value of reference: Logging and associated road-building activities have been a major form of
disturbance in the Western Forested Mountains, reducing large wood availability in stream
channels. This paper documents evidence that this loss of wood from streams has resulted in
consistent changes in physical habitat (large woody debris, low flow wetted width) between
1937 and -1990. The authors suggest that the condition of anadromous salmonid stocks is
linked, at least in part, to the logging disturbance histories of the basins upon which the fish
depend.

A major value of this reference is that it records changes in physical habitat conditions at the
same locations more than 50 years following logging, a primary form of anthropogenic
disturbance in the Coast and  Cascade Ranges of the Pacific Northwest.

Results relevant to EMAP: Most of the catchments in which timber harvest and road
construction had occurred in the upper South Umpqua River experienced widening of low-flow
wetted stream widths, perhaps attributable to a reduction in large woody debris in  active
channels. Streams that had not been historically logged generally had more wood within the
active stream channel than those in which logging had occurred.  Stream width was similarly
associated with both percent harvest (r2 = 0.44), and road density (r2 = 0.45).

Three of four anadromous salmonid stocks in the South Umpqua River basin are considered at-
risk for extinction, including Chinook salmon (Oncorhynchus tschawytscha), coho salmon
(Oncorhynchus kisutch), and  searun cutthroat trout (Oncorhynchus clarki).  The population  of
winter-run  steelhead remained healthy at the time of the publication.

These declines are attributed, in part, to impacts associated with  timber harvest. The at-risk
populations are found primarily in catchments impacted by silvicultural activities, while he
healthier steelhead population utilizes upstream portions of the basin protected from road
building and timber harvest.

Geographic location: Region 10, South Umpqua River Basin, Oregon, Western Forested
Mountains, mountains, ecol, eco4, eco78, Coast Range, Cascades, Klamath Mountains

Keywords: phab; aquatic ecosystems; forest hydrology; habitat alteration; channel width;
watershed management; logging; roads; salmonids; Chinook salmon (Oncorhynchus
tschawytscha); coho salmon (Oncorhynchus kisutch); steelhead trout (Oncorhynchus mykiss);
searun cutthroat trout (Oncorhynchus clarki); large woody debris

Abstract:  Recent stream survey data (1989-1993) from 31 stream segments within the South
Umpqua Watershed Oregon were compared to 1937 stream survey data collected from these
same stream segments. Concurrent low-flow wetted stream widths of 22 of the 31 surveyed
segments were significantly narrower. In only 1 of 8 tributaries to  the South  Umpqua River
                                         45

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which originated from the lands designated as timber emphasis were significantly wider than in
1937. The observed change in stream width was linearly related to timber harvest (r2 = 0.44),
road density (r2 = 0.45), and the amount of large organic debris remaining in the active stream
channel (r2 = 0.43). These findings suggest that timber harvest and road construction may have
resulted in changes in channel characteristics. These channel changes may also be a factor in
the observed decline of three of the four populations of anadromous salmonids within the basin.

Notes: For the historic site sample descriptions, see: Roth, A.R. 1937. A survey of the waters of
the South Umpqua Ranger District, Umpqua National Forest. U.S.D.A. Forest Service, Portland,
Oregon. (Also available from the Umpqua National Forest, Roseburg, Oregon, 97470.)
                                          46

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Author: Drost, C. A.; Fellers, G.M.
Year: 1996
Title: Collapse of a regional frog fauna in the Yosemite area of the California Sierra Nevada,
USA
Reference Type: Journal Article
Journal: Conservation Biology
Volume: 10
Issue: 2
Pages: 414-425

Value of reference: The primary value of this study is that it represents a careful resurvey of
the margins of streams, in addition to lakes and ponds, and documentation of change of seven
species of amphibians at sites in the Sierra Nevada that were originally surveyed in 1915. The
original survey was conducted prior to the majority of fish introductions or other types of
anthropogenic disturbances. This study is of particular value because of the level of historical
detail, and the range of taxa examined, and the implications related to changes in aquatic
vertebrate indices through time.

Results relevant to EMAP: Severe declines in most species  of sampled amphibians were
observed between  the 1915 and 1992 surveys. The broad scale decline of an entire frog fauna
over a diverse region is unprecedented. Intensive stocking offish into the area began following
the 1915 survey. Large lake populations of amphibians had historically provided opportunities
for amphibian recolonization of small, isolated habitats which are most susceptible to the effects
of natural drought cycles.

The authors hypothesize that large lakes function as reservoirs for amphibian populations, while
perennial streams function as corridors metapopulation dispersal. They suggest that major
reductions of amphibian populations in large lakes following fish introduction may have  reduced
the probability of recolonization of other habitat types, including perennial streams as well as
more isolated habitats following natural localized extinctions.

The authors provide evidence that the introduction of nonnative fish alone, however, is
insufficient to  explain the general trends in amphibian declines. Toads, for example, have also
declined, yet tend to breed in ephemeral waters lacking fish, and produce toxins that fish tend to
avoid. Other, unidentified causes of the observed declines  remain to be identified. The  results
have implications regarding interpretation of vertebrate metrics from  reference sites in this
ecoregion.

Geographic location: EPA Region 9, California,  Sierra Nevada, eco5, mountains

Keywords: amphibians; frogs; toads; introduced fish; nonnative species; amphibian decline;
mountain yellow-legged frog; Rana muscosa; foothill yellow-legged frog; Rana boylii;  red-
legged frog; Rana aurora; Yosemite toad; Bufo canorus; western toad; Bufo boreas; Great
Basin spadefoot; Scaphiopus intermontanus; Pacific treefrog;  Hyla regilla

Abstract: There  has been much concern about widespread declines among amphibians,  but
efforts to mine the extent and magnitude of these declines have been hampered  by the  scarcity
of comparative inventory data. We surveyed a transect of the  Sierra  Nevada mountains in
western North America that was carefully studied in the early  1900s. Our comparisons show
that at least five of the seven frog and toad species in the area have suffered serious declines.
One species has disappeared from the area entirely and a second species, formerly the most
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abundant amphibian in the area, has dwindled to a few small remnant populations. These
declines have occurred in a relatively undisturbed, protected area and show some of the same
patterns noted in other reports of amphibian declines. Introduced predatory fish, possibly
interacting with drought-induced loss of refuge habitats, have contributed to the decline of some
species. However, the overall cause of these dramatic losses remains unknown.
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Author: Duff, D. A.
Year: 1988
Title: Bonneville cutthroat trout: Current status and management
Reference Type: Book Section
Editor: Gresswell, R. E.
Book Title: Status and management of interior stocks of cutthroat trout.
City: Bethesda, Maryland
Publisher: American Fisheries Society
Volume: Symposium 4
Pages: 121-127

Value of reference: The book chapter outlines the historical distribution of the Bonneville
cutthroat trout, its presumed extinction, and the rediscovery of 39 pure strains in headwater
streams of the Bonneville Basin.

Results relevant to EMAP: The article discusses the historic importance of the Bonneville
cutthroat trout to Native American and early settlers' diets and an early commercial fishery. The
fish was once widespread in all available habitats surrounding the Bonneville Basin. The paper
includes a list of pure populations by state and state plans for managing the species, as well as
a map of present day occurrences in the 4 state area.
Fish numbers have been affected by dewatering of streams through irrigation, competition with
nonnative species, and fishing pressure. Trout numbers began their decline after construction of
early irrigation projects when large numbers of fish became trapped in irrigation ditches.

Geographic location: eco13, Utah, Wyoming, Nevada, Idaho, EPA Region 8, xeric, Bonneville
Basin

Keywords: fish, cutthroat trout, distribution, nonnative species, water diversion,  habitat
degradation

Abstract: Only one trout subspecies, the Bonneville cutthroat trout, Salmo clarki utah, is
endemic to the Bonneville Basin, the largest endorheic basin in the Great Basin of western
North America. The subspecies was historically abundant throughout all suitable habitat of a
vast area of Utah, Wyoming,  Nevada,  and Idaho until  about 8,000 years ago, when the
desiccation of ancient Lake Bonneville occurred. During this century, the subspecies suffered a
catastrophic decline from introductions of nonnative trouts and habitat alteration. Today, only 41
populations, primarily limited  to small headwater streams, are known to be genetically pure.
Habitat conditions existing in  waters containing the Bonneville cutthroat trout are marginal, and
the streams are generally small with depleted flows. Yet, in many of these streams,  Bonneville
cutthroat trout still survive. Introductions of nonnative trout have been largely unsuccessful in
these marginal streams, but they have led to the demise of the native cutthroat trout. The
Bonneville cutthroat trout has promising possibilities for enhancing wild trout fishery
management programs within the Great Basin states. As a result of the subspecies' limited
distribution and present threats to its survival, protection of the few remaining populations is
being considered. This paper summarizes the current status and management direction for this
subspecies.

Notes: Hickman, T. J. 1978. Systematic study of the native trout of the Bonneville Basin. MS
Thesis. Colorado State University, Fort Collins, Colorado, is a paper cited in Duff (1988) that
discusses the taxonomy of the Bonneville cutthroat trout, the search for pure populations, and
the reasons for the species' decline in more detail.
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Author: Eberle, Mark E.; Hargett, Eric G.; Wenke, Thomas L; Mankdrak, Nicholas E.
Year: 2002
Title: Changes in fish assemblages, Solomon River basin, Kansas: habitat alterations,
extirpations, and introductions
Reference Type: Journal Article
Journal: Transactions of the Kansas Academy of Science
Volume: 105
Issue: 3-4
Pages: 178-192

Value of reference: This paper summarizes changes in fish communities from likely early fish
assemblages to current assemblages. The study area is outside of the EMAP-West study area,
but is very similar to surrounding plains ecoregions with respect to landscape characteristics,
land  uses, human impacts, and numerous fish species. Therefore, some aspects from this
paper can be applied to plains  regions in EMAP-West, particularly those in Colorado.

Results relevant to EMAP: The authors reviewed  historic literature related to fish accounts to
establish likely native fish assemblages. Using this  baseline the study attempts to establish what
changes in fish assemblages have occurred in the Solomon River basin.  Within the whole
basin, 32% of the native species of fishes have been extirpated, and 51% of the present
assemblage was comprised of nonnative species.  Extant native species in the basin are more
tolerant of a wide range of conditions.

Segments of the historical headwater sections of the rivers and tributary streams had clear, cool
water maintained by springs and groundwater seepage. Conversion of grassland to cropland
increased turbidity in small streams, and most of the fish species extirpations occurred in these
streams.

Stream widths in the two tributary forks were 18-30 m in the 1860s, but were reduced to 2-20 m
by the 1990s,  and substrates contained more fine sediments in the 1990s. Lower stream flows
have resulted  from decreases in surface runoff and base flow.

Changes in fish populations are due to extirpations, range contractions, introductions, and range
expansions associated with alteration in physicochemical attributes of the streams as a
consequence  of agricultural developments and the  construction of impoundments.

Geographic location: Kansas, Solomon River basin, eco27, plains, Central Irregular Plains,
EPA region 7

Keywords: fish, habitat alterations, turbidity, stream discharge, extirpations,  introduction,
nonnative species, impoundment, agriculture, eco27

Abstract: We sampled fishes four times each year at 12 sites on the Solomon, North  Fork
Solomon, and South Fork Solomon rivers in north-central Kansas during 1996 and 1997. Kirwin
and Webster reservoirs are located on the North  Fork Solomon River and South Fork Solomon
River, respectively,  and Waconda Reservoir inundates the confluence of these two rivers at the
head of the Solomon River. Multivariate analyses identified two fish assemblages that were
related to stream discharge. One fish  assemblage was associated with stream segments that
had lower discharges, such as  those located upstream from Kirwin and Webster reservoirs.
This  assemblage was characterized by equal  numbers of extirpations of native species and
introductions of nonnative species.  The other fish assemblage was associated with the
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reservoirs and stream segments that had higher discharges. This assemblage was
characterized by a large number of species that were introduced or had immigrated into these
areas.  For the basin as a whole, 32% of the native species of fishes have been extirpated, and
51 % of the present assemblage was comprised of nonnative species.  Most of the extirpations
and introductions are associated with habitat changes caused by agricultural development and
the construction of impoundments. The relatively large component of the fish assemblage
comprised of nonnative species reflects the trend toward homogenization offish assemblages
throughout the United States.
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Author: Eby, L. A.; Pagan, W. F.; Minckley, W. L.
Year: 2003
Title: Variability and dynamics of a desert stream community
Reference Type: Journal Article
Journal: Ecological Applications
Volume: 13
Issue: 6
Pages:  1566-1579

Value of reference: Minimally disturbed reference streams in desert regions are rare. Aravaipa
Creek, a tributary to the San Pedro River in Arizona, retains its historic complement of native
fish species, and it is often studied to develop expectations for other desert streams.

Results relevant to EMAP: Seven native fish species inhabit Aravaipa Creek, including 2
federally listed species and five candidate species. The mid- and upper reaches retained the full
complement of fish species over the last 30 years, though there was variation in the proportional
abundances of the dominant fish species (longfin dace, Gila spikedace, and desert sucker). The
lower reaches of Aravaipa Creek did show a decline in species richness, likely due to the
invasion of eight exotic species. Two species, spikedace and loach minnow, have disappeared
from the lower reaches of Aravaipa Creek; both are susceptible to  replacement by the nonnative
red shiner

The authors  conclude that one of the major factors central  to maintaining a full complement of
native fish species in desert streams is flow variability. Flash floods and high spring runoff favor
native fish that are adapted to such conditions and discourage the  establishment and
domination of exotic (nonnative) species.

Geographic location: Aravaipa Creek, Sonoran Desert, Region 9, Arizona, San Pedro River,
eco23, eco81, xeric

Keywords: Aravaipa Creek, community  composition, conservation, desert stream, exotics, fish,
flow variability, measures of community change, Sonoran Desert, hydrologic variability, flash
floods, runoff, nonnative species

Abstract: Communities can be highly variable over a few years, but remain fairly constant over
the long term. Evaluating measures and  examining the variability associated with long term
change  is useful because it increases our understanding of and our ability  to predict responses
to disturbances. We used long term fish  community data from Aravaipa Creek, Arizona, USA, a
Sonoran Desert stream, to determine whether there had been long term changes in the
community composition, what measures best describe these shifts, and what environmental
factors are correlated with the changes. Aravaipa Creek is an intrinsically variable system and
one of the few remaining desert streams to support its complete historical assemblage of native
fishes. Multivariate analyses illustrated important changes  in composition of the native fish
community that were not described by traditional measures of persistence  and stability. In the
early 1980's, changes in community composition were correlated with alterations in base flow,
while more recent changes are likely associated with the presence of exotic species. Changes
in stream morphology,  hydrology, and climate have decreased flow variability, thereby
increasing the likelihood of exotic establishment, and may have increased  the downstream
connection between Aravaipa Creek and the San Pedro River thus increasing the likelihood of
repeated invasions by nonnative species. These results support previous research in
intrinsically variable desert systems, which conclude that retention  of high flow variability is
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important to conservation of the native fish community. In addition, although connectivity in
aquatic lotic systems is important, isolation from large river systems teeming with exotics may
be important in preserving these remnant native fish assemblages.

URL: www.esaiournals.org/esaonline/?request=get-toc&issn=1051-
0761&volume=013&issue=06
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Author: Echelle, A.A.; Luttrell, G.R.; Larson, R.D.; Zale, A.V.; Fisher, W.L.; Leslie, D.M., Jr.
Year: 1995
Title: The Great Plains: decline of native prairie fishes
Reference Type: Report
City: Washington, DC.
Institution: U.S. Department of the Interior, National Biological Service
Pages: 530

Value of reference: This  reports specifically on declines of the Arkansas River shiner and the
Arkansas River speckled chub, both of which once occurred in the upper Arkansas River in
Colorado, as well as other states that are outside the EMAP-West region. The text reports both
as historically inhabiting Colorado, although the historical range maps (Figures 1 and 2) do not
show historical collections in Colorado. The authors may have used anecdotal information to
define historical ranges even if the species were not formally sampled historically in some
portions of the basin; however, they do not cite these ancillary sources, if used. The reference
is one of very few that represent a modern synthesis of historical fish distributions in the Plains.

Results relevant to EMAP: The Arkansas River shiner was historically widespread in the
Arkansas River basin. It has been extirpated from about 75% of the river reaches in its range,
as assessed before 1985, and is now considered extirpated in Colorado.  It experienced great
decline between 1983 and 1985.

The speckled chub occurred throughout the Arkansas River basin, including Colorado.  By the
early 1990s, the chub had declined notably, and it is believed to be extirpated from Colorado
and reduced by about 75% of its total historic range.

Low stream flow during the breeding season, a period historically associated with peak flows,
has affected successful reproduction and recruitment.  Intensive agriculture has resulted in
demand for irrigation  water and creation of numerous reservoirs, resulting in degraded habitat
Impoundments fragment the landscape, limiting access to suitable habitat and isolating
populations.

Geographic location: Colorado, Arkansas River basin, eco26, eco25, plains, EPA region 8

Keywords: fish, habitat fragmentation, altered water flow regime, agriculture,  dams

URL: http://biology.usgs.gov/s+t/pdf/Plains.pdf
                                          54

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Author: Erman, N.A.
Year: 1996
Title: Sierra Nevada Ecosystem Project: Final Report to Congress, vol. II, Assessments and
scientific basis for management options. Status of Aquatic Invertebrates.
Reference Type: Report
City: Davis, CA
Institution: University of California, Centers for Water and Wildland Resources
Pages: 987-1008
Report Number: Report No. 39

Value of reference: An important paper based upon a systematic review of standard library
databases, including taxonomic studies, impact studies, geographic surveys of specific
taxonomic groups, and behavioral studies, unpublished, non-refereed reports, and experts on
specific taxonomic groups. Museum collection information was not examined.

This resource thoroughly reviews the types of anthropogenic disturbances (mining, logging,
damming,  diversions, roads, grazing) and associated stressors which have impacted Sierra
Nevada streams during the last 200 - 300 years. The author discusses changes in physical
habitat, macroinvertebrates, and elaborates on problems  associated with reconstructing historic
macroinvertebrate distributions in the face of limited reference collections and revisions of
taxonomic relationships. This document can be of use for guiding best professional judgment
regarding probable changes in macroinvertebrate assemblages and derived metrics following
anthropogenic disturbances characteristic to the region.

Results relevant to EMAP: Prior to the immigration of Europeans and Asians 200-300 years
ago, the Sierra Nevada systems contained macroinvertebrate taxa characteristic of continuously
flowing waters. Major changes in the  region have occurred in flow regimes as a result of dams
(see Fig. 35.1), sediment budgets, substrate characteristics, stream temperature, and channel
morphology. Over the last 200 years, many rock-bottomed perennial streams  have been filled
with sediment due to  hydraulic gold mining activities to the point where surface flow no longer
exists (Mount 1995). Dispersal barriers have been destroyed, major changes have occurred to
riparian vegetation, streams have been intentionally poisoned with rotenone and actinomycine,
and unintentionally contaminated with heavy metals, herbicides, and pesticides.  Nonnative
organisms have been both intentionally and unintentionally introduced.

As a result of these changes, the author uses deductive reasoning to conclude that there has
probably been a reduction in macroinvertebrate richness,  macroinvertebrate species diversity,
and relative abundance of certain species in streams.  In reservoirs, portions of streams that
once contained fauna characteristic of free-flowing water,  such as Plecoptera for example, are
now dominated by taxa characteristic of habitats where sediments accumulate, such as
burrowing  Chironomidae larvae, other midges, and oligochaetes.

Habitat destruction such as alteration of natural hydrology and accumulation of excess
sediment is of special concern due to the high degree of endemism in the region. Twenty five
percent of known Plecoptera species, 19% of Trichoptera, 9% of Blephariceridae midges, 25%
of Deuterophlebeiidae midges, 20% of molluscs, and 10% of fairy and brine shrimp (Anostraca)
are endemic. The author stresses, however, that a systematic survey of aquatic
macroinvertebrates has yet to be conducted in the Sierra  Nevada. While some groups have
been reasonably well surveyed, such as Plecoptera and Trichoptera, others require more
attention, such as  Diptera and Ephemeroptera.
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Geographic location: EPA Region 9, California, Sierra Nevada, mountains, Eco5

Keywords: macroinvertebrates; fish; pre-European; change; Sierra Nevada; California; dams;
water diversion; roads; mining; grazing; sediments; intentional invertebrate introductions;
opossum shrimp; Mysis relicta,  signal crayfish; Pacificasticus leniusculus; rotenone; antimycin

Abstract: The aquatic invertebrate fauna of the Sierra Nevada is diverse and extensive, with
many endemic species throughout the range. Aquatic systems differ widely in the Sierra
because of such natural factors as elevation, climate patterns, geology, substrate type, water
source, water volume, slope, exposure, and riparian vegetation. These differences are reflected
in the aquatic invertebrate fauna. Small, isolated aquatic habitats such as springs, seeps,
peatlands, and small permanent and temporary streams have  a high probability of containing
rare or endemic invertebrates. Aquatic invertebrates are a major source  of food for birds,
mammals, amphibians, reptiles, fish, and other invertebrates in both aquatic and terrestrial
habitats. Changes in a food source of such importance as aquatic invertebrates can have
repercussions in many parts of the food web. The life cycles of aquatic invertebrates are
intricately connected to land as well as water, and the majority of aquatic invertebrates spend
part of their life cycle in terrestrial habitats. Aquatic invertebrates are affected by human-caused
activities on land as well as activities in the water. Land and water uses and impacts are
reflected in species assemblages in streams and lakes. Changes in aquatic invertebrate
assemblages have been used for many decades to monitor impacts on land and in water.
However, the level of detail of most monitoring is not sufficient to track species  losses in aquatic
invertebrates. Aquatic invertebrates have not been inventoried or well-studied at the species
level in most of the Sierra. Aquatic invertebrates are rarely considered or evaluated in
environmental impact assessments in the Sierra. Major changes have occurred in aquatic and
terrestrial habitats in the Sierra of the last 200 years: we must  logically assume that
corresponding changes have occurred in aquatic invertebrate assemblages.

Notes: Mount, J.F. 1995. California rivers and streams: The conflict between fluvial process and
land use. Berkeley and Los Angeles: University of California Press.

URL:  http://ceres.ca.gov/snep/pubs
                                          56

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Author: Evermann, B.W.
Year: 1891
Title: A Reconnaissance of the Streams and Lakes of Western Montana and Northwestern
Wyoming
Reference Type: Journal Article
Journal: Bulletin of the United States Fish Commission
Volume: 11
Pages: 3-60

Value of reference: This is a primary data source that reports the physical and natural-history
features of the streams and lakes of the region, including size, depth, current, stream
obstructions, source of water, water temperature, water clarity, composition of bottom and
banks, human impacts, fish species, abundance, size, condition, and distribution, and
invertebrates (crustaceans, insects, mollusks) that could be fish prey.  The authors had a
particular focus on geographical distribution of fishes and attempted to trace the limits in the
range of species. All waters examined are given, which include locations on the Clarke Fork
and Snake River of the Columbia basin and the Yellowstone River, Madison, River, Gallatin
River, Jefferson River, and Prickly Pear Creek of the Missouri River basin.

The first part of the report is a series of description of the streams visited, including physical
habitat, and lists offish, invertebrates, and frogs present. The second part is an annotated list
of each fish species, including all the locations where it was found and the number of each that
were collected. This section also contains species descriptions and taxonomic notes.  The third
part is an annotated list of reptiles and batrachians collected.

This information is valuable for constructing the historical distribution of indigenous fish species
in the region and to assign the presence of invertebrates and amphibians to particular streams.
It may also be useful for comparing historical physical habitat attributes with current conditions.

Results relevant to EMAP: The total collection of indigenous fish obtained on this expedition
was only 16.  The author was confident that it represented the  fish fauna of the region fairly well.
The species included genera in the following families: Catostomidae,  Cyprinidae,  Salmonidae,
Cottidae, and Gadidae. Four introduced Salmonids  were also  noted.  Reports of amphibians
and reptiles were incidental, i.e., no time was devoted to searching for them.  Nevertheless,
over 2  pages of the report are devoted to reporting results of findings of (primarily) amphibians
in the genus Rana.

The report should be consulted for details of fish species occurrences and physical habitat
descriptions of the streams visited.

Geographic location: Montana, Wyoming, Columbia River basin, Missouri River basin, Clarke
Fork River, Snake River, Yellowstone River,  Madison River, Gallatin River, Jefferson River,
Prickly Pear Creek, EPA region 8,  mountains, eco17

Keywords: fish, amphibians, phab, macroinvertebrates, historical data, historical distribution,
primary source
                                           57

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Author: Evermann, B.W.
Year: 1896
Title: A report upon salmon investigations in the headwaters of the Columbia River, in the state
of Idaho, in 1895 together with notes upon the fishes observed in that state in 1894 and 1895
Reference Type: Report
City: Washington, D.C.
Institution: Government Printing Office

Value of reference: This report covers 2 areas in central Idaho: 1) the headwaters of the
Salmon River and 2) several inlets and outlet streams in the Redfish Lakes region on the west
side of the Salmon River Valley at the  east base of the Sawtooth Mountains.  The first part of
the report describes physical habitat (riparian vegetation, width, depth, sediment type, woody
debris, water temperature) and presence of salmon and other fish species, as well as extent of
spawning habitat in the inlet and outlets streams and in Salmon River headwater tributaries.

The second part is a detailed report on each species of fish observed, including information
about relative abundance and distribution and specific tributary streams where each species
was seen or collected. Known distribution and abundance of each species in other portions of
the Snake or Columbia basins is also mentioned for some of the species.  The focus of the
report is salmon, particularly the sockeye; therefore these species receive more treatment in the
text. The report is an important synopsis of historical fish distribution in an area that is not often
reported  in the historical literature (see other citation in Notes section below). It also documents
the distribution of Chinook and sockeye salmon and gives other detailed descriptions, such as
length and weight of individuals collected.

Results relevant to EMAP: The report covers 21 species offish from the central region of
Idaho, including lamprey, sturgeon, suckers, chubs, shiners, dace, whitefish, salmon, steelhead,
bull trout, and sculpins. Details about  distribution, relative abundance, and stream physical
habitat descriptions occur throughout;  the report should therefore be consulted for specific
information.

Geographic location: Idaho, eco16, EPA region 10, mountains, Salmon River basin

Keywords: fish, phab, historical data,  primary source, baseline information

Notes: A related document focusing on salmon in the same region:

Evermann, B.W. 1896. A preliminary report upon salmon investigations in Idaho in 1894.
Bulletin of the U.S/ Fish Commission 1896:253-284.
                                          58

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Author: Evermann, B.W.; Cox, U.O.
Year: 1896
Title: Report upon the Fishes of the Missouri River Basin
Reference Type: Report
City: Washington, D.C.
Institution: U.S. Commission of Fish and Fisheries

Value of reference: This  primary source is an excellent synthesis of the fishes known to the
Missouri River basin in the late 1800s.  The report is presented in four sections, beginning with
results of fish examinations done in various streams the authors visited  in South  Dakota,
Nebraska, and Wyoming in 1892-1893.  Results include physical habitat descriptions of streams
visited and a notations of  fish  in each location. Following that report is  an annotated
bibliography (in chronological order) of the ichthyology of the entire Missouri River basin,
including all known faunal lists at the time.  Complete citations of these works is given for further
consultation, if desired. Each entry lists the locations examined, a list of the fish  species found
and their locations. Next is an annotated list of the fishes based on sources listed in the
bibliography, including all  the locations in the basin where each species had been documented
prior to 1896. This section can be cross-referenced, by source, with the annotated bibliography
in the preceding section.  Finally, the table on pages 426-428 summarizes the occurrence of
143 fish species by state in the Missouri River basin.  In addition to these  143 species, a list of
74 nominal species is given on pages 424-425; of these,  52 had been recognized at the time of
this report.

This is an important historical synthesis and would be useful for reconstructing historical ranges
and fish communities before major fish introductions and interbasin transfers had occurred.  It
may also be useful for comparing historical and current physical habitat attributes of streams
and river tributaries.

Results relevant to EMAP: Lists of fish species, by sub-basin and state,  and physical habitat
descriptions (for sites visited in South Dakota, Nebraska, and Wyoming in the late 1800s) can
be found in detail in this report. The results synthesize what had been published on species
occurrences in the basin,  beginning with the explorations of Lewis and Clark in 1803-06.  The
report should be consulted for details.

The total number of species and subspecies of fishes known from the Missouri Basin in 1896
was  143.  These were distributed among 24 families and 68 genera (see table, pages 426-428),
and among 9 states.  The majority of species occurred in non-EMAP states in the lower basin
and in the eastern portion of the basin; only 55 species were known from North Dakota,
Montana, Wyoming, and Colorado, and 10 of those were endemic. The authors present a
section on the unique community of 15 species found in the isolated Black Hills region. They
also acknowledge introduced species-notably carp, rainbow trout VonBehr trout (brown trout),
and Eastern  brook trout. They note that there may be others that have  been introduced by state
fish agencies, but do not provide any further detail about nonnative species (possibly there were
not many to report).

Geographic location: Missouri River basin, Montana, North Dakota, South  Dakota, Wyoming,
Colorado, eco17, eco18, eco26, eco21, eco42, eco43, eco46, eco25, plains, mountains, xeric,
EPA region 8

Keywords: fish, phab, historical data, Missouri River basin, historical occurrence, primary
source
                                          59

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Notes: This report is Appendix 5 from the Report of the U.S. Commissioner of Fish and
Fisheries for 1894, pages 325-429. It was extracted and published as a stand-alone report.
                                         60

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Author: Evermann, B.W.; Rutter, C.
Year: 1894
Title: The Fishes of the Colorado Basin
Reference Type: Journal Article
Journal: Bulletin of the United States Fish Commission
Volume: 9
Pages: 473-486

Value of reference: This is a frequently-cited, early, primary data source that presents a
comprehensive synthesis of the earliest documentations of fishes in the Colorado River basin,
based on publications dating from 1848 to1891.  An annotated bibliography (18 citations) of the
ichthyology of the Colorado Basin is included to provide the background material the authors
use to construct, in chronological order, the different places in the Colorado Basin where each
species was recorded during the period of 1849-91. Since fish documentation was not based
on surveys or a systematic census, the data indicate only presence (not absence); the historical
accounts also differ in their geographic scopes. The paper lists, by species, locations where
present, as reported in the literature (all of which is referenced in the annotated bibliography).
Most of the historical collections on which this work was based were  made in river tributaries of
the Colorado River.

Results relevant to EMAP: Thirty-two native fish species, representing 5 families and 18
genera, were recognized for the Colorado Basin by 1891 (list by family and genus, with number
of species in each genus is given in this publication).  The Cyprinidae, by far, contained the
greatest number of species, comprising almost 60% of the species, followed by Catostomidae
with 25% of the species. Approximately 78% of the species of fishes known in 1891 from the
CO Basin were endemic.

The approximate locations where each species was documented on  each tributary are given in
tabular format for each species separately. These lists are cross-referenced with the citations in
the annotated bibliography. The text contains scattered notes about relative abundance (e.g.,
common, abundant...) for some of the  species.

Geographic location: Colorado River basin, EPA Region 8, EPA Region 9, xeric, mountains,
eco21, eco22, eco23, eco20,  eco18, eco81,  Colorado, Wyoming, Utah, Arizona, New Mexico

Keywords: fish, historical data, geographic distribution
                                          61

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Author: Fausch, Kurt D.; Bestgen, Kevin R.
Year: 1997
Title: Ecology of fishes indigenous to the Central and Southwestern Great Plains
Reference Type: Book Section
Editor: Knopf,  Fritz L; Samson, Fred B.
Book Title: Ecology and Conservation of Great Plains Vertebrates.
City: New York, NY
Publisher: Springer
Pages: 131-166
Series Title: Ecological Studies 125

Value of reference: Journals from early scientific expeditions, such as John C. Fremont's two
trips up the Platte River system in 1842 and 1843 are assumed to be accurate representations
of undisturbed  Plains ecosystems. However this information is sparse and does not include
detailed accounts of fish assemblages of the time.  Little is known about the indigenous fishes of
the Great Plains, especially considering the extensive modification of aquatic environments that
began about 1860.  Distributions of some species were likely altered by transfers among waters,
whereas others were probably locally extirpated before any specimens were collected.

This chapter attempts to draw together information about the distribution and  ecology of fishes
indigenous to the central and southern Great Plains, a  region encompassed largely by
upstream reaches of the Platte, Kansas, Arkansas, Canadian, and Pecos rivers; includes pre-
settlement and post-settlement information.

Chapter includes descriptions of the physical characteristics of Plains streams and what is
known of the original fish fauna and its characteristics, reproductive ecology of Plains fishes,
and factors influencing variability of populations and assemblages. Summary is a synthesis of
ecological mechanisms with broad implications for conservation of plains fishes of the region.

Results relevant to EMAP: Describes the ecology of the region; based on historic data and
current information about the biota, streams,  and physical characteristics of the streams and
landscape.

Chapter highlights what is known about the distribution of fish fauna and factors influencing
variability of populations and assemblages.

This provides a synthesis of the changes in fish distribution, assemblages, and habitat that have
occurred since settlement due to factors like; impoundments, water diversions; introductions,
etc.

Geographic location: Colorado, Platte River, Kansas River, Arkansas River, Canadian River,
Pecos River, eco 25, High Plains, eco27 Central Irregular Plains, plains, EPA region 8

Keywords:
Great plains, plains,  phab, fish, native species, pre-settlement, water diversion, impoundments,

Abstract: The  Great Plains of western North America are a harsh environment for fishes. Due
to the increasing aridity and general lack of permanent water one finds traveling westward
across the Plains, even trained biologists rarely consider fishes or their habitats when
transversing the region. The same was true of early explorers. For example, none of the four
scientific expeditions that ascended the Platte River in the first half of the 1800s described
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Plains fishes, whereas flora and other fauna were collected and described extensively (e.g.
Fremont expedition , 1843-1843; Jackson and Spence 1970). Indeed, no collections offish from
the Plains region of the South Platte River Basin in Colorado were preserved until 1873 (Cope
and Yarrow 1875).

It is therefore not surprising that relatively little is known about the indigenous fishes of the Great
Plains, especially considering the extensive modification of aquatic environments that began
about 1860 (Eschener et al. 1983). Distributions of some species were likely altered by transfers
among waters, whereas others were probably locally extirpated before any specimens were
curated (cf. Jordon 1891). Moreover, little is known about the basic life history of many fishes
that range widely throughout the Plains, and even less is understood about the ecology of other
biota in Plains streams and riparian zones (Matthews  1988, Zale et al.  1989, Brown and
Mathews 1995).  This information is urgently needed,  due to the continued acceleration of
human degradation and loss of species populations from these aquatic ecosystems (Cross and
Moss 1987).

Our goal in this chapter is to draw together information about the distribution and ecology of
fishes indigenous to the central and southern Great Plains,  a physiographic region
encompassed largely by  upstream  reaches of the Platte, Kansas, Arkansas, Canadian, and
Pecos  rivers (Cross et al. 1986) (Fig 6.1). We emphasize the Platte and Arkansas rivers  in
eastern Colorado and the Pecos River in New Mexico, because we have firsthand knowledge
and experience in these basins.  However, we incorporate literature from other Plains rivers and
from similar rivers in the adjacent Central Lowlands to the east, where  appropriate.

Because one can interpret little about the ecology of organisms without understanding the
physical template to which they are adapted (cf. Southwood 1988), we begin by describing the
physical characteristics of Plains streams. We then discuss what is known of the original fish
fauna and its characteristics, reproductive ecology of Plains fishes, and factors influencing
variability of populations and assemblages. We end by attempting a synthesis of ecological
mechanisms with broad implications for conservation of plains fishes of the region and by
summarizing needs for further research.
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Author: Fisher, R. N.; Shaffer, H. B.
Year: 1996
Title: The decline of amphibians in California's Great Central Valley
Reference Type: Journal Article
Journal: Conservation Biology
Volume: 10
Issue: 5
Pages:  1387-1397

Value of reference: This is one of a very few historical trend analyses of amphibians in the
western United States.

Results relevant to EMAP: Historical distribution data were compiled for six native species of
amphibians based on museum specimens (see Notes below) for the Sacramento Valley, San
Joaquin Valley, and the Coast Range near San Francisco. These data were compared with field
data collected  between  1986 and 1994 at 315 ponds distributed across  the same geographic
area to document species declines. Six amphibian species were historically widespread in this
habitat and a single aquatic breeding site would generally contain between two and five species.

Results record a statistically significant decline in the number of species currently found in most
counties compared with that found historically. Declines varied from 1 out of 28 counties lost for
Pacific treefrog (P. regilla) to 24 out of 28 counties lost for California red-legged frog (R. aurora).
Graphs and distribution maps are given for 5 species (four natives plus  introduced bullfrog)
showing historical records compared to recent detections. Table 1 shows that there is a
significant inverse relationship between introduced exotics and native amphibians. For three
species, historical localities were significantly lower in elevation than are current viable
populations.  Most of low elevation sites sampled were unoccupied by native species, compared
with their historical pattern of distribution, implying they have been lost from these areas.

Causes of decline are attributed to exotic and introduced species predation and competition,
pond alteration or loss.

Geographic location: xeric,  Central Valley, California, coast range, San Joaquin valley,
Sacramento valley, eco6, eco7, EPA Region 9

Keywords: amphibians, historical data, museum records, California newt, California tiger
salamander, Pacific treefrog,  western spadefoot toad, western toad, California red-legged frog,
bullfrog, nonnative species, habitat degradation, habitat loss

Abstract: Declines in amphibian populations are rarely reported on the  community or
ecosystem level. We combined broad-scale field sampling with historical analysis of museum
records to quantify amphibian declines in California's Great Central Valley. Overall,  amphibians
showed an unambiguous pattern of decline, although the intensity of decline varied both
geographically and taxonomically. The greatest geographical decline was detected in the
counties of the Sacramento and San Joaquin valleys. Two species, Rana aurora and Bufo
boreas, were identified as the most affected by decline, whereas Pseudacris regilla was the
least affected.  The Coast Range counties had  little or no detectable decline. We provide new
evidence implicating introduced predators as a primary threat. Introduced predators occur at
lower elevations than native species, and our data indicate that for some native species there
has been significant restriction to higher elevation sites from a formerly  broader distribution. Our
historical approach provides a strategy for identifying declining amphibian communities that
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complements more detailed, long-term monitoring programs and provides an assessment of the
pattern of change that is a necessary prerequisite for the development of field experiments that
test hypothesized mechanisms of change.

Notes: See Schaffer et al. 1998 in this bibliography for general discussion of the use of
museum specimens for reconstructing historical aquatic communities.
                                         65

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Author: Frissell, C.A.
Year: 1993
Title: Topology of extinction and endangerment of native fishes in the Pacific Northwest and
California (U.S.A.)
Reference Type: Journal Article
Journal: Conservation Biology
Volume: 7
Issue: 2
Pages: 342-354

Value of reference: Existing information is synthesized into a synoptic map of WA, OR, ID, and
CA with isopleths showing patches representing numbers of native fish species extinct,
endangered, or threatened. Also included is Table 1, listing basins in CA, OR, and WA, the
number of native fish taxa in each, and the proportions that are extinct, endangered, threatened,
or of special concern. The mapping procedure can identify regions and ecosystems at high risk,
which can be targeted for more  intensive monitoring.

Results relevant to EMAP: The native ichthyofauna that has become extinct, endangered, or
threatened (EET) is highest in CA (mean 48%), lower but still high in OR (mean 33%) and
lowest in WA (mean 13.5%); the proportion of native fauna that is EET declines as native
species richness in the basin increases.

The spatial patterns of EET are  influenced more by the many basin-specific population groups
of seven widely distributed species of anadromous salmonids than by the more than 60 locally
endemic species and subspecies of suckers,  minnow, pupfishes, and other fishes.

The simultaneous decline  of numerous taxa in basins with and without dams or diversions
suggests that cumulative damage to aquatic habitats caused by logging, grazing, urbanization,
and other land uses plays  a major role in ichthyofaunal impoverishment.

Geographic location: mountains, xeric, ecol, eco3, eco7, eco6, eco78, west coast, California,
Oregon, Washington, EPA Region 9, EPA Region 10

Keywords: fish, status, extinction, mapping, dams, logging, grazing, urban

Abstract:  Recent studies have provided a broad data base on extinction and endangerment of
species, subspecies, and distinct populations of inland fishes in western North America.
Development of a synoptic, regional-scale image of extinction and risk of extinction is
complicated by the small size and  linear distribution of fluvial aquatic habitats and by
interspecific variation in areal extent of populations.  I developed a regional map of extinction-
risk isopleths based on the number of extinct and persistently declining species in drainage
basins of the Pacific Northwest and CA.  This topological synthesis is useful for delineating and
monitoring areas of historic and ongoing loss of aquatic biodiversity, and for relating losses to
patterns of land use and habitat modification, climate, hydrology, and geomorphology.  From an
ecological perspective, endangerment of numerous indigenous populations of seven widely
distributed species of anadromous salmonids in this region is as important as the more local,
diffuse effects of declines in more than 60 endemic, non-anadromous species and subspecies.
The simultaneous decline  of numerous taxa in basins not afflicted with dams or diversions
suggests that cumulative damage to aquatic habitats caused by logging, grazing, urbanization,
and other land uses plays  a major role in ichthyofaunal impoverishment.
                                          66

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Author: Fulton, L.A.
Year: 1968
Title: Spawning areas and abundance of Chinook salmon (Oncorhynchus tshawytscha) in the
Columbia River Basin-past and present
Reference Type: Report
City: Washington, D.C.
Institution: U.S. Department of Interior. Fish  and Wildlife Service, Bureau of Commercial
Fisheries
Report Number: Special Scientific Report-Fisheries No. 571

Value of reference: This article shows status and trends based on run estimates for a middle
period of time (1930s to 1960s), as well as the commercial catch trend for the Columbia River,
1865-1962 (see Figure 1) as an indicator of Chinook salmon population changes through time.
Since much degradation had already occurred by the 30s, the 1930s numbers of salmonids are
probably lower than pre-settlement, but estimates still represents a period when Chinook salmon
were much more numerous and widely distributed than today.  The losses of spawning  areas
since the 30s indicate changes in distribution, reduction in range, habitat destruction, physical
barriers, and impacts on reproduction.  Locations of spawning areas and their status (past and
present) are given in a tabular format for multiple tributaries of the Columbia  River basin.

Results relevant to EMAP: Commercial catch trends for Columbia River 1865-1962 were
fluctuating but stable from the late 1800s through 1920, but then fell to about 1/3 the previous
numbers.  This decline was attributed  to advancing  civilization in the PNW-irrigation, logging,
mining, dam construction, and other activities reduced the size and capacity  of spawning areas;
for most species, many spawning areas had been completely lost by 1968.

Spring and summer runs of Chinook in the Columbia River 1939-55 (excludes catches by sport
fishery in the ocean and lower Columbia River, landings by the offshore troll  fishery, and
escapement to tributary streams entering the Col River below Bonneville Dam with the
exception of the Wllamette River run) had an increasing trend. Runs  of fall Chinook in the
Columbia R. and escapement to areas above Bonneville Dam (excludes same as above), 1938-
66, showed a fairly steep declining trend.

Geographic location: Columbia River basin, mountains, xeric, ecol,  eco3, eco4,  eco2, ecolO,
eco11, eco15, eco16,  eco12, eco17, eco9, Washington, Oregon, Idaho, EPA Region 10

Keywords: fish, Chinook salmon, water diversion, logging, mining, dams

Abstract: Chinook salmon, the most abundant species of salmon in the Columbia Basin,
formerly spawned  in nearly all tributaries of the Columbia River and in many  areas of the main
river.  Over the past 60 years, the construction of dams has inundated, impeded, or blocked
access to spawning areas.  Despite these heavy losses, large areas of spawning grounds in the
middle and lower portions of the drainage are still available to Chinook salmon.  Stream
improvements by State and Federal fishery agencies have rehabilitated some areas and have
brought others into production for the first time.  Important spawning areas are listed and
charted in this report according to their past use (before 1965) and present use (1966).
Estimates of recent spawning populations in major tributaries and in segments of the main stem
are also given. Former and present levels of abundance are listed according to three major
runs-spring, summer, and fall.

Notes: This reference is a companion to Fulton  1970, which  provides  synopses for steelhead
                                         67

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trout, coho, chum, and sockeye salmon
                                       68

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Author: Fulton, L.A.
Year: 1970
Title: Spawning areas and abundance of steelhead trout and coho, sockeye, and chum salmon
in the Columbia River Basin-past and present
Reference Type: Report
City: Washington, D.C.
Institution: U.S. Department of Commerce, National Oceanic and Atmospheric Administration,
National Marine Fisheries Service
Report Number: Special Scientific Report-Fisheries No. 618

Value of reference: Conditions in the mid to late 1800s are scattered throughout this
document, much in the form of commercial catch or production records, which are used as
surrogates of relative population sizes. Also shown are status and trends for 1930s to 1960s,
using run counts. Spawning areas and their status (past/present) are given per creek or river in
a tabular format.

Results relevant to EMAP: The Columbia river run  and commercial catch estimates have
fluctuated  greatly with time, but the general trends have been substantial declines for all four
species since the turn of the century.  Coho had a slight rebound in the early 60s; chum were
practically extinct at the end of the 1960s. Tabular detail in the paper shows how the changes in
spawning ranges contributed to the declines in each tributary in the Columbia River drainage, by
species, for 1938-66 (fish runs) and 1890/1900 -1966  (commercial catch).

Declining catches and loss of spawning areas are attributed to logging, highway construction,
agricultural cultivation, placer mining,  and dumping of wastes. Report  lists parts of
subwatersheds where these fish species once spawned and where they no longer occurred in
1969.

Geographic location: Columbia River basin, mountains, xeric, Oregon, Washington, EPA
Region 10, ecolO, eco4, eco11, eco 15, eco16. eco3, eco9

Keywords: fish, salmonids, logging, roads, agriculture, mining, pollution, dams, water diversion

Abstract:  Past spawning areas (those removed from use before  1969) and present ones (those
in use in 1969) are described for steelhead, trout, Salmo gairdneri; coho salmon, Oncorhynchus
kisutch; sockeye salmon, O. nerka; and chum salmon,  O. keta. The different species
characteristically spawn in the following areas: 1) steelhead trout-in streams of all sizes (widely
dispersed  throughout the watershed, 2) coho salmon-in small streams (mostly in the lower
tributaries) and in a few areas in the middle watershed, 3) sockeye salmon-in lakes and
tributaries  of lakes (in the middle portion of the watershed),  and 4) chum salmon-in lower
portions of tributaries that enter the Columbia River below The Dalles dam. All four species
have lost many spawning areas because of water-use  developments and changes  in the
watershed resulting from logging, highway construction, agricultural cultivation, placer mining,
and dumping of wastes. Serious depletion of the runs  of all four species is evident from the
available data (the commercial catches before 1938  and since 1938 augmented by information
on escapement and sport catch). The future prospects are fair for steelhead trout, good for
coho salmon, and poor for sockeye and chum salmon.

Notes: This reference is a companion to  Fulton 1968, which provides similar synopses for
Chinook Salmon
                                          69

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Author: Gerstung, E.R.
Year: 1988
Title: Status, life history, and management of the Lahontan cutthroat trout
Reference Type: Journal Article
Journal: American Fisheries Society Symposium
Volume: 4
Pages: 93-106

Value of reference: This is the most complete summary found of the decline of the Lahontan
cutthroat trout  (Oncorhynchus clarki henshawi) and its causes.  It thoroughly describes the
historic distribution and decline separately for 5 sub-basins:  Truckee River, Carson River,
Walker River, Humboldt River, and Smoke Creek/Black Rock sub-basins.  Populations that
have been established outside their native waters of the Lahontan Basin, as a result of stocking
hatchery-reared fish, are also covered.

Although possibly not of as much use to EMAP, this publication also summarizes the life history
of Lahontan cutthroat trout, including migration, breeding, habitat preferences, feeding, and
growth.  In full, it is an excellent synopsis of the species and its historical and current status (as
of 1988).

Results relevant to EMAP: At the time of early settlement of the region, Lahontan cutthroat
trout reportedly existed in waters throughout the basin, including most cooler perennial streams
downstream from impassable falls, totaling at least 6,100 km of stream habitat (as well as in 11
lakes). A map is included (Figure 1) that shows the probable historic and present distribution of
the trout in the 5 sub-basins of the region. Also shown are the locations of introgressed
populations.  Following European settlement, the species was extirpated from much of the
native range. Currently (1982) self-sustaining populations are found in a total of only 490  stream
miles, which represents only 7% of the historic range in stream habitats.

Historical distributions are described in detail for each of the sub-basins and contrasted with the
subspecies' current distribution; reasons for decline are given for each as well.  Table 1 gives
the probable historic and present (1982) habitat extent (stream km) for each of the sub-basins.
From this,  one could calculate the percent of probable historic stream km occupied presently.

There is dispute among authors over whether the Humboldt River sub-basin populations are the
same subspecies as those in other sub-basins, but they are  covered here as if they are the
same. The Humboldt populations differ taxonomically and also seem better adapted for life in a
fluvial system than in a lacustrine one.

Reasons for severe decline of this subspecies include over-fishing, competition and
interbreeding with nonnative trout, construction of dams, water diversions, and general habitat
degradation.

Geographic location: Nevada, California, Lahontan basin, ecoSO,  eco13,  eco5, EPA Region  9,
xeric, mountains

Keywords: fish, fishing, nonnative species, dams, water diversion,  habitat degradation

Abstract:  The Lahontan cutthroat trout Salmo clarki henshawi is believed to have occupied at
least 6,100 km of stream habitat and 135,000 ha of lake habitat in its historic range. Some lake
populations such as those in  Lake Tahoe, California-Nevada and in Pyramid and Walker  lakes
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in Nevada were large enough to support thriving commercial fisheries.  Pure self-sustaining
stocks of Lahontan cutthroat are now limited to headwater streams within the Humboldt River
drainage, to Summit and Independence lakes, and to several small tributaries of the Truckee,
Carson, and Walker rivers. A small number of additional populations have been established
outside the Lahontan Basin in both California and  Nevada by transplants and hatchery
production in each of these states. Self-sustaining Lahontan  cutthroat trout populations are
known to occur in 100 locations, representing about 7% of the historic stream  habitat and 0.4%
of the historic lake habitat. Competition from and hybridization with introduced nonnative trout,
the construction of dams and diversions on important spawning streams, and water quality
deterioration are largely responsible for the decline of Lahontan cutthroat trout. Restoration
efforts in California and Nevada will involve, eliminating nonnative trout from selected streams,
restocking with endemic stocks where possible, and improving and protecting  habitat.
Hatchery-reared stocks will continue to be utilized  in various lake and reservoir recreational
fishing programs, including those existing in Pyramid and Walker lakes.

Notes: Dunham et al. (1997) (citation below) discuss the effects of habitat fragmentation and
loss of connectivity throughout the range of this trout as being a major obstacle in its survival as
a subspecies.

Dunham, J.B., G.L. Vinyard, and B.E. Rieman. 1997.  Habitat fragmentation and extinction risk
of Lahontan cutthroat trout.  North American Journal of Fisheries Management 17:1126-1133.
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Author: Gilbert, C.H.; Evermann, B.W.
Year: 1894
Title: A report upon investigations in the Columbia River basin, with descriptions of four new
species of fishes
Reference Type: Journal Article
Journal:  Bulletin of the United States Fish Commission
Volume:  1
Pages: 169-207

Value of reference: This is a detailed primary literature source reporting fish specimens
collected as part of a survey begun in 1892 to locate a hatchery site in the Columbia basin.  It
contains a list of the river tributaries and streams examined and a report on each, including brief
descriptions of physical habitat (substrate, riparian vegetation, water temperature, channel
width, depth,  nature  of banks, pools, and current), general abundance of fish, and a short list of
the dominant  fish species.  Following stream descriptions is a list of fish species, the locations
where they were collected, and the numbers collected. Results are useful for determining
historical presence and distribution.  Report contains scattered anecdotal notes on what was
known about  distribution  and abundance based on surveys or other work prior to 1892.

The information about fish presence and relative abundance would be useful for reconstructing
historical ranges and fish assemblages in river tributaries.  Some reconstruction of taxonomy
based on type specimens and location from the historical text would be  necessary for
interpreting results and making comparisons with present-day taxonomy. A variety of physical
habitat information can also be extracted from this  source for use in reconstructing historical
physical conditions for specific streams in the Columbia basin.

Results relevant to EMAP: A variety of baseline data can be extracted from this document,
including fish  species presence, relative abundance, and dominance in various tributary basins,
as well as physical habitat features of streams.

The specimens collected include lamprey, sturgeon, suckers, minnows, chub, squawfish,  dace,
salmon, steelhead, trout, and sculpin; mention also of carp, which at that time had been recently
introduced.

Geographic location: Columbia River basin, Oregon, Washington, Idaho, EPA Region 10,
mountains, xeric, ecolO,  eco11, eco12, eco16, eco15, eco9, eco4, eco3, ecol

Keywords: fish, phab, historical data, fish presence, fish abundance
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Author: Gilbert, C.H.; Scofield, N.B.
Year: 1895
Title: Notes on a collection of fishes from the Colorado basin in Arizona
Reference Type: Journal Article
Journal: Proceedings of the U.S. National Museum
Volume: 20
Issue: 1131
Pages: 487-499

Value of reference: This account details the occurrence in the Colorado River basin of 19 fish
species in the late 1800s. It also makes corrections to a previous collection and archival
account by Evermann and Rutter (1894, this bibliography).

Results relevant to EMAP: The primary objective of the research expedition was to investigate
the alleged occurrence of shad in the Lower Colorado. In the process, the authors made
reports and descriptions of other fish they found and their locations in the lower basin.
Therefore, this was not a complete or systematic survey of the river basin,  but it can be used for
developing a list of species and general locations where species were present in the late 19th
century.

The number of specimens (or relative number, e.g., "numerous specimens"), collection
locations, and sometimes the relative abundance at the location are given at the beginning of
each species account for each of 19 species. Locations are specified very generally, e.g., "in
the Salt River at Tempe,  AZ"; "Chino, AZ, in a tributary of the Rio Verde". The great majority of
text is descriptions of fish and not of much use to EMAP.  It is a good supplement to the 1894
account of Colorado Fishes by Evermann and Rutter (in this bibliography) for describing
historical fish community composition and species distributions.

Geographic location: Colorado River Basin, Arizona, eco81, eco23, eco22, eco14,eco20, EPA
Region 9, xeric

Keywords: fish, historical data

Notes: This reference is  a supplement to Evermann and Rutter (1894)--in this bibliography
                                          73

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Author: Gilbert, E.W.; Litt, B.
Year: 1966
Title: The exploration of Western America 1800 - 1850
Reference Type: Book
City: New York
Publisher: Cooper Square Publishers, Inc.
Number of Pages: 233
Original Publication: 1933
Reprint Edition: 1966

Value of reference: These early explorations of the west are the first observations of the region
by European-Americans. Observation of the landscape and plants and animals of the area help
establish what pre-settlement conditions were like. This book contains documentation of
several explorations ranging from  1800 to 1850 and provides good descriptions of the physical
habitat, geology, flora and fauna of the region..

Results relevant to EMAP: The book contains chapters on the Physical geography, climate,
natural drainage, natural vegetation, and animals of the region. In addition to overall
descriptions of the landscape, many of the expeditions include information about the
characteristics of the streams and rivers. This mainly consists of physical characteristics
including: flow, sinuosity, riparian vegetation, and some fish information. This baseline is helpful
in establishing pre-settlement condition of the streams before navigation and irrigation
modifications  had been made.

The chapters  require some sifting through to extract pieces of anecdotal information or to
reconstruct stream  related attributes, however; the information is  quite valuable and may be the
only  source of pre-settlement conditions  of the region. This is a good broad reference and
inventory that includes specific information about pre-settlement conditions.

Geographic location: Western United States, North Dakota, South Dakota, Nebraska, Kansas,
Missouri, Colorado, Wyoming, Oregon, Washington,  Utah, EPA Region 7, EPA Region 8, EPA
Region 9, eco47, eco27, eco25, eco44, eco42, eco46, eco17, eco18, eco21, eco17, ecoSO,
eco16, eco15, eco3, eco4, ecolO, eco11

Keywords: exploration, phab, resource inventories, pre-settlement condition, historic condition,
historical geography, geology, expeditions
                                          74

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Author: Gregory, S.C; Deacon, J.E.
Year: 1994
Title: Human induced changes to native fishes in the Virgin River drainage
Reference Type: Book Section
Editor: Marston, R.A.
Book Title: Effects of Human Induced Changes on Hydrologic Systems.
City: Middleburg, VA
Publisher: American Water Resources Association
Pages: 435-444
Series Title: Technical  Publication Series No. 94-3

Value of reference: Article addresses the native fish of the Virgin River, the impacts that have
caused their declines beginning in the 1930s, and the reduction of these species from different
parts of the drainage. It is a good and thorough synopsis, including graphics of the trends in
native and nonnative species abundances, and describing the trends in species distribution in
different sections of the drainage as a result of multiple impacts.

Results relevant to EMAP: Despite early settlement of the Virgin River, (1850s-90s), the six
native fish species of the Virgin River remained relatively unaffected until large scale habitat
changes  occurred, beginning in 1935 with the Hoover Dam, which eliminated the native fish
community in the lower 25 miles of the river.

Tributary populations were depleted in the 1960s and  1970s due to reservoir construction and
dewatering (diversions) and poisoning offish, followed by introduction of trout and cattle
grazing, while middle mainstream fishes were most affected during 1980s by municipal and
agricultural water management that altered both variability and volume of flow and by the
upstream invasion by the introduced red shiner.

Today, the Virgin chub and woundfin are federally endangered, and the Virgin spinedace is a
candidate for threatened status-all three are endemic to the Virgin River.  Water diversions and
dewatering is the greatest threat to native fish, followed by dams and other flow alterations;
more recently, population pressures and municipal water development projects have put
demands on the river.

Geographic location: xeric, eco20, eco22, eco14,  Nevada, Utah, Arizona, Virgin River basin,
EPA Region 8, EPA Region 9

Keywords: fish, historical data, dams, nonnative species, grazing, water diversion, fish
poisoning, endangered  species, Federal Reserved Water Rights

Abstract: The Virgin River originates in southwestern Utah and joins the Colorado River in
southern Nevada where it flows into the Overton Arm of Lake Mead.  Analysis of a considerable
database on native fishes collected over the past 17 years, supplemented by historical records,
reveals reductions in both distribution and abundance of the native fish community.  Following
construction of Hoover Dam, Lake Mead flooded the lower 25 miles of the Virgin River,
eliminating the native fish community in the 1930s.  Reservoir construction, development of trout
fisheries, and cattle grazing, depleted native fish communities in tributary streams during the
1960s and 1970s. The  middle mainstream fish fauna was most severely affected during the
1980s following upstream invasion by the introduced red  shiner and  construction of a 45,000
acre-foot off-stream  reservoir.  The native fish community of the Virgin River Drainage maintains
relatively natural abundance today only in Zion National Park and for a short distance
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downstream, and in a segment of the Santa Clara River above Gunlock Reservoir.  Water
development plans for the future threaten the fish community in those areas.  Federal Reserved
Water Rights, management of endangered species, sport fish management, irrigation rights,
and pressure to provide water for urban growth place conflicting demands on the Virgin River
and highlight ethical dilemmas of a human population faced with adjusting to a world with limits.
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Author: Gresh, T.; Lichatowich, J.; Schoonmaker, P.
Year: 2000
Title: An estimation of historic and current levels of salmon production in the Northeast Pacific
ecosystem
Reference Type: Journal Article
Journal: Fisheries
Volume: 25
Issue: 1
Pages: 15-21

Value of reference: This work reviews estimates of historic salmonid run sizes in western North
America, based upon historic cannery records and previously published estimates of historical
abundance dating back to 1866. It also provides an estimate of the amount of marine-derived
nitrogen and phosphorous that were delivered to regional streams annually in the form of
salmon carcasses, which, the authors argue, were important for the survival of juvenile
salmonids in nutrient-poor streams. It provides a review of what is known about the influence of
marine-derived carbon (MDC) upon algal growth, macroinvertebrate abundance, growth and
survival of juvenile coho salmon (Oncorhynchus kisutch). This paper may be helpful in
reconstructing 'reference conditions'  in stream systems that were historically dependent upon
marine-derived nutrients.

Results relevant to EMAP: Marine-derived nitrogen, phosphorous, and carbon, which play an
important role in algal growth, macroinvertebrate abundance, and juvenile salmonid growth and
abundance in western streams, have dropped to 6 - 7% of historic (1880s) levels, associated
with the decline of historic salmon (Oncorhynchus spp.) runs.  Regionally, the Pacific salmon
biomass return has dropped from  an estimated 156 - 254 million kilograms to 12 -13 million
kilograms. Anthropogenic disturbances such as extirpation of beaver, logging, irrigation,
grazing, pollution, dams,  sport and commercial fishing have contributed to the decline of
salmonids, and possibly a spiraling ecosystem failure in streams of Washington, Oregon, and
California.

Geographic location: Region 10, Region 9, Washington, Oregon, California, Sacramento
River, Columbia River, Fraser River, Coastal Oregon Rivers, Klamath River, Coastal
Washington Rivers, ecol, eco2, eco3, eco4, eco78, eco6, eco7, eco9, ecolO, eco11,  eco77,
Coast Range, Puget Lowland, North Cascades, Wllamette Valley, Cascades, Klamath
Mountains, Southern and Central  California Chaparral and Oak Woodland, Central California
Valley, Eastern Cascades Slopes  and Foothills, Columbia Plateau, Blue Mountains, mountains

Keywords: fish, phab, salmon populations; coho; Oncorhynchus kisutch; fishing; logging;
agriculture; grazing,  pollution; dams; nutrient deficit; nitrogen; phosphorous

Abstract:  We used historical cannery records and current escapement and harvest records to
estimate historical and current salmon escapement to western North American river systems, in
order to determine the biomass and marine-derived  nitrogen and phosphorous levels delivered
by adult salmon, and deficits corresponding to the diminished returns of adult salmon over the
past century. We have estimated the  historic biomass of salmon returning to the Pacific
Northwest (Washington, Oregon, Idaho, and California) to be 160-226 million kg. The  numbers
indicate that just 6-7% of the marine-derived nitrogen and phosphorous once delivered to the
rivers of the Pacific Northwest is currently reaching those streams. This nutrient deficit may be
one indication of ecosystem failure that has contributed to the downward spiral of salmonid
abundance and diversity  in general, further diminishing the possibility of salmon population
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recovery to self-sustaining levels.
                                              78

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Author: Haden, G. A.; Shannon, J. P.; Wilson, K. P.; Blinn, D. W.
Year: 2003
Title: Benthic community structure of the Green and Colorado rivers through Canyonlands
National Park, Utah, USA
Reference Type: Journal Article
Journal: Southwestern Naturalist
Volume: 48
Issue: 1
Pages: 23-35

Value of reference: The authors suggest a model of the pre-settlement benthic flora and fauna
of the Colorado  River system by examining the invertebrate communities in the free flowing
sections of the Green and Colorado Rivers in Canyonlands National Park. These river reaches
are the farthest downstream of large impoundments and they retain similar hydrographs to pre-
dam condition.

Results relevant to EMAP: This study provides the first description of the abundance, standing
mass, taxa, feeding guilds, and  primary carbon sources for benthic macroinvertebrates at six
remote sites on  the Green and Colorado  rivers and provides an example of how the pre-dam
Colorado River system might have functioned. The authors hypothesized that the aquatic
community adjusted to flooding  and high  suspended sediment and that macroinvertebrate
standing mass was relatively stable  even with seasonal community composition changes.
They found that macroinvertebrate food resources were limited to allochthonous sources due to
high suspended sediment concentrations; however, there was an invertebrate assemblage that
processed this form of carbon and provided food for higher trophic levels.
Hard substrates were limited, but the complexity of riverine habitats, such as side channels,
backwaters,  and wetlands, and  the presence of wood might have augmented the standing mass
and species  richness of the invertebrate assemblage.

Geographic location: Region 8, Utah, Green River, Colorado River, eco20, xeric, Canyonlands
National Park

Keywords: macroinvertebrates, phab, dams, sediment, hydrologic variability, historic reference

Abstract: We sampled the aquatic benthos at 6 remote sites on the Colorado and Green rivers
through Canyonlands National Park, Utah, USA. This study provides the first published
description of benthic standing mass, invertebrate community composition, and primary carbon
source for this portion of the Colorado  River system. High suspended sediment concentrations
prohibited growth of primary producers. The primary carbon source for benthic invertebrates
was terrestrial organic matter. The invertebrate community was composed of 49 taxa, mostly
mayflies, caddisflies, and Diptera, which were dominated by filterer/collector species. A smaller
portion of the community was made up of predatory stoneflies and odonates. Standing mass of
invertebrates on cobble substrates within a given site was stable over the multiyear sample
period (1993 through 1996) and was comparable with other southwestern streams (overall
mean = 0.41 g/m2 ash-free dry mass).  Invertebrate standing mass at each site was controlled by
the availability of primary carbon. Primary carbon availability was controlled by supply to the site
and retention within the site. Both aspects might be influenced by anthropogenic alteration of
the river basin and discharge patterns  upstream of the study site.
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Author: Hamilton, J.B.; Curtis, G.L.; Snedaker, S.M.; White, O.K.
Year: 2005
Title: Distribution of anadromous fishes in the upper Klamath River watershed prior to
hydropower dams--a synthesis of the historical evidence
Reference Type: Journal Article
Journal: Fisheries
Volume: 30
Issue: 4
Pages: 10-20

Value of reference: This publication uses a variety of historical information to reconstruct the
distribution of anadromous fish above the Iron Gate Dam, which now restricts fish passage to
the upper Klamath River  basin.  It is significant in its use of multiple sources as lines of evidence
of fish species' historical  presence at multiple sites throughout the upper basin. Detailed
historical documentation  about presence and distribution in the upper basin is provided for:
Chinook salmon (spring and fall runs), steelhead, coho salmon, anadromous Pacific lamprey,
sockeye salmon, green sturgeon, eulachon, cutthroat trout, chum salmon, and pink salmon

Results relevant to EMAP: Prior to dam construction on the Klamath system, anadromous fish
migrated beyond the current site of Iron Gate dam (closed in 1962).  This dam, at river km 307,
is the current limit of upstream passage.

Numerous sources of information (many dating to the 19th century) are presented regarding the
occurrence of Chinook salmon, steelhead, coho salmon, and Pacific lamprey above the current
location of Iron Gate Dam.  A map (Figure 1) plots the cited incidents of each species  in the
upper basin, with cross-references to the literature documentation used as evidence (listed in
Table 1).

Chum salmon, pink salmon, eulachon, and cutthroat trout were limited historically to the lower
Klamath River, well below current location of Iron Gate Dam.

Geographic location: Klamath River basin, Oregon, California, eco78, eco4, eco9, EPA
Region 10, mountains

Keywords: fish, dams, anadromous fish distribution, historical documentation, historical
photographs, fish passage

Abstract: Knowledge of the historical distribution of anadromous fish is important to guide
management decisions regarding the Klamath  River including ongoing restoration and regional
recovery of coho salmon  (Oncorhynchus kisutch). Using various sources, we determined  the
historical distribution of anadromous fish above Iron Gate Dam.
Evidence for the largest,  most utilized species, Chinook salmon (Oncorhynchus
tshawytscha), was available from multiple sources and clearly showed that this species
historically migrated upstream into tributaries of Upper Klamath Lake. Available information
indicates that the distribution of steelhead (Oncorhynchus mykiss) extended to the Klamath
Upper Basin as well. Coho salmon and anadromous lamprey (Lampetra tridentata) likely were
distributed upstream at least to the vicinity of Spencer Creek. A
population of anadromous sockeye salmon (Oncorhynchus nerka) may have occurred
historically above Iron Gate Dam. Green sturgeon (Acipensermedirostris), chum salmon
(Oncorhynchus keta), pink salmon (Oncorhynchus gorbuscha), coastal cutthroat trout
(Oncorhynchus clarki clarki), and eulachon (Thaleichthys pacificus) were restricted to  the
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Klamath River well below Iron Gate Dam. This synthesis of available sources regarding the
historical extent of these species' upstream distribution provides key
information necessary to guide management and habitat restoration efforts.

URL: http://www.fisheries.org/html/fisheries/F3004/F3004p10-20Hamilton.pdf
                                          81

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Author: Hasse, Adelaide R.
Year: 1899 (digital version: 2003)
Title: Reports of Explorations Printed in the Documents of the United States Government: a
Contribution Toward a Bibliography
Reference Type: Electronic Source
Producer: U.S. Government Printing Office
Access Year: 2005
Access Date: August 25, 2005
Last Update Date: Aug. 25, 2005

Value of reference: A great source of surveys, reports, and exploration made during the mid to
late 1800's by the US government.  This listing is a comprehensive source of any type of
resource inventory, observation, report,  etc. made throughout the US and could be a valuable
look at the "historic conditions" of these  areas.

This is a digitized edition of Reports of Explorations Printed in the Documents of the United
States Government taken from a 1st edition (1899) copy held by the University of Minnesota
libraries:

Reports of Explorations Printed in the Documents of the United States Government: a
Contribution Toward a Bibliography. Compiled by Adelaide R. Hasse. (Washington, D.C.: U.S.
Government Printing Office, 1899. (GP 3.5:2 1899)). Transcription and encoding by Jennifer
Claybourne Torkelson, 2000. XML Source Encoding. Navigation elements added by Amy West,
Government Publications Library, 2003.

Results relevant to EMAP: A good source to locate available pre-settlement literature and
references. This web site includes  listings of many early exploration accounts and
observations, which may be the only sources for pre-settlement conditions in some areas of the
Western United States. Stream conditions and species inventories may be limited; however,
some baseline information can be gleaned from some of these references.

Geographic location: western United States

Keywords: Explorations, phab, resource inventories, pre-settlement condition, historical data,
historical condition, geography, geology, expeditions

URL: http://govpubs.lib.umn.edu/digdoc/hasse.phtml
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Author: Hassemer, P. F.; Kiefer, S. W.; Petrosky, C. E.
Year: 1997
Title: Idaho's salmon: Can we count every one?
Reference Type: Book Section
Editor: D. J. Stouder; P. A. Bisson; R. J. Naiman
Book Title: Pacific Salmon and their Ecosystems: Status and Future Options.
City: New York, NY
Publisher: Chapman and Hall
Pages: 113-125

Value of reference: The article's main focus is present day salmonid status and monitoring, but
there is a section on habitat loss over the last 100 years.

Results relevant to EMAP: Dam construction has been the major factor resulting in loss of
access to salmon spawning and rearing habitat in Idaho. About 62% of Idaho's historical
spawning and rearing habitat for spring/summer Chinook and steelhead remains available, but
only 17% of the historical habitat remains available for Snake River fall Chinook salmon due to
the construction of the 3 dam Hell's Canyon complex in the 1960's.

The 62% that is still accessible to spring and summer Chinook and steelhead represents approx.
6055 river km out of 9741 km estimated to exist in predevelopment times. Similarly, 172 km of
suitable habitat is available to fall Chinook out of and estimated 989 river km (17% of
predevelopment km).

Approximately  30% of Idaho's stream kilometers inhabited by salmon and steelhead are located
within designated wilderness areas or waterways classified as wild  and scenic rivers.

Geographic location: Idaho, Salmon River, Snake River, Clearwater River, mountains,
Columbia River, eco15, Northern Rockies, EPA  Region 10

Keywords: fish, habitat loss, phab, dams, Chinook salmon, spawning habitat

Abstract: Since the late 1950's, Idaho  Dept. of Fish and Game (IDFG) biologists have collected
standardized information about the status of salmon (Oncorhynchus spp.) in Idaho to assist
fisheries management. Currently, IDFG uses indices of production such as  redd and parr counts
for streams, and adult salmon counts at dams and weirs, to assess the recent history of our
salmon runs. We depict Idaho anadromous salmon trends using indices for sockeye, spring,
summer, and fall Chinook salmon, and steelhead. Counts of redds in index areas provide the
best historical indicator of trends and status of spring and summer Chinook salmon. Numbers of
redds have declined sharply through the last 33  years. All of the naturally reproducing Snake
River anadromous salmonid populations, excluding Chinook salmon in the Clearwater River
drainage and Snake River steelhead, have been listed as endangered pursuant to the federal
Endangered Species Act. Hydroelectric development of the mainstem Snake and Columbia
rivers is widely recognized as the major factor causing the decline of these populations.

Aggregated trend information is useful, but alone does not provide information needed for future
management. We must augment historical information with knowledge about brood-year
performance of multiple populations. We are using our indexed production information for life
cycle modeling to assess productivity, a key to assessing recovery actions.  Increased
monitoring and analyses of indicator populations will better describe salmon status and trends to
meet management needs for the future.
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Author: Hatch, M. H.
Year: 1949
Title: A century of entomology in the Pacific Northwest
Reference Type: Book
City: Seattle
Publisher: University of Washington Press
Number of Pages: 43

Value of reference: This short reference provides the best historical overview of who collected
what types of macroinvertebrates, where, and when in the Pacific Northwest. The author divides
entomological activities into four periods, including (1) the period of itinerate collectors, (2) the
period of resident collectors, (3) the period of established laboratories from 1890-1930, and the
'present' (4) 1930 -1949. The work contains a taxonomic index by order to guide readers to
references to specific historic materials.

This is baseline information, and, although sparse in coverage,  it should help to define the
limitations of historical reconstructions of aquatic macroinvertebrate assemblages in this region.
It also lists important literature for macroinvertebrates in the region by order. [Note: Many of the
collections mentioned in this reference have subsequently been assembled in the entomological
museum collection housed at Oregon State University]

Results relevant to EMAP: Macroinvertebrates were first collected in the Pacific Northwest in
the mid 1830's, but most collection activities were focused upon certain terrestrial orders
(Coleoptera, Lepidoptera) or those of importance to humans at that time, such as horticultural
pests, rather than aquatic macroinvertebrates.  References to aquatic orders discussed in this
reference  include Coleoptera, Diptera, Hemiptera, Neuroptera, Odonata, and Plecoptera.

Geographic location: Oregon, Washington, Idaho, Region 10, Mountains, Xeric, Eco1, Eco2,
Eco3, Eco4, Eco9,  Eco78, Eco77, EcolO, Eco11, Eco12, Eco15, Eco16, Eco17, EcoSO

Keywords: Macroinvertebrates; historical data; taxonomy; Coleoptera;  Diptera; Hemiptera;
Neuroptera; Odonata;  Plecoptera; Pacific Northwest
                                          84

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Author: Hatch, M. H.
Year: 1953
Title: The beetles of the Pacific Northwest
Reference Type: Book
City: Seattle, WA
Publisher: University of Washington
Volume: 16
Number of Pages: 340

Value of reference: There are few works which synthesize early information on aquatic
macroinvertebrates other than taxonomic keys. Keys such as this one provide a brief overview
of the history of the collection and study of specific groups within the western United States,
bringing together links to hundreds to thousands of individual published taxonomic records. This
key contains records of Coleoptera collected in the Pacific Northwest as early as 1834. It
provides the  starting point for identifying who collected aquatic Coleoptera, where, when, and
who described the taxa, dating back to the 1850s. The key provides information on generalized
occurrence information by state, and qualitative abundance. This may be useful for beginning to
reconstruct expected macroinvertebrate faunal composition and diversity metrics.

Results relevant to EMAP: Coleoptera were among the first insect orders collected in the
western United States. By the end of the 1870s, 500-600 species of Coleoptera were  known
from the Pacific Northwest, most of which were terrestrial. Descriptions of the families
Amphizoidae and Dytiscidae, which inhabit stream margins date to the early 1850s (LeConte
1852).

Geographic location: EPA Region 9, EPA Region 10, mountains, xeric, Oregon, Washington,
Idaho, California

Keywords: macroinvertebrates; historical data; Coleoptera; Amphizoidae; Dytiscidae

Notes: LeConte, John L. 1852.  Descriptions of some new species of Coleoptera from  California.
Ann. Lye. Nat. Hist. N. Y. V:125-216.
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Author: Henshall, J.A.
Year: 1906
Title: A list of the fishes of Montana with notes on the game fishes
Reference Type: Report
City: Missoula, MT
Institution: University of Montana
Pages: 13
Report Number: Bulletin of the University of Montana, No. 34-11

Value of reference: This is a compilation from multiple sources of the 36 native fish known in
Montana in 1906.  It is arranged by family and species and gives the names of rivers and
streams or general portion of the state where each species had been documented up to that
time.  Several species were identified from descriptions of Lewis and Clark; but most species
were collected on U.S. government railroad surveys and, more recently, by the U.S. Bureau of
Fisheries. The list is followed by the list of species that had been introduced in Montana at that
time.  The final section,  notes on game fish,  is not as relevant to EMAP as the initial list. The
location information can be used to reconstruct historical ranges of species and species
composition of major tributaries

Results relevant to EMAP: As of 1906, 36 species of fishes had been recorded as native in
Montana, and numerous introductions had occurred. The locations for each species listed here
might not be the complete list of where they  actually occurred; however, this list can provide
information on general historical distribution  of the fish species (primarily in the Missouri River
basin of Montana) and might be useful cross-referenced with Evermann and Cox 1896 (in this
bibliography)

Geographic location: Missouri River basin, Montana, EPA region 8, eco17, eco42, eco43,
mountains, plains

Keywords: fish, historical data, geographic distribution, primary source, baseline information
                                          86

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Author: Holden, P. B.; Deacon, J. E.; Golden, M. E.
Year: 2005
Title: Historical changes in fishes of the Virgin-Moapa River system: Continuing decline of a
unique native fauna
Reference Type: Book Section
Editor: J.N. Rinne; R.M. Hughes; Calamusso, B.
Book Title: Historical Changes in Large River Fish Assemblages of the Americas.
City: Bethesda, Maryland
Publisher: American Fisheries Society
Pages: 99-114

Value of reference: The chapter gathers what is known about the historical distribution of
native fishes in the Virgin-Moapa Rivers and their tributaries, and compares that with more
recent trends from the 1970's to the present. The river valleys  were populated with settlers in
the 1850's but were little studied until the 1930's (Hubbs and Miller) and 1970's (Cross).

Results relevant to EMAP: The authors describe the native fish species and their typical
habitats in both the mainstem and the tributary streams of the  Virgin and Moapa Rivers. They
present very limited evidence of fish collections from early surveys (1870's) and attribute the
shrinking habitat left for native fish to irrigation diversions, drowning of the lower rivers by Lake
Mead, and competition from warm water exotics and introduced  trout.

Of the 9 native fish species and subspecies in the Virgin-Moapa  River system 5 are endemic,
which is indicative of the unique habitats in these rivers. Map (p.  100) showing refugia for native
fishes in 1970 compared with 2002. Table (p. 104) of native and  nonnative species in the Virgin-
Moapa Rivers, listing extirpated species (desert sucker, woundfin) and endangered species
(Moapa dace, Virgin River chub).

Geographic location: EPA Region 9,  EPA Region 8, Utah, Nevada, Arizona, Virgin River,
Moapa River, eco19, eco13, eco14, xeric, mountains

Keywords: fish, nonnative species, water diversions, agriculture, dams, urban

Abstract: The Virgin-Moapa River system supports nine native fish species or subspecies, of
which five are endemic. Woundfin (Plagopterus argentissimus) and Virgin River chub (G/7a
seminuda) are endemic to the main-stem Virgin River, whereas cooler and clearer tributaries
are home to the Virgin spinedace (Lepidomeda mollispinis). Moapa dace  (Moapa  coriacea) and
Moapa White River springfish (Crenichthys baileyi moapae) are found in thermal springs that
form the Moapa River, and Moapa speckled dace (Rhinichthys osculus moapae) is generally
found below the springs in cooler waters. The agricultural heritage of the Virgin-Moapa River
system resulted in numerous diversions that increased as municipal demands rose in recent
years. In  the early 1900's,  trout were introduced into some of the cooler tributary streams,
adversely affecting Virgin spinedace and other native species. The creation of Lake Mead in
1935 inundated the lower 80 km of the Virgin River and the lower 8 km of the Moapa River.
Shortly thereafter, nonnative fishes invaded upstream from Lake Mead, and these species have
continued to proliferate. Growing communities continue to compete for Virgin River water.
These anthropogenic changes have reduced distribution and abundance  of the native Virgin-
Moapa River system fish fauna. The woundfin, Virgin River chub, and  Moapa dace are listed as
endangered, and the Virgin spinedace has been proposed for  listing. In this paper we document
how the abundance of these species has declined since the Endangered  Species Act of 1973.
Currently, there is no strong main stem refugium for the Virgin River native fishes, tributary
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refugia continue to be shortened, and the Moapa River native fishes continue to be jeopardized.
Recovery efforts for the listed and other native fishes, especially in the Virgin River, have
monitored the declines, but have not implemented recovery actions effective in reversing them.
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Author: Hoppe, G. N.
Year: 1938
Title: Plecoptera of Washington
Reference Type: Journal Article
Journal: University of Washington Publications in Biology
Volume: 4
Issue: 2
Pages: 139-174

Value of reference: This valuable reference provides a well documented example of the
paucity of knowledge of aquatic macroinvertebrates prior to the period of systematic surveys
conducted between the 1920s - 30s, long after settlement of the region. Although this
represents only one order, it reflects the level of familiarity with western macroinvertebrate fauna
prior to the 1930s. The author also describes the general distribution, and the location of
specific recorded samples dating back to  1895, although  most of the early descriptions date
from the early 1920s to 30s.

Results relevant to EMAP: The diversity of aquatic macroinvertebrates is poorly represented in
early literature. Prior to 1930, for example, only 30 species of  Plecoptera had been recorded
and described from Washington State. Following a series of surveys between 1930 and 1937,
an additional 41 species were collected and recorded, representing 137% increase in recorded
Plecoptera diversity for that state. This clearly illustrates the challenges facing those interested
in reconstructing changes in macroinvertebrate assemblage characteristics from pre-settlement
or early settlement conditions and suggests that a later time frame, although confounded by
human alteration that occurred after European settlement, may be a more realistic benchmark
for historically reconstructing macroinvertebrate distribution.

Geographic location: RegionIO, Washington, mountains, xeric, ecol, eco2, eco3, eco4, eco9,
ecolO, eco15, eco77

Keywords: macroinvertebrates; Plecoptera; Washington; change detection

Notes: Hatch, M. H. 1949. A century of entomology in the Pacific Northwest. University of
Washington Press. 43 pp. (in this bibliography)
                                          89

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Author: Jewett, Jr., S. G.
Year: 1959
Title: The Stoneflies (Plecoptera) of the Pacific Northwest
Reference Type: Book
City: Corvallis, OR
Publisher: Oregon State College Press
Number of Pages: 95

Value of reference: The primary value of this document is that it makes reference to the
original description and relevant taxonomic references.  The author provides basic geographic
range information in addition to relative abundance and seasonal occurrence of adults, although
it is difficult to determine both time frame and geographic localities for which this abundance
information is relevant. Unfortunately, papers devoted to distributional records that lack
taxonomic treatment were not included in the preparation of this resource. This may be useful
for beginning to reconstruct expected macroinvertebrate faunal composition and diversity
metrics.

Results relevant to EMAP: Of the approximately 400 species of Plecoptera identified in the
United States, 146 were reported in Washington, Oregon, Idaho, and British Columbia by  1959.

Geographic location: EPA Region 10, Washington, Oregon, Idaho, mountains, xeric, Eco1,
Eco2, Eco3, Eco4, Eco78, Eco77, Eco9,  EcolO, Eco11, EcoSO, Eco15, Eco16, Eco12, Eco17

Keywords: macroinvertebrates; stoneflies; Plecoptera; Oregon; Washington; Idaho; Pacific
Northwest
                                          90

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Author: Jewett, S.G., Jr.
Year: 1960
Title: The Stoneflies (Plecoptera) of California
Reference Type: Journal Article
Journal: Bulletin of the California Insect Survey
Volume: 6
Issue: 6
Pages:  125-177

Value of reference: This very useful resource contains county-level records of 101 species of
Plecoptera in California. It also provides an overview of the Plecoptera literature relevant to the
state ca. 1960. Most of the citations date from the 1930s -1950s. The primary value of this
document is that it synthesizes collection information on each species, including location, date,
often elevation, and occasionally stream size. Some information on relative abundance by
locality is also provided, although it is difficult to determine the time frame for which this
information is relevant.  This may be useful for beginning to reconstruct expected
macroinvertebrate faunal  composition and diversity metrics.

Results relevant to EMAP: Of the 6 families and 350 species of Plecoptera described in the
United States, all 6 families and 101 species have been recorded in California. The California
stonefly fauna is very similar to that throughout the western cordilleran region. More than 70
percent of the species are also found in Oregon, and approximately 60 percent in Washington.
None of the holarctic species of Plecoptera have been collected in California. The author reports
that many species have limited range, and distinct regional differences in stonefly faunal
assemblages are apparent.

Geographic location: California, EPA Region 9, mountains, xeric, Eco1, Eco4, Eco5, Eco6,
Eco7, Eco8, Eco9,  Eco13, Eco14, EcoSO, Eco81

Keywords: macroinvertebrates;  Plecoptera
                                          91

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Author: Johnsgard, Paul A.
Year: 2003
Title: Lewis and Clark on the Great Plains: A Natural History
Reference Type: Book
City: Lincoln, Nebraska
Publisher: University of Nebraska Press

Value of reference: This book chronicles the Lewis & Clark expedition and summarizes the
extensive natural history information collected over the Great Plains. In addition the web page
access to the book includes links to other journals and texts associated with the expedition.

Results relevant to EMAP: A summary of the many plants, mammals, fish, and other natural
history data collected on the expedition. The book includes geographical information that uses
present day locations to correlate where the original observations occurred.  This is a very good
broad reference that also includes very specific information about pre-settlement conditions in
the Great Plains.

Geographic location: Kansas, Missouri, Nebraska, Iowa, North Dakota, South Dakota,
Montana,  Missouri River Basin, EPA region 7, EPA region 8, eco47, eco42, eco43, eco46,

Keywords: Lewis & Clark expedition, pre-settlement, mammals, phab, birds, fish, natural
history

Abstract: Lewis and Clark on the Great Plains is an easy-to-use reference on the wildlife that
Meriwether Lewis and William Clark encountered during their 1804-6 Corps of Discovery
expedition. Over one hundred animals and plants that were first carefully described and in some
cases discovered by Lewis and Clark are identified here. More than an expedition reference
guide, Lewis and Clark on the Great Plains also examines the lasting importance of the
expedition's discoveries, the significance of the  Plains plants and animals to local Native
Americans, and the current status of Plains wildlife. Lavishly illustrated with Paul A. Johnsgard's
drawings of mammals, birds, fish, reptiles, and plants, the book also includes a guide to the
Lewis and Clark sites of botanical and zoological interest and more than seventy sites where
readers can follow in the footsteps of two of America's greatest pioneering naturalists. Visit the
Journals of the Lewis and Clark Expedition Online Project, based on Gary E. Moulton's
celebrated edition of the Lewis and Clark Journals. Initially offering almost two hundred pages
from volume 4, the site will eventually feature the full text of the Journals-almost five thousand
pages. Also view a gallery of images and hear acclaimed poet William Kloefkorn reading
selected passages. Wth full-text searchability and ease  of navigation, the Journals of the Lewis
and Clark Expedition Online Project is a useful tool for students and scholars and an engaging
website for the general public. Sponsored by the University of Nebraska Press, the Center for
Great Plains Studies, and the University of Nebraska E-Text
Center.lewisandclarkjournals.unl.edu

URL:
http://libtextcenter.unl.edu/examples/servlet/transform/tamino/Library/lewisandclarkiournals?& x
mlsrc=http://libtextcenter.unl.edu/lewisandclark/files/xml/lc.iohnsgard.01.xml& xslsrc=http://libte
xtcenter.unl.edu/lewisandclark/LCstvles.xsl#ch1
                                           92

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Author: Johnson, W.C.
Year: 1992
Title: Dams and riparian forests: case study from the upper Missouri River
Reference Type: Journal Article
Journal: Rivers
Volume: 3
Issue: 4
Pages: 229-242

Value of reference: This article reports the effects of altered flow and meander rate on
floodplain forest composition along the Missouri River in central North Dakota as a result of the
closing of the Garrison Dam in 1953. Several historical time periods,  dating back to the late
1800s, were used to reconstruct changes due to construction of the dam.  Over time, river
dynamics have changed due to hydrological alteration, which has changed forest cover
composition and succession.

Erosion and deposition over time are estimated. General Land Office Survey notes and maps
were used to determine the proportional composition of riparian forest successional categories
at the time of settlement.  Pre-settlement data for meander and forest successional rates are
used to create a model to predict future forest compositional shifts.

Results relevant to EMAP: Mean annual flows have changed slightly in the 25 post-dam years,
as compared with the early 1900s, while peak flows  have changed dramatically (see Figure 3).
The seasonal timing of peak and  minimum flows has been reversed.  Flooding now occurs only
on very low terraces.  The mean annual flood has  been reduced by about  70%, while the
maximum annual flood has reduced 81%.  Historically, the Missouri River  was a rapidly
meandering stream. Post-dam erosion rates were 25% of pre-dam rates,  while deposition rates
were only 1% of pre-dam rates. The result was a reduction in new alluvium for formation of bars
for colonization by cottonwood and willow.

On the upper Missouri River, pioneering young forests occupied only  6% of the total forest area
in 1979, down from 47% prior to settlement.  In contrast, transitional forests occupied 48% of
the area in 1979, as compared with 21% pre-settlement (see Table 5). Over 90% of pre-
settlement forests had cottonwood as a significant member of the forest overstory.  By 1938,
approximately 38% of the floodplain forest had been cleared. In 1979, forest vegetation
comprised about 44% of the area.

Model simulations showed that the pre-settlement dominance of the floodplain by cottonwood
and willow cannot be maintained  under current low meander rates. The prediction is a rapid
increase  in proportion of equilibrium forests as pioneer forests  age  and are not replaced. River
regulation and agriculture are given as the primary impacts bringing about this change.

Geographic location: North Dakota, EPA region 8,  eco43, eco42, Missouri River basin, plains

Keywords: phab, dams, agriculture, meander rates, deposition, erosion, riparian forest
composition, forest succession

Abstract: This research examined the  effects of altered flow and meandering rate of the
Missouri  River in central North Dakota  on the compositional dynamics of floodplain forests. This
was  accomplished by estimating the rates of river erosion and  deposition during pre-dam and
post-dam periods from historical maps  and aerial photographs. Future changes in forest
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composition were simulated using a simple mathematical model based on measured rates of
forest succession and river meandering for pre- and post-dam periods. Simulations indicated a
future decline in the areal extent of pioneer forests (cottonwood, willow) due to river regulation.
Later successional species (primarily green ash) will dominate the future forests.
Experimentation  is needed in order to regenerate pioneer forests to maintain current levels of
species diversity on the floodplain. (DBO)

Notes: A general overview and comparison of the effects of river regulation on meandering
(e.g., Missouri River)  vs. braided (e.g., Platte River) channels in areas of differing water usage is
given by Johnson, 1998, who synthesizes  results from this publication (Johnson 1992) and
Johnson 1994 (also in this bibliography), as well as other publications.

Johnson, W.C. 1998.  Adjustment of riparian vegetation to river regulation in the Great Plains,
USA. Wetlands 18(4):608-618.

Another relevant and  cited article:

Bragg, T.B. and A.K.  Tatschl. 1977. Changes in flood-plain vegetation and land use along the
Missouri River from 1826 to 1972.  Environmental Management 1(4):343-348.
                                          94

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Author: Johnson, W.C.
Year: 1994
Title: Woodland expansion in the Platte River, Nebraska: patterns and causes
Reference Type: Journal Article
Journal: Ecological Monographs
Volume: 64
Issue:  1
Pages: 45-84

Value of reference: This article uses historical sources (GLO notes, time-series photographs)
to reconstruct pre-settlement vegetation along the Platte River and its tributaries, including
areas in Colorado, Wyoming, and similar Ecoregion 25 in western Nebraska. The causes of
riparian vegetation changes are discussed. The results are notable because, rather than loss of
woodland, there has been an increase in woodland, despite regulation of the river.  This is in
marked contrast to historic changes on the Missouri River in South Dakota (see Rumble et al.
1998 in this bibliography) and in many other places in the West where river regulation has led to
a decline in cottonwood and willow recruitment.

Results relevant to EMAP: Prior to settlement, scattered trees occurred on river banks and on
islands in central Nebraska, but farther upstream on the South Platte River in Colorado,
woodland was scarce and few trees were present; thus, riparian woodland decreased in a
westward direction. Cottonwood, American elm, and willow were the dominant trees; minor
species were box elder, ash, and oak in central Nebraska and pine and cedar in western
Nebraska. The river was described as a very shallow stream that could be crossed at any point
in most seasons and filled with islands of all sizes covered with  grass,  bushes, and small trees.

Woodland began to expand into the North Platte River about  1900, occurring earliest in
upstream reaches.  By the late 1930s, much of the pre-settlement active channel in the North
and South Platte rivers had transformed to woodland, resulting in a reduction of channel area.
This process occurred in a west to east direction from the Colorado and Wyoming tributaries
into central Nebraska.  Woodland expansion rates since the 1930s have been highly variable,
and the river has become more homogenous from east to west with respect to the mix of
channel and woodland cover. The  system appears to have reached a new equilibrium between
flow and forest successional stage. The author postulates that the balance between woodland
extent  and active channel area was quite dynamic historically, changing during climatic cycles
and sensitive to small but persistent changes in flow.

Irrigation and impoundments, beginning on a  large scale in the early 1900s, may have set this
process into motion. The effect of consistently-reduced flows, in combination with tree life
histories, climatic factors, and hydrogeomorphology, provided conditions more amenable to
establishment and recruitment of trees.  The factors that restricted tree growth in the pre-
settlement period were high June flows (which would have restricted seedling recruitment) and
ice on sand bars (which would have reduced survivorship of tree seedlings). Water
developments curtailed  both of these factors, and woodland expansion was the result.  The
system is now reaching a new equilibrium, and the process of forest expansion is actually
reversing itself to some  extent; for example, some of the forests that have expanded into the
upper tributaries have already declined substantially in recent years.

Geographic location: Wyoming, Colorado, eco25, EPA region 8, Platte River basin, plains

Keywords: phab, dams, agriculture, demography, geomorphology, hydrology, management,
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Populus, primary succession, remote sensing, riparian woodland, Sa//x, sandbar colonization

Abstract: This research was conducted to identify the factors that have permitted Populus-Salix
woodland to expand into the formerly active channels of the Platte River and its two major
tributaries, the South and North Platte rivers. The research included: pre-settlement vegetation
reconstruction based on the General Land Office survey notes, a statistical comparison between
historic rates of woodland expansion from aerial photographs and environmental variables, and
a field study of seedling demography to isolate the factors controlling recruitment and survival  in
the modern river. Woodland expansion began in the South and North Platte rivers around 1900
and spread downstream into the Platte River. By the late 1930s, vegetation had occupied most
of the former channel area of the South and North Platte rivers and was expanding  into Platte
River channels. Rates of channel loss in the Platte River have been as great as 10%/yr during
droughts. By 1986, channel-to-woodland proportions were relatively uniform throughout the
Platte River system. Statistical models indicated that sandbar succession to woodland was
regulated by three environmental factors: June flows, summer drought, and ice. June flow
regulated seedling recruitment and initial survival because it coincided with the main Populus-
Salix seed germination period. Historic reductions in flow at this time for irrigation and to fill
reservoirs exposed much of the riverbed and  elevated recruitment and  seedling survivorship.
Late-summer seedling survival was regulated by factors that affect seedling water balance,
including river stage, seedling elevation in the riverbed, and rainfall. Winter conditions exerted
the largest effect on seedling survivorship. Dominant factors were air temperature, stream flow,
and seedling elevation in the riverbed. Lowest survivorship occurred during cold, icy winters with
relatively high flow and when most seedlings were growing on low sandbars. The dominant
historic trend, of losses in channel area and gains in woodland area, has ceased in recent
years. No significant declines in channel area have occurred since 1969; in several reaches
channel area has significantly increased since 1969. Comparatively small changes  in channel
and woodland proportions are expected in the future as long as water use and climate do not
change markedly. The steady state has developed because flows have come into balance with
active channel area, thereby reducing recruitment and increasing the mortality of tree seedlings.
Because of the importance of wide, unvegetated channels to certain avifauna, it may be
desirable to manage future flows to ensure no further reduction in channel widths, even if
narrowing is only temporary. Dominance  by Populus and Sa//x on new  sandbars can be
explained by life history characteristics. These include large and dependable seed crops that
are effectively dispersed by wind and water to optimal germination sites; rapid germination;
rapid root and height growth to withstand flooding, drought, and sedimentation; tolerance of low
soil fertility; and the ability of Sa//x to reproduce vegetatively. Pioneer vegetation and
geomorphic processes (principally sedimentation) facilitate succession  on floodplains by
modifying the highly variable riverbed environment suitable for early successional species into
relatively stable surfaces favorable for recruitment of later successional species. Much of the
extensive Populus-Salix woodlands that now occupy the Platte River will be replaced by later
successional tree and shrub species with lower associated faunal diversity. Maintenance of the
current biotic diversity may require artificial regeneration, as is taking place along other river
systems in western North America. The response of the Platte River to altered flow differed from
that of other rivers.  This divergent response despite similar disturbances points out the complex
interrelationships among plants and hydrogeomorphic processes operating on floodplains and
the difficulties associated with understanding, generalizing, and predicting the effects of human
modification of stream flow on natural ecosystems.

Notes: A general overview and comparison of the effects of river regulation on meandering
(e.g., Missouri River) vs. braided (e.g.,  Platte  River) channels in areas of differing water usage is
given by Johnson, 1998, who synthesizes results from this publication (Johnson 1994) and
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Johnson 1992 (also in this bibliography), as well as other publications.

Johnson, W.C. 1998. Adjustment of riparian vegetation to river regulation in the Great Plains,
USA.  Wetlands 18(4):608-618.

For further supporting documentation of physical changes in the Platte River system, see
Knopf, F.L.  1986.  Changing landscapes and the cosmopolitism of the eastern Colorado
avifauna. Wildlife Society Bulletin 14:132-142.
                                          97

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Author: Jordan, D.S.
Year: 1878
Title: Report on the collection of fishes made by Dr. Elliott Coues U.S.A. in Dakota and Montana
during the seasons of 1873 and 1874.
Reference Type: Journal Article
Journal: Bulletin of the U.S. Geologic and Geographic Survey of the Territories
Volume: 5
Pages: 777-799

Value of reference:  This report is an inventory of the fish species collected during 1873 and
1874 in northern Montana and North Dakota and surrounding areas into Canada. Its focus is on
taxonomy. It adds Dr. Coues findings to existing museum records.  It includes descriptions,
relative abundance of specimens collected, and (rarely) location observed.  The report is broken
down by family and then  species.

Results relevant to  EMAP: This is one of the few baseline inventories to be found for the
northern plains. Any information found in this inventory is helpful in establishing the pre-
settlement species and "historic range" for the fishes of the Great Plains.

Geographic location: Montana, North Dakota, EPA Region 8, eco43, eco42, Missouri River
basin, Red River, Milk River, Mouse River, Saint Mary's River, Plains

Keywords: fish, historical data, plains
                                          98

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Author: Jordan, D.S.
Year: 1889
Title: A Reconnaissance of the Streams and Lakes of the Yellowstone National Park, Wyoming,
in the Interest of the United States Fish Commission
Reference Type: Journal Article
Journal: U.S. Fish Commission Bulletin
Volume: 9
Pages: 41-63

Value of reference: This is a primary source that contains much detail about the fish species
and physical habitat of streams at the headwaters of the Missouri and Columbia basins.  Since
this area had been little explored and not yet settled at the time of this report, this is good
baseline  information for constructing pre-settlement, high-elevation stream conditions and fish
communities. Although its  focus is in Yellowstone National Park, it covers streams that originate
outside the park, spanning  2 major basins on either side of the continental divide.

The report is aimed at identifying waters where trout could be introduced.  Its focus is therefore
on current trout distribution; nevertheless, it contains much baseline information about the
streams and fish community at the headwaters of the Missouri and Columbia River basins, a
region  influenced by geothermal activity.

Results relevant to EMAP: The author lists 10 fish species that were found and the locations
where specimens were collected in and surrounding the Park, as well as those species that had
been introduced prior to this exploration. Following that are notes,  by species, of the fish found,
including locations  and  relative abundance, with notes on physical barriers to some of the
streams.  There is also discussion of a common parasitic worm on the suckers and trout of the
warmer waters.

The last section is a description of all the creeks and rivers in the Park, categorized by 3 major
drainages: Yellowstone basin, Missouri River drainage, and Columbia River drainage.  This
section includes notes on fish species and abundance, stream physical habitat, vegetation,
invertebrate abundance, stream width and depth, water temperature, waterfalls as physical
barriers to fish movement, water permanence, and known fish introductions.  Some of the
information is second-hand. This section is summarized with a list  of the streams in the Park
suitable for trout and those where trout were not found (primarily due to barriers). The article
should be consulted for specific details.

Geographic location: Wyoming, eco17, EPA region 8, Columbia River basin, Missouri River
basin, mountains

Keywords: fish, macroinvertebrates, phab, historical data, geographic distribution,  primary
source, baseline information
                                          99

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Author: Jordan, D.S.
Year: 1891
Title: Report of explorations in Colorado and Utah during the summer of 1889, with an account
of the fishes found in each of the river basins examined
Reference Type: Journal Article
Journal: U.S. Fish Commission Bulletin
Volume: 89
Pages: 1-40

Value of reference: Reference is a useful primary historical reference of the presence and
relative abundance offish in main stem and tributaries of 6 major river basins encompassing
areas of Colorado and Utah on both sides of the continental  divide in 1889.  It reports early
stream conditions and is valuable as a reference, since it represents a condition that is relatively
close to pre-settlement and largely before major extinctions or changes in fish communities
(although some fish  species were already experiencing mortalities due to early impacts).

Results relevant to EMAP: Reference systematically describes the historical condition in
basins of Colorado and Utah.  River and tributaries were examined in the following basins:
Platte River, Arkansas River, Rio Grande, Colorado River, Salt Lake Basin, Sevier Lake Basin.
The physical character (e.g., water clarity, substrate, flow, width, depth, general fish community)
of each stream is briefly described, and a summary is given, by species, offish  distribution in
the various tributaries and relative abundance in the late 1800s. Abundance is described as
scarce, not common, common, very common, abundant, very abundant, etc.

Geographic location: eco19, eco20,  eco21, eco26, eco25,  eco26, Colorado, Utah, xeric,
mountains, plains, Platte River basin, Arkansas River basin,  Rio Grande River basin, Colorado
River basin, Salt Lake Basin, Sevier Lake Basin, EPA Region 8, EPA Region 9

Keywords: fish, phab, fish distribution, fish abundance, historical data, primary  source, baseline
data
                                          100

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Author: Katibah, E. F.
Year: 1984
Title: A brief history of riparian forests in the Central Valley of California
Reference Type: Book Section
Editor: Warner, R. E.; Hendrix, K. M.
Book Title: California Riparian Systems:  Ecology, Conservation, and Productive Management.
City: Berkeley, California
Publisher: University of California Press
Pages: 23-29

Value of reference: A comprehensive treatment of pre-settlement hydrology, riparian
vegetation, and patterns of degradation of Central Valley riparian forests over the last 150
years.

Results relevant to EMAP: The chapter gives a description and map of surface hydrology of
the Central Valley circa 1850 (page 24) recording flow and flood regimes. There are also
descriptions of the pattern of natural riparian forest growth on natural levees, the riparian
species found there, and the history of decline of riparian forests.

Estimates of extent of riparian forest circa 1848 from literature:
Sacramento Valley - 324,000 ha (800,000 ac)
San Joaquin Valley - 57,000 ha (140,600 ac)
Tulare sub-basin (Kings, Kaweah, Tule, Kern  rivers) - 20,000 ha (50,000 ac)
Tributary streams, sloughs, marshes - 40,500 ha (100,000 ac)
Author's revised estimate of the total 1848 riparian forest coverage in the Central Valley -
373,000 ha (921,000 ac)

Estimates of present day riparian forest from a mapping project begun in 1979 - 41,300 ha
(102,000 ac) remaining in the Central Valley.  19,800 ha (49,000 ac) were in a disturbed or
degraded condition. 21,500 ha (53,000 ac) were  identified then as mature riparian forest, no
condition specified.

Geographic location: California, xeric, San Joaquin River, Sacramento River, eco6, eco7, EPA
Region 9

Keywords: phab, riparian vegetation,  historical, EPA Region 9, pre-settlement, agriculture,
water diversion, channelization, dams

Abstract: Riparian forests once occupied substantially greater areas in the Central  Valley of
California than they do today. This paper explores the hydrologic influences which allowed the
original riparian forests to establish  themselves, the extent and the reasons for the decline of the
pre-settlement forests, as well as an estimate of the extent of today's remaining  forests.
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Author: Knapp, R.A.
Year: 1996
Title: Non-native trout in natural lakes of the Sierra Nevada: an analysis of their distribution and
impacts on native aquatic biota.
Reference Type: Report
City: Davis, CA
Institution: University of California, Centers for Water and Wildland Resources

Value of reference: Although the focus of this article is on fish introductions in lakes, the effects
of these introductions on biota in associated streams is also addressed.  Native trout,
amphibians, and invertebrates occurring in watersheds of formerly fishless lakes have been
impacted by trout introductions in this region when introduced fish move into stream habitats
and compete with native biota that are not adapted to compete.

This reference presents a map of the region above 1800 m that was formerly fishless.

Results relevant to EMAP: Historically, trout were absent above approximately 1800 m in the
Sierra Nevada. Trout introductions to streams and lakes began in the mid-1800s and all
watersheds currently contain as many as 5 nonnative trout species.  Although stocking has
been terminated in the National Parks of the region, data from Yosemite NP suggest that trout
are likely to occur in at least 60% of all streams. The effects of introductions on naturally
fishless ecosystems can have severe impacts on native trout in perimeter streams, amphibians,
and macroinvertebrates; this paper provides some support for this, although limited quantitative
examples.  Native trout are impacted by introductions due to hybridization/introgression and
resource competition.

Historically, the mountain yellow-legged frog was widespread throughout the Sierra Nevada at
elevations above 1500 m, and found in all major watersheds, whereas it is now present in fewer
than 15% of the sites where it was found  in 1915.  The decline is attributed to predation by
nonnative trout.

Geographic location: California, eco7, EPA region 9, mountains, Sierra Nevada, nonnative
species, predation, competition, fishless streams

Keywords: fish, nonnative species, alpine habitats, biodiversity, cold water fisheries, lakes,
streams, recreation, watersheds, wilderness, food chains, amphibians, aquatic invertebrates,
introduced  species, plankton, Sierra bioregion, conservation biology, endangered species,
federal lands, geographic information systems, land management, park management,
restoration.

Abstract: The objective of this  study was to describe the current distribution of introduced trout
in the Sierra Nevada relative to the historic fish distribution, and to review the impacts of
introduced trout on native aquatic biota. Historically, trout were absent above approximately
1800 m in the Sierra Nevada. In the mid-1800's, however, widespread trout introductions were
begun to move fish into formerly fishless lakes and streams to  enhance recreational fishing.
Trout stocking is now conducted by the California Department of Fish and Game, and the
current program is intended to supplement and maintain existing populations of non-native trout.
As a result  of past and current trout stocking, the proportion of trout-containing lakes in the
Sierra Nevada has increased from less than 1% of all lakes larger than 1 ha (N=4000+) to
approximately 63% of all such lakes. National forests have a much higher proportion of lakes
containing non-native trout than national parks, with trout in at  least 85% of the lakes larger than
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1 ha. Only 7% are known to be fishless. In Sequoia, Kings Canyon, and Yosemite National
Parks, the proportion of lakes with fish has increased from less than 1% to approximately 35-
50% of such lakes. The greater number of fishless lakes in the national parks than national
forests is due in part to the termination of fish stocking in park lakes in the 1970's. Recent
surveys in Sequoia, Kings Canyon, and  Yosemite National Parks show that trout have
disappeared from 29-44% of previously  stocked lakes. Although data on the distribution of non-
native trout in Sierran streams is generally lacking, data from Yosemite National Park suggests
that trout are likely to occur in at least 60% of all streams. Given the current ubiquity of trout in
the formerly fishless portion of the Sierra Nevada, their impacts on native aquatic biota are likely
widespread.

Introduced trout are affecting the distribution of a wide range of native aquatic species in the
Sierra Nevada, including native fishes, amphibians, zooplankton, and benthic
macroinvertebrates. The introduction of  non-native trout has caused widespread declines of
native trout species such as golden trout as a result of hybridization, competition, and predation.
The decline of at least one amphibian species, the mountain yellow-legged frog, has been
attributed largely to predation by introduced trout. Predation by introduced trout has also caused
dramatic changes in zooplankton and benthic invertebrate species composition in lakes, shifting
the dominant species in these communities from large-bodied to small-bodied forms.

The majority of lakes stocked by the California Department of Fish and Game lie within
designated wilderness areas, areas managed for their natural values. Given that trout stocking
serves to maintain an artificial fishery that has substantial impacts on native aquatic biota, and
that continuation of this fishery  is strongly supported by portions of the public, the ongoing
stocking of trout poses inherent management conflicts. Resolution of these conflicts will require
additional research on the ecological and sociological consequences of alternatives to the
current trout stocking program that provide a better balance between the needs of aquatic
ecosystems and those of recreational interests.
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Author: Knapp, R. A.; Matthews, K.R.
Year: 2000
Title: Non-native fish introductions and the decline of the mountain yellow-legged frog from
within protected areas
Reference Type: Journal Article
Journal: Conservation Biology
Volume: 14
Issue: 2
Pages: 428-438

Value of reference: Although the focus of this paper is on the impact of introduced trout on
yellow-legged frogs, the greater value of this study may be that it represents a very large space-
for-time investigation of the impact that introduced fish species can have upon native biota. This
study investigates patterns of amphibian distribution across multiple spatial scales to better
investigate alternate explanations for observed amphibian declines. This reference provides
strong support for the interpretation that fish introductions have influenced aquatic vertebrate
assemblages, and derived indices.

Results relevant to EMAP: After factoring out the influence of habitat conditions, there was a
negative correlation between trout and yellow-legged frogs at the landscape scale; at the
watershed-scale,  the presence of introduced trout accounted for approximately 60% of the
variance in the distribution of yellow-legged frogs; and at the scale of the individual water body
(n =  1728), the effect of trout on frog presence or absence was very significant (p < 0.0001).
Although the species has disappeared from sites lacking trout, there is some evidence to
indicate that these areas may represent marginal habitat containing non-equilibrium
metapopulations.  The authors surmise that the decline of the yellow-legged frog in the Sierra
Nevada began shortly after fish introductions in the 1850s.

Geographic location: California; Sierra Nevada; mountains; eco5;  EPA Region  9

Keywords: amphibians; introduced fish; nonnative species; predation; yellow-legged frog; Rana
muscosa

Abstract: One of the most puzzling aspects of the worldwide decline of amphibians is their
disappearance from within protected areas. Because these areas are ostensibly undisturbed,
habitat alterations are generally perceived as unlikely causes. The introduction of non-native
fishes into protected areas, however, is a common practice throughout the world  and may exert
an influence on amphibian distributions. We quantified the role of introduced fishes (several
species of trout) in the decline of the mountain yellow-legged frog (Rana muscosa) in
California's Sierra Nevada through surveys of >1700 sites in two adjacent and historically
fishless protected areas that differed primarily in  the distribution of introduced fish. Negative
effects of fishes on the distribution of frogs were  evident at three spatial scales. At the
landscape scale, comparisons  between the two protected areas indicated that fish distribution
was  strongly negatively correlated with the distribution of frogs. At the watershed scale, the
percentage of total water-body surface area occupied by fishes was a highly significant predictor
of the percentage of total water-body surface area occupied by frogs. At the scale of individual
water-bodies, frogs were three times more likely  to be found and six times more abundant in
fishless than in fish-containing water-bodies, after habitat effects were accounted for. The strong
effect of introduced fishes on mountain yellow-legged frogs appears to result from the unique
life history of this amphibian which frequently restricts larvae to deeper water bodies, the same
habitats into which fishes have most frequently been introduced. Because fish populations in at
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least some Sierra Nevada lakes can be removed with minimal effort, our results suggest that the
decline of the mountain yellow-legged frog might be relatively easy to reverse.
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Author: Lavier, D.C.
Year: 1976
Title: Distribution of salmon and steelhead in the Columbia River Basin, 1850-1976: a summary
of data from maps prepared for the Columbia Fisheries Project, Pacific Northwest Regional
Commission
Reference Type: Report
City: Olympia, WA
Institution: Washington Department of Game

Value of reference: This is a series of tabular synopses of river miles available to and in use by
steelhead, spring, summer, and fall Chinook, coho, chum, and sockeye salmon in 8 different
river sections  of the Columbia, Snake, Yakima, and Willamette Rivers in 1850 vs. 1975. The
tributaries  included in each river section are listed with each table.

Since this  is a summary from maps, the original mapped areas of use by each species are
presumably available from the Columbia River Fisheries Project, but the maps are not part of
this particular summary. There is also  no text, explanation of methods, or interpretation,
although the tabular results are straightforward and can be very useful for quantitative
comparisons of pre-settlement and 1970s conditions. For more detail and clarification, this
tabular summary may need to be supplemented with background information or reporting from
the Washington Department of Game or the Columbia River Fisheries Project..

Results relevant to EMAP: A wide range of information can be extracted from these tables
including: river length (miles), miles accessible to fish, miles blocked to fish, and miles in use by
several species of salmonids in 1850 and 1975. River miles accessible to fish can be compared
to accessibility prior to major impacts (1850). For example, sockeye salmon used 320 miles of
the Yakima drainage in 1850, but did not use any of the river miles in 1975.  In comparison to
1850, an additional 136 miles of the basin were blocked to fish in 1975.  Between 1850 and
1975, steelhead use decreased by 143 miles (22%), spring Chinook use by 232 miles (40%),
and coho use by 61 miles (19%) in the Yakima River basin. All river miles can easily be
converted  to proportions or percentages of a basin. The summary does not address causes of
decline, but increases in blockage to fish since 1850 were likely associated with dams.

Geographic location: Washington, Oregon, Idaho, EPA region 10, eco3, eco4, eco9,  ecolO,
eco11, eco12, eco15, eco16 ecoSO, Columbia River basin, mountains, xeric

Keywords: fish, blockage to fish, fish use, map summaries
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Author: Lee, D.; Sedell, J.; Rieman, B.; Thurow, R.; Williams, J.; others
Year: 1997
Title: A broad-scale assessment of aquatic species and habitats [Chapter 4]
Reference Type: Report
City: Portland, OR
Institution: USDA Forest Service, Pacific Northwest Research Station
Report Number: General Technical Report PNW-GTR-405

Value of reference: This  long and detailed chapter represents a very large synthesis of current
data, knowledge (including professional judgment), historical information, and predictive
modeling. Current status  is given in relation to historical range, reconstructed from 1) actual
samples and 2) predicted occurrences based on landscape features (i.e., potential range),
using classification tree analysis.  The report synthesizes an immense literature and, along with
professional judgment and predictive modeling, reconstructs and maps the historical ranges of
46 fish species in the Columbia Basin and  compares them with current ranges; habitat
requirements and key factors influencing status are also discussed for each. A separate section
presents  historical changes in pool habitats.

Results relevant to EMAP: Approximately 50% of the native fish taxa in the assessment area
has exhibited significant declines from historical levels. Presently, 45 of the 88 native fish taxa
(51%) in the assessment area are identified as threatened, endangered, sensitive, or of special
concern by state or Federal agencies or by the American Fisheries Society.  Overall changes in
composition, distribution, and status of fishes are dramatic and extensive; a wide range of
human impacts on these populations are given in discussions of each species.

Example status conclusion: "Bull trout are known or predicted to occur in 45% of watersheds in
the historical range and to be absent in 55%. We found bull trout less widely distributed within
the potential historical range than other non-anadromous salmonids...Watersheds believed or
predicted to be strong spawning and initial  rearing areas represented only 6% of the historical
range..."

In managed  streams, roads and accompanying human activities including timber harvest,
highway construction, grazing, agricultural  practices, and loss of riparian vegetation have
combined to create major decreases in pool habitats, which appear to have been the greatest in
the low-gradient, biologically productive areas of river basins most disturbed by humans.

Geographic location: eco 10, eco11, eco15, eco16, ecoSO, eco12, mountains, xeric, Oregon,
Washington, Idaho, Interior Columbia Basin, EPA Region 10

Keywords: fish, human impacts, historical  range

Notes: A 9-page Executive Summary of this chapter is in Volume I, Chapter 1 of this series.

The portion of this reference discussing pool habitats is largely from Mclntosh 1995. In addition,
see Mclntosh 1994 in this bibliography.

Mclntosh, B.A. 1995.  Historical changes in stream habitats in the Columbia River Basin.
Corvallis, OR: Oregon State University. Ph.D. dissertation.
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Author: Leidy, R.A.; Becker, G.; Harvey, B.N.
Year: 2005
Title: Historical status of coho salmon in streams of the urbanized San Francisco estuary,
California
Reference Type: Journal Article
Journal: California Fish and Game
Volume: 94
Issue: 4
Pages:  1-36

Value of reference: The article represents an in-depth investigation and synthesis of historical
literature, museum specimens, agency files, and long-term data records to reconstruct the
relative  probability of the past presence of coho salmon in 65 watersheds around San Francisco
estuary. Probability of presence was based on a combination of documented historical
presence of the species and the likelihood of occurrence of essential habitat requirements
historically.

The information in this document is useful for reconstructing the historical range of the species
and its presence in specific estuary watersheds of the region.

Results relevant to EMAP: Coho salmon were last documented from an estuary stream  in the
early to  mid-1980s.  Coho salmon populations have experienced declines throughout California
attributable primarily to human activities, including water diversions, creation of migration
barriers, streambed alteration for flood control, impaired water quality, removal of riparian
vegetation, disruption of natural hydrological  processes, and reduced instream habitat
complexity.

At least  4 of 65 estuary watersheds (6%) historically supported coho salmon. A minimum of an
additional  11 watersheds (17%) may also have supported coho salmon.  These 15 watersheds
and supporting evidence for the occurrence of coho salmon are summarized in Table 1. Habitat
characteristics of the 15 watersheds are shown in Table 2.

Although broadly distributed, the environmental characteristics of streams known historically to
contain  coho salmon shared several characteristics: cool summer water temperatures, suitable
spawning and juvenile rearing habitat, distinct surface water connections to the estuarine  and
marine environments, as well as stream flows during the months of February through May
suitable for smolt out-migration.

Estuary  coho salmon typically were members of three-to-six species assemblages of native
fishes, including Pacific lamprey, steelhead, California roach, juvenile Sacramento sucker,
threespine stickleback, riffle sculpin, prickly sculpin, and/or tidewater goby.

Geographic location: California, eco6, EPA Region 9, local watersheds of the San Francisco
Bay Estuary, xeric

Keywords: fish, urban, water diversion, dams
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Author: Lichatowich, J. A.
Year: 1997
Title: Evaluating salmon management institutions: The importance of performance measures,
temporal scales, and production cycles
Reference Type: Book Section
Editor: D.J. Stouder; P. A. Bisson; Naiman, R. J.
Book Title: Pacific Salmon and their Ecosystems.
City: New York, New York
Publisher: Chapman and Hall
Pages: 69-87

Value of reference: The article makes an argument for historical reconstruction to set
meaningful goals for restoration of salmon runs and to evaluate the success of management
strategies  to date.

Results relevant to EMAP: Lichatowich uses salmon productivity  graphs to show what
happens when managers work on short temporal scales without considering the historic
baseline. A short time frame, particularly during favorable climatic conditions, may make
managers overly optimistic in their predictions of increased productivity when the real result is
the preservation of the status quo or a continual adjustment of the baseline downward to
extinction. An ecosystem's history determines the system's present state and helps establish
the range of possibilities for future development trajectories. Developing  baselines from
historical reconstruction of salmon abundance and  habitats is a critical step in salmon
restoration.

By considering only the currently available habitat,  Oregon and Washington have compressed
the habitat baseline. There is no historical component. Past habitat loss is not taken into
account in either definition. The implication is that we are satisfied with the status quo, the
current condition of salmon habitat. This has led to  stocks being listed as healthy that have
exhibited dramatic declines. For example, the Tillamook Bay chum salmon is listed as a healthy
stock even though the annual run declined from an average of 92,000 fish in the late 1940's and
early 50's to an  average of 17,000 fish in recent years.

If each generation is allowed to reset the temporal scale of the baselines used to evaluate
management performance, the result will be no evaluation or accountability, a misinformed
public, and a spiral of decline for which the  outcome will be the inevitable extinction of Pacific
salmon in  much of their range.

Geographic location: mountains, xeric, Columbia  River,  coastal rivers, ecolO, ecol, eco4,
eco3, Oregon, Washington, EPA Region 10

Keywords: historic fish abundance,  historical reconstruction, baseline, Chinook salmon, coho
salmon, temporal scale, institutional  learning, management expectations

Abstract:  Management of renewable resources from an ecosystem perspective will require
institutional changes. Management institutions will have to enhance their ability to learn, use
what they  learn, and promote more effective evaluation of performance. Development of
appropriate management baselines is an important prerequisite to  institutional learning and
evaluation. Three important components of management baselines are biological performance
measures, temporal scale of institutional evaluation, and natural environmental fluctuations in
the ecosystems that produce Pacific salmon. Performance measures should broaden the
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traditional focus on harvest and economics to include measures of the condition of important
ecological processes. Temporal scale will have to include the entire history of management
institutions. Compressing the temporal scale and shifting baselines forward will create inevitable
extinction of the resource. Natural cycles in production require flexibility in management
programs and the development of realistic expectations.
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Author: Liknes, G. A.; Graham, P. J.
Year: 1988
Title: Westslope cutthroat trout in Montana: Life history, status and management
Reference Type: Book Section
Editor: Gresswell, R. E.
Book Title: Status and management of interior stocks of cutthroat trout.
City: Bethesda, Maryland
Publisher: American Fisheries Society
Pages: 53-60

Value of reference: The authors compare the historic and present range of the westslope
cutthroat trout, identify the locations of pure populations, and list the important factors
responsible for the decline of the subspecies.

Results relevant to EMAP: The historic range of the westslope cutthroat trout in Montana both
east and west of the Continental Divide is estimated at 25,547 stream kilometers. The present
distribution is at 6993 stream km or 27.4% of the historic range (includes hybridized trout).
Genetically pure populations are present in 72 streams (nine river drainages) representing 2.5%
of their historic range.

Westslope cutthroat trout are sensitive to riparian disturbance, and they are often replaced by
the alien brook trout following disturbances such as logging, grazing, or mining.

As with other cutthroat trout populations (Lahontan and Bonneville, see references Duff
(1988)and Gerstung (1988)), the authors believe that the major factor in the trout's decline is
hybridization with rainbow trout, golden trout, and Yellowstone cutthroat trout.

Geographic location: Region 8, Montana, mountains, Flathead River, eco17, eco41

Keywords: fish, westslope cutthroat trout, historic distribution, habitat degradation, nonnative
species

Abstract: The historic range of westslope cutthroat trout Salmo clarki lewisi included western
Montana, central and northern Idaho,  a small portion of Wyoming, and portions of three
Canadian provinces. The distribution and abundance of westslope cutthroat trout have
drastically declined from its historic range during the last 100 years. Although previous studies
in Montana identified strongholds of populations, the status of westslope cutthroat trout over its
complete range is uncertain. Three life history forms are found within this range: 1) lacustrine-
adfluvial  stocks, 2) fluvial-adfluvial populations, and 3) fluvial fish. Migratory adults travel long
distances during periods of high stream flow and spawn when water temperatures are near 10
degrees C. Most migratory adults quickly leave the spawning grounds following the spawning
act. Sexual maturity is attained at age 3 or older. In some drainages, repeat spawning occurs
predominantly in alternate years. Westslope cutthroat trout are opportunistic in their food habits,
but are not highly piscivorous; they tend to specialize as invertebrate feeders. The decline of
westslope cutthroat trout has been attributed to overexploitation, genetic introgression,
competition from or replacement by nonnative species, and habitat degradation. Westslope
cutthroat trout occupy only 27.4% of their original range in Montana, and genetically pure
populations are present in only about 2.5% of their historic range. As a whole, westslope
cutthroat trout populations in Idaho and British Columbia, Canada, have fared better than in
Montana. Management programs designed to protect the westslope cutthroat trout have helped
to maintain or increase existing populations, and even to create new populations.
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Author: Lytle, D. A.
Year: 2003
Title: Reconstructing long term flood regimes with rainfall data: Effects of flood timing on
caddisfly populations
Reference Type: Journal Article
Journal: The Southwestern Naturalist
Volume: 48
Issue: 1
Pages: 36-42

Value of reference: This article is one of several that demonstrate how natural flow regimes
(e.g., flash floods, spring runoff) historically affected desert stream biota. The author integrates
short term flood data with long term rainfall data to infer patterns of the influence of flooding on
caddisfly populations. This approach is particularly useful for a biological indicator for which
there is little or no historical data.

Results relevant to EMAP: There is a large interannual variation in caddisfly population sizes
due to the stochastic nature of flash floods.
"Mortality of aquatic insects from flash floods exceeds 90% for most taxa, and some species are
locally extirpated by floods, so recolonization of flooded streams from adjacent, non-flooded
drainages might also be important for maintaining species diversity."

"The timing of individual floods relative to the long term average strongly affected caddisfly
populations; early and timely floods had little affect on population size in the next year, but late
floods significantly reduced population size in the next year."

Geographic location:  Region 9, eco79, Arizona, Chiricahua Mountains, xeric

Keywords: desert streams, hydrographic variability, flash floods, macroinvertebrates, phab,
precipitation, flood frequency, caddisfly, recruitment,

Abstract: Flash floods  are a defining feature of desert streams, but flow records are not always
available to characterize long term flood dynamics. In this study, rainfall data spanning 100
years were used as a proxy to quantify long term flood regimes for southeastern Arizona (USA)
streams. The frequency and seasonal timing of severe floods (>50% substrate movement) were
highly variable at short  temporal scales (days to several years), but clear patterns emerged in
the long term (several years to a century). To explore the ecological effects of flood timing,
populations of the caddisfly Phylloicus aeneus were monitored in 2 streams over 3 years. The
timing of individual floods relative to the long term average strongly affected P. aeneus
populations: early and timely floods had little effect on population size in the next year, but late
floods significantly reduced population size in the next year. Thus, flood timing might play a role
in regulating populations of desert stream organisms.
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Author: MacCoy, D.; Blew, D.
Year: 2005
Title: Impacts of land-use changes and hydrologic modification on the lower Boise River, Idaho,
USA
Reference Type: Book Section
Editor: LR. Brown; R.H. Gray; R.M. Hughes; M. Meador
Book Title: Effects of Urbanization on Stream Ecosystems.
City: Bethesda, MD
Publisher: American Fisheries Society
Volume: 47
Pages: 133-156

Value of reference: This research uses cadastral survey notes from the late 1800s to recreate
the historical lower Boise River and assess changes in the  structure and function.  Historical
hydrogeomorphology and riparian conditions were reconstructed: average bankfull width,
channel forms, parafluvial surfaces, sloughs, and riparian vegetation.  The changes in these
features since the 1800s, as a result of human alteration, are described.

Results relevant to EMAP: Today, the average bankfull width is about one-quarter to one-half
the historical width, and parafluvial surfaces are stabilized by trees and shrubs. Historically, an
extensive network of sloughs was present, with numerous surface connections between sloughs
and the main channel.  Between  1868 and 1939, many sloughs were filled or converted to
agricultural drains or canals.  Today, many river channels are incised.

River bottom substrate was historically dominated by cobble and gravel, and the banks were
subject to frequent inundation and scouring; cottonwood stands were extensive, in some places
reaching 900 m in width. In contrast,  current flows do not produce adequate shear stress to
mobilize bed material, resulting in sandy bottoms and embeddedness over 50% in many places;
alien species dominate in most sections of river.  Table 2 compares physical features (average
bank-full width, channel forms, parafluvial  surfaces, sloughs,  and vegetation) of the historic
(1867-1868) versus current (1994-2002) in four reaches  of the lower Boise River,

Modifications due to urbanization and agriculture have stabilized the river and reduced
parafluvial surfaces and bankfull  widths. Three large dams in the upper basin have altered flow
regime and sediment supply to the river. Increased abundance of tolerant and alien species
has lowered the quality of natural aquatic assemblages.  Alien hardwoods have replaced native
cottonwood stands, and alien herbaceous species are present along most of the lower river.

Geographic location: Idaho, Boise River basin, eco12,  EPA region 10, xeric

Keywords: phab, hydrogeomorphology, riparian vegetation, cadastral surveys, urban,
agriculture, dams

Abstract:  In less than two centuries, the lower Boise River below Lucky Peak Dam in
southwestern Idaho has been transformed from a meandering, braided, gravel-bed river that
supported large runs of salmon to a channelized, regulated, urban river that also provides
irrigation water to more than 1300 km2 of land. The construction of three large dams in the
upper basin dramatically altered the flow regime and sediment supply to the lower river.  Flows
are no longer sufficient to mobilize bed sediments and have allowed cottonwood trees and alien
hardwoods to stabilize parafluvial surfaces, thereby narrowing sections of the river channel.
Cadastral survey notes of 1867 and 1868 were used to recreate features associated with the
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lower Boise River Valley and identify characteristics of the river channel prior to dam
construction and urbanization.  Gravel and sand bars, historically present throughout the river,
which are necessary to maintain biodiversity and productivity, are currently scarce.  Sloughs
were a dominant feature on the floodplain of the late 1800s, but today have been converted to
irrigation canals, drains, or residential and commercial land uses.  Flow alterations, water quality
degradation, and habitat loss due to urbanization near the lower Boise River have resulted in
macroinvertebrate and fish assemblages dominated by tolerant and alien species.
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Author: Martin, B. A.; Saiki, M.K.
Year: 1998
Title: Effects of ambient water quality on the endangered Lost River Sucker in Upper Klamath
Lake, Oregon
Reference Type: Journal Article
Journal: Transactions of the American Fisheries Society
Volume: 128
Pages: 953-961

Value of reference: This paper reviews historic literature documenting the dramatic changes in
fish abundance and community characteristics in the upper Klamath River Basin, resulting from
the cumulative effects of overharvest, mining,  grazing, agriculture, impoundments, and water
diversions. It also identifies the primary causal factors associated with recent fish mortality in the
basin.

Results relevant to EMAP: The Lost River sucker (Deltistes luxatus) was the most important
food fish in the Klamath Lake region for the Klamath and Modoc Indians prior to the turn of the
twentieth century (Gilbert 1898),  and heavily used  by white settlers for food and livestock feed
(Cope 1879). It has subsequently been pushed to the edge of extinction by human impacts
associated with damming of rivers, draining of marshes, water diversions, competition with or
predation by exotic species, loss and isolation of habitat, and impacts on water quality by
logging, agriculture, and grazing. In this study, hypoxia, associated with a dissolved oxygen
deficit, was identified as the primary factor currently influencing juvenile Lost River sucker
mortality.

Geographic location: Upper Klamath River Basin, Oregon, California, eco78, Klamath
Mountains, Region 10, mountains

Keywords: fish; water quality; Lost River sucker; Deltistes luxatus; Shortnose sucker;
Chasmistes brevirostris; Klamath largescale sucker; Catostomus snyderi; mortality; dissolved
oxygen; population decline; logging; grazing; agriculture; dams, water diversion, nonnative
species

Abstract:  Populations of the Lost River sucker Deltistes luxatus have declined so precipitously
in the Upper Klamath Basin of Oregon and California that this fish was recently listed for federal
protection  as an endangered species. Although Upper Klamath Lake is a major refuge for this
species, fish in the  lake occasionally experience mass mortalities during summer and early fall.
This field study was implemented to determine if fish mortalities resulted from degraded water
quality conditions associated with seasonal blooms of phytoplankton, especially
Aphanizomenon flos-aqua. Our results  indicated that fish mortality did not always increase as
water temperature, pH, and un-ionized  ammonia concentration increased in Upper Klamath
Lake. Little or no mortality occurred when these water quality variables attained their  maximum
values. On the other hand, an  inverse relation existed between fish mortality and dissolved
oxygen concentration.  High mortality (>90%) occurred whenever dissolved oxygen
concentrations decreased to 1.05 mg/L, whereas mortality was low (<10%) when dissolved
oxygen concentrations equaled or exceeded 1.58 mg/L. Stepwise logistic regression  also
indicated that the minimum concentration of dissolved oxygen measured was the single most
important determinant of fish mortality.

Notes: Gilbert, C. H. 1898. The fishes of the Klamath basin. U.S. Fish Commission Bulletin
17:1-13.
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Cope, E. D. 1879. The fishes of Klamath Lake, Oregon. American Naturalist 13:784-785.
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Author: McAllister, K.R.; Leonard, W.P.; Hays, D.W.; Friesz, R.C.
Year: 1999
Title: Washington state status report for the northern leopard frog
Reference Type: Report
City: Olympia, WA
Institution: Washington Department of Fish and Wldlife
Pages: 36

Value of reference: Report contains known historical records and distribution of the species,
dating back to 1881. Reduction in distribution is  assessed and reason for decline are
discussed.

Results relevant to EMAP: Museum specimens indicate that northern leopard frogs were
found historically in 8 counties in eastern Washington (see Table 1).  They were considered
abundant in the Walla Walla basin in 1960. The  Snake River and its associated flood plain
wetlands may have provided an aquatic corridor  to historically abundant leopard frog
populations in Idaho and Montana.  In addition to the Walla Walla River populations, the link may
have been responsible for colonization along the Columbia River downstream to Fort Dalles,
Oregon.  The species seems to have occurred in few locations, but in large numbers.

Geographic location: Washington, EPA Region 10, mountains, xeric, Columbia River basin,
ecolO, eco77, eco15

URL: http://wdfw.wa.gov/wlm/diversty/soc/status/leopfrog/nlepfrog.pdf
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Author: McDowell, P. F.
Year of Conference: 2000
Title: Human impacts and river channel adjustment, northeastern Oregon: Implications for
restoration
Reference Type: Conference Proceedings
Editor: P.J. Wigington; R.L Beschta
Conference Name: Riparian Ecology and Management in Multi-Land Use Watersheds
Publisher: American Water Resources Association, Middleburg, VA
Pages: 257-261

Value of reference: Though the title implies that the article is about the future rather than the
past, the paper contains an example of reconstructing past river channel configuration.
McDowell reconstructs channel changes for a 30 km section of the Middle Fork John Day River
in eastern Oregon using 1881 land survey records, and aerial photos from 1939 and 1989.

Results relevant to EMAP: The paper outlines human impacts contributing to declining salmon
numbers in the John Day basin over the last 125 years, but it also provides a quantitative
measure of sinuosity taken from aerial photographs in 1939 (prior to major changes in the
segment) and 1989. Sinuosity decreased on all seven study channel segments. Not
unexpectedly, there has been more direct human modification of the channel and riparian zone
in wide valley (unconstrained) segments than in narrow valley (constrained) segments.

1881 survey notes show dense willow thickets, or riparian communities of willow, cottonwood,
and alder, in many places along the Middle Fork that today have little or no woody riparian
vegetation (and no  large woody debris). 1881 notes show that anabranching reaches with two
or three active channels were present in 3 study segments.

The only major human  caused change between 1881 and 1939 was a km of channel cut off by
the construction of the  railroad. Between 1939 and  1989 sinuosity was reduced in every
segment with wide valley segments experiencing the largest reductions  in sinuosity. Other
segments have dredged artificial channels and bank stabilizing structures that harden the banks
and eliminate the possibility of future lateral migration of the channel. The segments with the
most structures today had unconfined sinuous channels in 1881 and 1939.

Geographic location:  John Day River, eco11, Blue Mountains, mountains, Northern Rockies,
EPA Region 10, Oregon

Keywords:  phab, fluvial geomorphology, human impacts, channel adjustment, riparian
restoration, bank stabilization, sinuosity, historical, mining, channelization

Abstract: Historical data were used to reconstruct channel change in the Middle Fork John Day
River, a tributary of the Columbia River. Human impacts on the channel from the 1800s to
present include: beaver trapping, early alluvial gold mining, dredge mining,  livestock grazing,
haying and irrigation, railroad building, road building, and placing of bank stabilization
structures. 1881 land survey records, 1939 aerial photos, 1989 aerial photos, and a detailed
1996 channel habitat inventory were used to identify the extent and location of channel change,
and to compare direct human modification of the channel with channel self-adjustment by fluvial
processes. Channel change and human impacts have been expressed differently in wide valley
segments, which are inherently sinuous with abundant pools, compared to narrow valley
segments, which are inherently less sinuous. The major effects of human activities include loss
of sinuosity, loss of riparian woody vegetation, probably loss of large woody debris and pools,
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and reduced potential for adjustment because of bank stabilization structures. Wide valley
segments have more potential for fish habitat, but also have been the most affected by human
impacts. Implications for restoration are discussed.

Notes: Also see Welcher, K.E. 1993.  Channel restoration plan and geomorphology of the
Middle Fork John Day Preserve.  Report prepared for The Nature Conservancy, Portland, OR
(unpublished). 88 p.  + appendices.
                                         119

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Author: McFarling, L.
Year: 1955
Title: Exploring the Northern Plains
Reference Type: Book
City: Caldwell, Idaho
Publisher: The Caxton Printers, Ltd.
Number of Pages: 441

Value of reference: The early explorations into the northern Great Plains contain descriptive
information of the landscape, geology, vegetation, and general river conditions within the region.
There is also mention of the wildlife present. These accounts help establish what was present
prior to and during settlement of the region.

Results relevant to EMAP: Descriptions of the Platte River, James River, White River,
Missouri River, Niobrara River, and Ponca Creek (among others within the Missouri River basin)
include physical characteristics, geology, flora, and large fauna. These early expeditions
contain valuable  baseline information of what landscape and riverine conditions were like prior
to settlement of the region. The information is presented as descriptive text, maps, and explorer
narratives including explanatory footnotes.

The chapters require some sifting through to extract small  pieces of anecdotal information or to
reconstruct stream related attributes, however; the information present is quite valuable and
may be the only source of pre-settlement conditions of the plains and plains streams. This is a
good broad reference and inventory that includes specific information about pre-settlement
conditions in the  plains.

Geographic location: Nebraska, Wyoming, South Dakota, Montana, North Dakota, Niobrara
River, Ponca Creek, Missouri River, James River, White River, eco43, eco42, eco17,  plains,
EPA region 7, EPA region 8

Keywords: explorations, phab, resource inventories,  pre-settlement condition, historic
condition, geography, geology, expeditions
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Author: Mclntosh, Bruce A.; Sedell, James R.; Smith, Jeanette E.; Wissmar, Robert C.; Clarke,
Sharon E.; Reeves, Gordon H.; Brown, Lisa A.
Year: 1994
Title: Management History of Eastside Ecosystems: Changes in Fish Habitat Over 50 Years,
1935 to 1992. Volume III: Assessment
Reference Type: Report
City: Portland, OR
Institution: USDA Forest Service, Pacific Northwest Research Station
Pages: 55
Report Number: General Technical Report PNW-GTR-321

Value of reference: The most useful data from this publication (and reliable, in terms of its
relevance to a true pre-settlement condition) are the historical run estimates given for coho,
Chinook, and steelhead in the Upper Grand Ronde, Yakima River, Metthow River, and
Wenatchee River basins. For comparison, the present day (late 1980s) runs are given, but not
consistently. In addition to historical runs, this publication reports changes in pool habitats
between the 1930s and 1990s (see Notes section below for suggested citations).  In some
areas, the  1930s condition was quite degraded already.

Results relevant to EMAP:  Grand Ronde Basin historically had large runs of spring  Chinook
and summer steelhead (see  Northwest Power Planning Council 1990), which have been
reduced to a small fraction of their predevelopment numbers  (spring Chinook are listed as
threatened) due to dams, habitat degradation (from numerous human impacts), and over
exploitation of mixed-stock fisheries.

Yakima River Basin historic salmon runs were estimated at 790,000 adults before the 1870s
(break down by species and  run is included-also see Northwest Power Planning Council 1989).
By 1900, >90% of runs were thought to be depleted as a result of dams, irrigation canals, log
drives, local overfishing; present runs are estimated at only 7018.

Wenatchee Basin historical runs (1850s): chinook=41,300; coho=3900; sockeye=228,100;
steelhead=7300. Numbers for 1967-87 were higher but distributed much differently: coho=0,
Chinook=204,800; sockeye=93,700, steelhead=8200 (from Mullan et al.  1992).

Methow Basin historical runs (1850s): chinook=24,200, coho=36,000, steelhead=3600.  1967-
1987: chinook=86,100, coho=0; steelhead=5000 (see Mullan et al. 1992).  Coho were near
extinction by 1941, while the other species increased by the 1980s; decline of coho was due to
impassable dams, unscreened irrigation diversions, overharvest, and the indiscriminate use of
coho eggs for early hatchery programs.

Geographic location: mountains, xeric, Washington, Oregon, eco11, ecolO, eco77,  Grande
Ronde River basin, Yakima River basin, Wenatchee River basin, Methow River basin, EPA
Region 10

Keywords: fish, anadromous, fish habitat, historical changes, land-use practices, pools, stream-
flow, fish, mountains, arid, general human impacts

Abstract: From  1934 to 1942, the Bureau of Fisheries surveyed over 8000 km of streams in the
Columbia River basin to determine the condition of fish habitat. To evaluate changes  in stream
habitat over time, a portion of the historically surveyed streams in the Grande Ronde, Methow,
Wenatchee, and Yakima River basins were
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resurveyed from 1990 to 1992. Streams were chosen where the primary impacts were natural
disturbance (unmanaged), such as wilderness and roadless areas, and where human impacts
(managed) were the major disturbances. In addition, historical changes in land-use, stream-
flow, and climate regimes were also analyzed. Many of these streams had been degraded from
land-use activities (riparian timber harvest, splash dams, stream channelization, livestock
grazing, and mining) prior to the historical survey. While the general trend throughout the
Columbia River basin has been towards a loss in fish habitat on managed lands and stable or
improving conditions on unmanaged lands, the data for these four river basins suggest there is
a regional pattern to this change. Based on this information, along with data on the status of
anadromous fish runs in these basins, fish habitat has shown some improvement from past
abuses in eastern Washington, while continuing to decline in eastern Oregon. This appears to
be the result of different land-use histories in the two regions. The river basins of eastern
Washington apparently had a period of recovery after World War I from past land-use practices,
as the impacts of development decreased. In contrast, river basins of eastern Oregon have
been affected continuously by land-use practices over the entire development period (1850-
present). From this information, it is clear that land-use practices have degraded fish habitat
throughout eastern Washington and Oregon. Strategies to protect,  restore, and maintain
anadromous and resident fish populations and their habitat, must be based on a watershed
approach that protects the remaining habitat and restores historical habitats.

Notes: Mullan, J.W. et al. 1992. Production and habitat of salmonids in mid-Columbia River
tributary streams.  Leavenworth, WA: U.S. Department of Interior,  Fish and Wildlife Service.
Monograph I. 489 pp.

Northwest Power Planning Council. 1989. Yakima River sub-basin salmon and steelhead plan:
draft report. Portland, OR, 212 p.

Northwest Power Planning Council. 1990. Grande Ronde River sub-basin salmon and
steelhead production plan: draft report.  Portland, OR. 129 p.

Additional information on changes in fish habitat (namely pools) since the 1930s in basins of the
Columbia River basin can be found in:

Mclntosh, B.A., J.R. Sedell, R.F. Thurow, S.E. Clarke, and G.L. Chandler. 2000.  Historical
changes in pool habitats in the Columbia River Basin.  Ecological Applications 10(5): 1478-1496.

Mclntosh, B.A., J.R. Sedell, J.E. Smith, R.C. Wissmar, S.E. Clarke, G.H. Reeves, and L.A.
Brown. 1994. Historical changes in fish habitat for select river basins of Eastern Oregon and
Washington. Northwest Science 68 (Special lssue):36-53.
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Author: Meengs, C.C.; Lackey, R.T.
Year: 2005
Title: Estimating the size of historical Oregon salmon runs
Reference Type: Journal Article
Journal: Reviews in Fisheries Science
Volume: 13
Pages: 51-66

Value of reference: This research estimates pre-settlement salmon (coho, Chinook) runs for the
west coast of Oregon using 2 methods: 1) converting estimated aboriginal population levels into
numbers of salmon; and 2) extrapolating cannery pack into numbers of salmon. It is unique in
that its focus is on the streams and rivers that drain to the Pacific Ocean on Oregon's West
Coast, excluding the Columbia River basin.

The authors calculate estimates of coho and Chinook salmon populations for the Oregon coastal
rivers in 1850, before major European influence or impacts had altered salmon habitat, and the
data are thus notable as  pre-settlement conditions. The authors compare these estimates with
today's estimates to obtain estimates of population losses. Based on spawning habitat loss,
potential populations are also estimated.

Past publications and methods of estimating salmon populations in a similar  manner are
reviewed and provide good additional data and references.  Some of the past estimates are also
used in the calculations of this publication (e.g., Craig and Hacker 1940, estimates of aboriginal
consumption and proportion of a run that was harvested).

Results relevant to EMAP: Total pre-settlement salmon runs along the Oregon coast were
estimated to be 1.75-5.36 million fish.  Salmon runs may have been larger in the 1850s than any
other time in post-glacial  history because of the rapid decline in the aboriginal population and
the resulting decline in harvest just prior to major European impacts such as  gold mining,
farming, and logging.

The pre-1850 estimates were1.5-2.5 million fish in the coho run and 290,000-517,000 in the
Chinook run.  During "poor" ocean years, the current run size for coho  is 3-6% of the historical
run size,  whereas  in "good" ocean years it is 11-19% of the historical run size.  Overall, on the
Oregon coast, coho runs have been reduced by 80-95% since the 1850s.  Current population
estimates are far below potential salmon numbers, which were calculated based on available
habitat remaining. The authors conclude that, since spawning habitat has declined, ocean
conditions are the dominant factor affecting fluctuations in run size.

Reasons given for decline include deteriorating ocean conditions, competition with nonnative
fish,  predation, pollution,  and past or current fishing levels. Mining, logging, and agriculture
beginning in the 1800s have also impacted salmon populations.

Geographic location: Oregon, Coastal Oregon  rivers and streams, EPA Region 10, ecol,
mountains

Keywords: fish, mining, logging, agriculture, habitat degradation, nonnative species, urban,
fishing

Abstract: Increasing the abundance of salmon in Oregon's rivers and streams is a high priority
public policy objective. Salmon runs have been reduced from pre-development conditions
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(typically defined as prior to 1850), but it is unclear by how much. Considerable public and
private resources have been devoted to restoring salmon runs, but it is uncertain what the
current recovery potential  is because much of the freshwater and estuarine habitat for salmon
has been altered and there is no expectation that it will be returned to a pre-development
condition. The goals of all  salmon recovery efforts are based on assumptions about the size of
the runs prior to significant habitat alteration, coupled with an estimate of the amount and quality
of freshwater and estuarine habitat currently available. We estimated the historical aggregate
salmon run size in rivers along the Oregon coast (excluding the Columbia River)  using two
methods: (1)
Converting estimated aboriginal population levels into numbers of salmon; (2) Extrapolating
cannery pack into numbers of salmon. Annual aboriginal harvest of all salmon species is
estimated to have been approximately 10 million pounds per year (4,500,000 kg) or 1.75-5.36
million salmon, a harvest level similar to that occurring during the height of commercial fishing
on Oregon's coastal rivers in the late 1800s and early 1900s. Extrapolating cannery pack data,
the estimated size of the late  1800s aggregate runs of coho salmon (Oncorhynchus kisutch)
was 1.5-2.5 million. The estimated size of aggregate runs of Chinook salmon (Oncorhynchus
tshawytscha) runs was 290,000-517,000. Compared to our estimates of mid-1800s coho
salmon levels, early 2000  runs (during favorable ocean conditions), were 11-19% of the
historical level.
During poor ocean conditions (1990s), current coho salmon runs were 3-6% of the historical
size.

Notes: Craig, J.A. and R.L. Hacker. 1940.  The history and development of the fisheries of the
Columbia River.  Bulletin of the Bureau of Fisheries 49:133-216.

URL:  http://www.epa.gov/wed/pages/staff/lackey/recntpub.htm
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Author: Miller, A.I.; Counihan, T.D.; Parsley, M.J.; Beckman, L.G.
Year: 1995
Title: Columbia River Basin White Sturgeon
Reference Type: Electronic Source
Producer: U.S. Department of Interior, National Biological Service
Access Year: 2005
Access Date: May 18

Value of reference: This web site addresses a particular species (white sturgeon) in a large
basin (Columbia River) and graphically shows the population status in sections of that basin in
rough comparison with historical population levels.  This might not have a wide application
within EMAP-West, since the sturgeon is a large river fish, and EMAP focuses on smaller
streams.

Results relevant to EMAP: Historically, white sturgeon inhabited the Columbia River from the
mouth upstream into Canada, the Snake River upstream to Shoshone Falls, and the Kootenai
River upstream to  Kootenai Falls; they also used the extreme lower reaches of other tributaries,
but not extensively.

A commercial fishery that began in the 1880s peaked in 1892 when 2.5 million kg (5.5 million Ib)
were harvested (Craig and Hacker 1940).  By 1899 the population had been severely depleted
due to overfishing; more recent causes for populations declines include dam-building (which
affects spawning habitat), and continued over-harvest.

The  Figure included on this web site shows portions of the Columbia River Basin in the U.S.
where white sturgeon are currently abundant (lower Columbia River only), abundant but below
historical levels (portion of Columbia River above Bonneville Dam, upper Columbia near
Canadian border, between Lower Granite Dam and Hells Canyon Dam, and portion of upper
Snake  River), sparse, endangered, extirpated, and  unknown.

Geographic location: ecol, eco3, eco4, ecolO,  eco11, eco15, eco12, Columbia River Basin,
xeric, mountains, Washington, Oregon, Idaho, EPA Region 10

Keywords: fish, dams, fishing

URL: http://biology.usgs.gov/s+t/noframe/e065.htm
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Author: Miller, R.R.; Williams, J.D.; Williams, J.E.
Year: 1989
Title: Extinctions of North American fishes during the past century
Reference Type: Journal Article
Journal: Fisheries
Volume: 14
Issue: 6
Pages: 22-38

Value of reference: Information about extinct species can be used to reconstruct a more
complete species list to describe historical fish diversity. This article profiles 40 species or
subspecies of North American fish that have become extinct.  The list includes 14 species or
subspecies from states within the EMAP-West 12-state region, plus 3 species in that region that
inhabited only lakes.

The article discusses human impacts that are thought to have caused extinction,  and
summarizes  these,  by  species, in Table 2. It also lists erroneously reported extinctions of fishes
from North America and their current (1989) status, e.g., endangered, threatened...)(Appendix).

Results relevant to EMAP: The following 14 species, originally found in streams of the EMAP-
West region, have gone extinct as of 1989:  Oncorhynchus clarki ssp., G/'/a bicolor isolata, Gila
crassicauda, Lepidomeda altivelis, Pogonichthys ciscoides, Rhinichthys deaconi, R. osculus
reliquus, Chasmistes I. liorus, C. muriei, Cyprinodon nevadensis calidae, C. sp., Empetrichthys
latos concavus, E. I. pahrump, E. merriami.  Species were lost from Colorado, Wyoming, Utah,
Nevada, Oregon, California, and Arizona

Most of these were originally known from a very small locale or number of streams or springs
and may have had very specific geographic ranges and/or habitat requirements.  Some had
been known  for only a  short time and were presumably in decline for many years prior to being
described, and therefore the original geographic ranges will never be fully  known for most of
these species or subspecies

Reasons for extinction include physical habitat alteration, introduction of species, chemical
alteration or  pollution, hybridization, and overharvest.

Geographic location: westwide, Colorado, Wyoming, Utah, Nevada, Oregon, California,
Arizona, EPA region 8, EPA region 9, EPA region 10, mountains, plains, xeric

Keywords: fish, habitat degradation, nonnative species, pollution, fishing

Abstract: Extinctions of 3 genera, 27 species, and 13 subspecies of fishes from North America
are documented during the past  100 years. Extinctions are recorded from  all areas except
northern Canada and Alaska. Regions suffering the greatest loss are the Great Lakes, Great
Basin, Rio Grande,  Valley of Mexico, and Parras Valley in Mexico. More than one factor
contributed to the decline and extinction of 82% of the fishes. Physical habitat alteration was the
most frequently cited causal factor (73%). Detrimental effects of introduced species also were
cited in 68%  of the extinctions. Chemical habitat alteration (including pollution) and hybridization
each were cited in 38% of the extinctions, and over-harvesting adversely affected 15% of the
fishes. This unfortunate and unprecedented rate of loss of the fishery resource is expected to
increase as more of the native fauna of North America becomes endangered or threatened.
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Author: Minckley, W.L.; Deacon, J.E.
Year: 1968
Title: Southwestern fishes and the enigma of "endangered species"
Reference Type: Journal Article
Journal: Science
Volume: 159
Pages: 1424-1432

Value of reference: This paper is about extinction primarily, but in this context it gives
examples of declining species and fauna and the changes in distribution that have occurred in
the Gila basin. Paper describes historical ranges for a number of native fish of the Gila basin,
the changes in distribution that had occurred as of 1968, and the causes of the declines in
native fish.  The historical and current distributions of several selected species are depicted in
maps and juxtaposed with range maps for exotic species.  Conditions in the Gila drainage are
presented as an example of what was postulated to be happening in the Colorado River basin
overall (in 1968).

Results relevant to EMAP: As an example of the  changes in a whole fish fauna, data for
occurrence or probable occurrence are given for 34 species in the Salt River tributary of the Gila
basin from 1900 to 1960 (natives and exotics listed separately), showing the decline of natives
(all but 2) and the appearance and increase in 20 exotics beginning in 1920 (see Table 1).

Two  other examples: 1) the Gila spinedace once occurred throughout the upper Gila River basin
but more recently it has drastically declined, apparently replaced by the introduced red shiner
(see  historical maps Figure 2); 2) the Gila topminnow lived in off-channel habitats from a high-
elevation in western New Mexico to the area near Dome AZ and throughout the Gila drainage;
once considered very common, they were considered rare in 1968 (see historical distribution
map  Figure 3).

Historical distributions of larger river (mainstem) species-squawfish, humpback suckers, and
woundfish~are also described.

Declines have been the result of habitat destruction-including water diversions, impoundments,
erosion and downcutting, agriculture, and pollution~and competition with introduced fish
species.  These impacts are discussed in more detail by Molles 1980 with respect to their
present and likely future influences in the upper Colorado River basin.

Geographic location: Gila River basin, Arizona, eco81, eco79, eco23, xeric,  EPA Region 9

Keywords: fish, nonnative species, dams, water diversion, erosion, agriculture

Notes: Molles, M.  1980.  The impacts of habitat alterations and introduced species on the native
fishes of the upper Colorado River basin. Pages 163-81 IN Spofford, W.O., Jr., A.L. Parten,
A.V.  Kneese (eds.), Energy development in the southwest.  Research paper 18. Resources for
the future, Washington, D.C.
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Author: Minckley, W.L.; Marsh, P.C.; Brooks, J.E.; Johnson, J.E.; Jensen, B.L.
Year: 1991
Title: Management toward recovery of the razorback sucker
Reference Type: Book Section
Editor: W.L. Minckley; Deacon, J.E.
Book Title: Battle Against Extinction: Native  Fish Management in the American West
City: Tucson, AZ
Publisher: The University of Arizona Press
Pages: 303-357

Value of reference: The first portion of this chapter summarizes what is known about the
historical distribution of the razorback sucker in the Colorado River basin and chronicles the
species' decline. It is extensively researched, using both peer-reviewed and published literature
as well as personal contacts. The historical summary is largely a literature review, which
includes many historical survey references and an overview of historical abundance in various
portions of the river basin (see subsection 'Abundance in Aboriginal and Early Historical Times',
on page 307).   Other relevant sections summarize survey records from the 1900s, which
provide evidence of declining populations, and reasons for decline.

Results relevant to EMAP: Although it is estimated that the species began declining before
1912, much of the concern regarding the species status is more recent, beginning in the  1930s
after closure of the Hoover Dam.

Possible reasons for declining populations include dewatering, dams, water diversions, lower
water temperatures, competition with non-native fishes, predation, and hybridization

Historical records of presence and abundance are cited throughout the text.  Figure 17-2 shows
a map of present and historic distribution of the sucker in the Colorado River basin.

Geographic location: Colorado River basin, xeric, mountains, eco20,  eco18, eco22, eco14,
eco23, eco81,  EPA Region 8, EPA Region 9, Colorado, Wyoming, Arizona, California, Utah,

Keywords: historical distribution, fish, razorback sucker, dams, water diversion, nonnative
species
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Author: Minckley, W.L.; Rinne, J.N.
Year: 1985
Title: Large Woody debris in hot-desert streams: an historical review
Reference Type: Journal Article
Journal: Desert Plants
Volume: 7
Issue: 3
Pages:  142-153

Value of reference: This work provides a good historical review of desert riparian communities
in the mid 1800s.  Many selected quotations from early literature help to illustrate riparian
conditions. The fate of large wood in desert systems and the changes in human impacts
between the late 1800s and late 1900s are addressed. The influence of wood and organic
particulates on macroinvertebrates is also treated to link the physical and biological aspects of
desert streams.

Results relevant to EMAP: Historically, large wood contributed to heterogeneity of the desert
stream ecosystem. Lithographs, photographs, and written historical documentation provide
evidence of dense riparian gallery forests, marshlands, densely-vegetated floodplains, and
accumulations of large, woody debris along Sonoran Desert streams, much of which originated
in the upper basin.  Conditions along smaller tributaries included large stands of riparian trees
(including cottonwood, mesquite, willow), and thus presumably substantial amounts of downed
timber.  Based on historical accounts, the authors conclude that substantial amounts of
vegetative debris, including fine particulates, were available to streams of the Sonoran Desert.
Extensive literature citations are given for historical documentation.

A large  percentage of southwestern riparian communities, especially at low elevations, have
now been replaced by introduced saltcedar (Tamarix chinensis).  Riparian communities have
been further destroyed by woodcutting, agricultural development, urbanization, and desiccation
from stream incision,  impoundment, channelization, and over-grazing.  In central AZ, cleared
and irrigated agriculture land increased from less than 200 hectares in 1862 to many thousands
of hectares in 1982., while the population of Phoenix grew from 100 to over a million.  Dams
now trap most particulate materials.

Geographic location: xeric, Arizona, California, EPA Region 9, Sonoran Desert, lower
Colorado River basin, eco14, eco81, eco23, eco22, eco20

Keywords: phab, large wood, riparian vegetation,  particulate organic matter,  Sonoran Desert,
historical documentation, agriculture, urban, grazing, impoundment

Abstract: Large-particulate organic debris is denied to present-day desert streams because of
interception by impoundments and as a results of decimation of formerly extensive riparian
vegetation. Historical records indicate a substantial, but sporadic, input of coarse debris, which
was reduced to finer particles through molar action in canyon-bound reaches  of desert rivers.
Historical changes, functions of large debris in the system, and probable future conditions are
reviewed.
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Author: Minshall, G. W.; Jensen, S. E.; Platts, W. S.
Year: 1989
Title: The ecology of stream and riparian habitats of the Great Basin region: A community
profile
Reference Type: Report
Institution: U.S. Fish and Wildlife Service
Pages: 142
Report Number: Biological Report 85(7.24)

Value of reference: The reference provides a good overview of the fish of the Great Basin with
an emphasis on the post-Pleistocene distribution of cutthroat trout and a timeline offish
introductions. It also has a section on the history of livestock grazing in the Great Basin.

Results relevant to EMAP: Introduction of exotic fish into Bonneville basin waters began in the
late 1880's. Table 22 p. 86, lists fish presently established in the Great Basin with native species
noted. In the Carson River system, nonnative trout introduced in the 1880's displaced the native
cutthroat trout within a few decades, except where the natives had been stocked above
impassable falls. The west face of the Ruby Mountains and East Humboldt Range in Elko
County show the most significant impact of past trout stocking practices. Native cutthroat trout
have been replaced by other salmonids, principally the eastern brook trout.

Lahontan cutthroat trout have been eliminated from 95% of their native habitat as a result of
human activity, p. 92. In the Humboldt River drainage Lahontan cutthroat trout still live in the
headwaters, but occur in only about 12% of their former range. Lahontan cutthroat trout of the
Humboldt River drainage fared better than the trout in the Truckee-Walker drainages because
they were better adapted to stream life with its flood/drought cycle. The trout in the Humboldt
drainage also have not experienced as much displacement or hybridization with other stocked
trout species.

Geographic location: xeric, Nevada, Utah, Bonneville Basin, Lahontan Basin, eco13, ecoSO,
Truckee River, Humboldt River basin,  Carson  River, EPA Region 9, EPA Region 8

Keywords: fish, cutthroat trout, nonnative species,  riparian vegetation, grazing
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Author: Mongillo, P.E.
Year: 1993
Title: The distribution and status of bull trout/Dolly Varden in Washington state June 1992
Reference Type: Report
City: Olympia, WA
Institution: Washington Department of Wldlife Fisheries Management Division
Report Number: Report No. 93-22

Value of reference: A rough estimate of past distribution of bull trout/Dolly Varden is presented,
based on personal knowledge of the individuals interviewed and on historic creel records.
Extrapolation and assumptions were made, based on limited location information from historical
sources; therefore historical absence might only mean that no historical documentation was
found for certain  drainages or streams. The report is more of a current status of 77 populations
of the species, but changes since pre-settlement are also embedded; Figure 1 gives the current
knowledge on present and past distribution of bull trout/Dolly Varden.

Results relevant to EMAP: Most of the Columbia River was previously utilized by bull
trout/Dolly Varden, whereas only sections of the river associated with larger tributary
populations commonly contain bull trout/Dolly Varden today (see Figure 1); the species was
likely never abundant in the mainstem River and never seems to have been present in the
Cowlitz River drainage of southwest WA or the Quileute system below Solduc Falls on the
coast.

The Okanogan, Lake Chelan, and Lower Yakima River populations have been lost, while other
populations or groups of populations have become fragmented or isolated, for example in the
streams in the Blue Mountains of southeast WA, the upper Yakima River in central WA, the
Lewis River in southwest WA, and the Cedar River near Seattle.

Easy public access,  poaching and presence of nonnative fish species (brook trout, brown trout,
rainbow trout) are adversely impacting approximately the same number of populations;
interbreeding between small resident populations of bull and brook trout will likely lead to
elimination of bull trout. A number of human impacts harming the species are discussed; forest
management is affecting the greatest number of populations, and grazing the least.

Geographic location: Washington, eco77, eco15, ecolO, ecol, eco2,  eco4, Pacific Northwest,
EPA Region 10, mountains, xeric

Keywords: fish, nonnative species,  logging, roads, fishing

Abstract: Bull trout (Salvelinus confluentus), and Dolly Varden (Salvelinus malma), are
generally present in  all parts of Washington State except the area east  of the Columbia River
and north of the Snake River in eastern Washington (Columbia Basin) and the extreme
southwest portion of the state.  Distribution losses from historical levels have been confined
mainly to eastern Washington. In addition to a reduced distribution from historical levels,
several populations in both eastern and western Washington have become fragmented because
lower river reaches are no longer utilized.  A total of three populations have become extinct.  It
is estimated that  a minimum of 77 distinct bull trout/Dolly Varden populations remain in
Washington.  Nine are at high risk of extinction, six are at moderate risk, 13 are at low risk and
six are believed to be at no immediate risk. The remaining 43 populations do not have sufficient
data on them to assign a level of risk.  Additionally, the habitat and non-habitat factors affecting
each population are  identified and summarized.
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Author: Moyle, P.B.; Nichols, R.D.
Year: 1974
Title: Decline of the native fish fauna of the Sierra Nevada foothills, central California
Reference Type: Journal Article
Journal: American Midland Naturalist
Volume: 92
Issue: 1
Pages: 72-83

Value of reference: Historical data from three historical surveys were synthesized and
compared to the 1970 survey.  The results, shown in Table 2, show how the fish assemblage
changed over time in reference to the construction of Friant Dam (1942) and with respect to the
proportions of native and introduced species. Distribution  maps, showing pre-1900 and 1970
locations are presented for the most abundant species. General changes in numbers and
distribution are discussed briefly for each species.

The study was confined to streams between 90 and 1100 m elevation with a mean elevation of
401 m.

Results relevant to EMAP: The San Joaquin foothill fish fauna has change dramatically in
many areas as native fishes are replaced by introduces species. Table 2 illustrates the changes
that have occurred since 1989, as documented in 4  surveys,  published in 1898, 1934, 1941,
and 1970 (present study). The 1898 survey indicates that the areas originally had a fish fauna
transitional between those of the Valley floor and the foothills.

The San Joaquin River systems experienced modification due to dam construction and the
introduction of numerous fish species. By 1970, the river below Friant Dam (closed in 1942)
was dominated by introduced species.  Healthy populations of native fishes occurred only in a
restricted region of relatively undisturbed foothill streams.

Geographic location: xeric, eco7, California, EPA region 9,  San Joaquin River basin

Keywords: fish, nonnative species, dams, habitat fragmentation

Abstract:  A survey was made of the  fishes occurring in streams of the Sierra Nevada foothills
above the San Joaquin Valley, California. Twenty-four species were collected, 12 native, 12
introduced. The present distributions of these fishes were compared to their pre-1900
distributions, as inferred from old records. Overall, the ranges of introduced species and
rainbow trout have expanded while the ranges of native species, especially California roach,
hardhead, Sacramento squawfish and Sacramento sucker, have contracted. Healthy
populations of native fishes were found  only in a rather narrow middle elevation band of
comparatively undisturbed sections of foothill streams.  The native fish populations in different
foothill stream systems are now isolated from each other and are, thus, in danger of local
extinction as foothill development proceeds. The study indicates that populations of native
stream fishes, even if they do not contain endangered species, should be protected, to make
sure that severe natural conditions, when combined with human alterations to the streams, do
not destroy unique assemblages of fishes.
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Author: Moyle, P.B.; Williams, J.E.
Year: 1990
Title: Biodiversity loss in the temperate zone: decline of the native fish fauna of California
Reference Type: Journal Article
Journal: Conservation Biology
Volume: 4
Issue: 3
Pages: 275-284

Value of reference: This article synthesizes information and reports on the status of 113 native
fish taxa in California, in a manner similar to that of Nehlsen et al. 1991 (this bibliography).  It
does not present historical information specifically, but uses historical information and
knowledge of declining populations, based  on past status, and assigns a status ranking of 1-6
for each of several ratings of natural and artificial factors influencing the species distribution.
Causes of decline are also summarized briefly.

Results relevant to EMAP: Of 113 native fish taxa in California, 6% are extinct, 57% are in
various stages of decline, and 36% appear to be stable. Much of the decline has been recent,
rapid, and unexpected. Fish taxa at particular risk are most likely to be endemic, restricted in
range, part of a small fish assemblage, or found in isolated springs, warm water stream, or big
rivers. Entire regional faunas are threatened with extinction or with being confined to isolated
fragments of habitat.

Cause for decline is attributed mainly to water diversions and  introduced species, acting in
concert.  Habitat alterations associated with agricultural practices, grazing, and channelization
are other contributors.

Geographic location: California, ecol, eco78,  eco4, eco9, eco5, eco7, eco6, eco8, eco14,
eco81, EPA Region 9, Mountains, Xeric. Non-specific to river basin, although some summaries
used ichthyological provinces.

Keywords: fish, status, water diversion, nonnative species, agriculture, grazing, channelization
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Author: Moyle, P.B.; Yoshiyama, R.M.; Knapp, R.A.
Year: 1996
Title: Status of Fish and Fisheries
Reference Type: Report
City: Davis, CA
Institution: University of California, Centers for Water and Wildland Resources
Pages: 953-973

Value of reference: This is a good synthesis of changes in native fish populations in the Sierra
Nevada range. Historical (pre-European) distributions (largely affected by elevation) are
discussed briefly for each of four major basins and summarized in general in Figure  1.  Current
status and short species accounts of 40 native fish species are presented.  Factors contributing
to declines and the importance of their impact on native fishes of the region are summarized in
Table 4.  A special section  is included for Chinook salmon, although a more thorough treatment
of this species can be found in Yoshiyama et al. 1998, in this bibliography.

Fish introductions in this region are treated in detail, since they are a major factor in  the decline
of native species.  The effect of trout introductions on native biota-native trout, amphibians, and
invertebrates-is included, although few specific details are presented.

Results relevant to EMAP: Since 1850, anadromous fishes have been excluded from most
west side rivers; most resident native fishes have declined and aquatic communities have
become fragmented; 30 species  of nonnative fishes have been introduced or have invaded
most waters, including historically fishless, high-elevation areas; and fisheries now focus on
nonnative fish, rather than natives. Chinook salmon have lost 62% of the stream length
originally available to them for spawning in the Central Valley  (Table 3).

Historically, all four of the major basins in the region were fishless at high elevation.  Chinook
salmon, steelhead trout, and Pacific lamprey were abundant in the Sacramento-San Joaquin
drainage. The Lahontan drainage supported 10 native fish species and all were widespread
and abundant. Known historical  elevation limits are given for  a number of species.

Of the 40 fishes native to the Sierra Nevada,  15% have been  listed as threatened or
endangered, 30% are listed as species of special concern by  Moyle et al. 1996, 10% are in
severe decline in this region, and 45% seem to be stable or expanding.  Chinook salmon,
steelhead, and 5 native trout have mostly disappeared from the region.  The mountain yellow-
legged frog is found at fewer than 15% of the high-elevation sites at which it was present in
1915 (Drostand Fellers 1994).

The biggest declines in native fish abundance occurred between  1850 and  1950 as a result of
hydraulic mining, construction  of dams and diversions, and introductions of nonnative fish.
Other factors include road building/urbanization, channelization, grazing, logging, and pollution.

Geographic location: California, eco5, eco6, eco7, Sierra Nevada, EPA region 9, mountains,
xeric, Sacramento-San Joaquin basin, Owens basin, Lahontan basin, Eagle Lake basin

Keywords: fish, status, distribution, nonnative species, dams, urban,  water diversion, logging,
grazing, channelization, pollution

Notes: Moyle et al. 1996.  Fish species of special concern in California.  California Department
of Fish and Game, Sacramento, CA.
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Drost and Fellers 1994. Decline of frog species in the Yosemite section of the Sierra Nevada.
U.S. Department of the Interior Technical Report NPS/WRUC/NRTR-94-02.  Government
Printing Office, Washington, D.C.
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Author: Mueller, G.; Marsh, P.
Year: 1995
Title: Bonytail and Razorback Sucker in the Colorado River Basin
Reference Type: Electronic Source
Producer: U.S. Department of Interior, National Biological Service
Access Year: 2005
Access Date: June 21

Value of reference: This is a summary paper printed by the National Biological Service on a
web site. It is a comprehensive summary of the decline of razorback suckers and bonytails in
the CO River basin.  It reports the extent of their historical ranges, the tributaries where they
were once common to abundant, and the major causes of their declines.

Results relevant to EMAP: Both species were common historically; today, no measurable
recruitment is evident for either species, and old individuals are reaching the end of their
lifespan.

Bonytails were historically common in mainstem CO, Green, Gunnison, Yampa, Gila, and Salt
rivers before construction of large dams.  They now exist only in Lake Mohave, which comprises
<2% of their former range (see Figure 3).
Razorback suckers were historically common to abundant in the CO mainstem and portions of
the Green  San Juan, Animas, Duchesne, Gila,  Salt, and Verde rivers, but today are very rare
and found  in <25% of the former  range (see Figure 3).

Declines have been caused by physical and biological changes to habitat cause by large dams,
reservoirs, and diversion canals,  direct competition with introduced fish species, and predation
on young fish by non-native fishes.  Promotion  of recreational fisheries, introduction of sport fish
more adapted to colder water, and poisoning compromised the native fish.

Geographic location: Colorado  River Basin, eco18, eco19, eco20, eco21, eco13, eco22,
eco23, eco81, eco14, Wyoming,  Utah, Colorado, Arizona, Nevada, xeric, mountains, EPA
Region 8, EPA Region 9

Keywords: fish, endangered species, dams, channelization, water diversion, nonnative species

Notes: A related, but less current publication documenting historical range and the 1970s
distribution in the Colorado R. system is:
McAda, C.W. and R.S. Wydoski.  1980. The Razorback Sucker, Xyrauchen texanus, in the
Upper Colorado River Basin, 1974-76. U.S. Department of Interior, Fish and Wildlife Service,
Technical Paper 99.  Washington, D.C.

URL: http://biology.usgs.gov/s+t/noframe/r166.htm
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Author: Mueller, G.; Marsh, P.
Year: 2002
Title: Lost, A Desert River and Its Native Fishes: A Historical Perspective of the Lower Colorado
River
Reference Type: Report
City: Fort Collins, CO
Institution: Geological Survey Fort Collins Science Center
Pages: 80
Report Number: Information and Technology Report USGS/BRD/ITR--2002-0010

Value of reference: This detailed report documents the history, exploration, settlement, and
historical fish community of the lower Colorado River basin, as well as the story of water
development of the basin and the changes in physical habitat and the native fish community that
followed. Information includes descriptions of channel characteristics, sediment loads,
backwater habitats, vegetation, river dynamics, and flooding patterns typical of the undisturbed
river.  Changes occurring during the settlement and development period are chronicled in detail.
The changes in physical properties of the water, channel configuration, riparian habitat, and
aquatic biota as a result of human impacts are discussed at length. This discussion includes
the survival strategies and life histories of all native fish of the lower river.  Table 5 gives the
relative historical abundance and current federal/state status of these species.  Numerous
historical accounts and photographs are included.

Results relevant to EMAP: Prior to 1880,  only 9 freshwater species were found in the lower
CO river, representing 4 families and two marine species in the lower river (in 1880, this would
have been in Mexico and not relevant to EMAP). Most fish were found in off-channel habitats
where there  were fewer suspended sediments and effects  of flooding were less severe. Fish
kills were common due to a hostile and unpredictable river environment. Fish communities
periodically disappeared from the broader floodplains and extended portions of tributaries.
Populations  that numbered in the millions could be reduced to only a few dozen fish in a single
season.

In contrast to other reports, the authors claim that the majority of natives were lost long before
the Hoover Dam was built in 1935, but the  larger water developments after 1935 likely
guaranteed their demise. Irrigated agriculture led to stranding of fish in fields.  Commercial
fishing, loss  of habitat, migration  barriers (dam construction, diversions, dewatering), and
introduction  of carp,  bullhead, and channel catfish occurred before 1935.

Profiles of past abundance and distribution in the basin and estimates of what remains are
described for each of the native species (beginning  on page 62, summarized in Table 5).

Geographic location: Arizona, California,  Utah, Colorado, eco81, eco23,  eco22, eco20, lower
Colorado River basin, Region 8, Region 9,  xeric

Keywords: human impacts, historic documentation, lower  basin, native fish, agriculture, fishing,
dams, water diversion, channelization, nonnative species,  historical photographs, fish, phab

Abstract: The Colorado River had one of the most unique  fish communities in the world.
Seventy-five percent of those species were found nowhere else in the world. Settlement of the
lower basin brought  dramatic change to both the river and  its native fish. Those changes began
more than 120 years ago as settlers began stocking nonnative fishes. By 1930, nonnative fish
had spread throughout the lower basin and replaced native communities. All resemblance of
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historic river conditions faded with the construction of Hoover Dam in 1935 and other large
water development projects. Today, few remember what the Colorado River was really like.
Seven of the nine mainstream fishes are now Federally-protected as endangered. Federal and
state agencies are attempting to recover these fish. However, progress has been frustrated due
to the severity of human impact. This report represents testimony, old descriptions, and
photographs describing the changes that have taken place in hopes that it will provide
managers, biologists, and the interested public a better appreciation of the environment that
shaped these unique fish.

URL:  http://www.stormingmedia.us/23/2322/A232214.html
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Author: Mueller, G.A.; Marsh, P.C.; Minckley, W.L.
Year of Conference: 2005
Title: A legacy of change: the lower Colorado River, Arizona-California-Nevada, USA, and
Sonora-Baja California Norte, Mexico
Reference Type: Conference Proceedings
Editor: Rinne, J.N.; Hughes, R.M.; Calumusso, B.
Conference Name: Historical Changes in Large River Fish Assemblages of the Americas
Conference Location: Phoenix, AZ
Publisher: American Fisheries Society
Volume: 45
Pages: 139-156

Value of reference: This chapter is a concise synopsis of what has happened to the Colorado
River and its native fish community.  The section on 'Native Fish Assemblage' describes the
historical fish community and provides citations of numerous original historical documents and
reports.

A section on 'Physical Description' includes a few riparian descriptions.

Factors causing the decline of native fish are discussed.

Results relevant to EMAP: Historically, the lower CO river had only 9 native fish species,
which are today extirpated, federally endangered, or being reintroduced through stocking.
Eighty alien species have been introduced to the lower basin, and 20 of these have become
common.  Predation by nonnative species and physical habitat degradation were the primary
causes of the decline of native fauna.

Table 1 summarizes historical abundance and current status of the native fish species.

Geographic location: Colorado River basin, Colorado, Utah, Wyoming, Arizona, EPA Region
8, EPA Region 9, eco18, eco19, eco20, eco21, eco22, eco23, xeric,  mountains

Keywords: fish, nonnative species, habitat degradation, historical abundance, status
                                         139

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Author: Murphy, Peter J.; Randle, Timothy J.; Fotherby, Lisa M.; Daraio, Joseph A.
Year: 2004
Title: The Platte River Channel: History and Restoration
Reference Type: Electronic Source
Producer: U.S. Department of the Interior; Bureau of Reclamation Technical Service Center
Access Year: 2005
Access Date: July 26, 2005

Value of reference: Good summary of the human impacts and physical changes that have
occurred to the  Platte River valley since settlement (mid -late 1800's).  Changes in
geomorphology, flow and sediment transfer of the river are the main focus of the study. Includes
an extensive bibliography.

Results relevant to EMAP: The emphasis of this study is a  historic review and analysis of the
geomorphology of the  central Platte River. This analysis is based primarily on existing historic
field data, historic mapping, aerial photos, written narrative, historic photos, recorded
information on Platte River Basin development, and some recent field data collection associated
with this study. Historic and recent field data include measurements of river discharge, climate
indicators, bed-material size gradations, average un-vegetated channel widths or active channel
widths, and stage-discharge relationships.

Initial anthropogenic influences on the central Platte River in  the 1800s are primarily raised
sediment inputs from land use beginning in the 1840s, and flow depletions in the last decades of
the century.  The beaver trapping industry eradicated almost all beaver in the area  by the mid
1800s. The impact of this harvest may have contributed small increases in sediment load in the
Rocky Mountain tributaries, through the gradual elimination of sediment-trapping beaver dams.
Extensive gold mining  and timber harvesting in the South Platte tributaries and some activity in
the North Platte tributaries, may have increased sediment loads to the central Platte River.

Reaches of the  present channel have an un-vegetated or active channel width that is 50 to 90
percent narrower than  the channel that existed in the 1860s and in the period 1898 to 1902. The
central Platte River has generally experienced channel narrowing throughout its length with
greater reductions in un-vegetated or active channel width in the upper reaches.

Geographic location: plains, Platte River Valley, Nebraska, Wyoming, Colorado, eco25,
eco27, eco43, EPA region 7, EPA region 8

Keywords: Platte River, phab, channel width, channel stability, pre-settlement,
geomorphology, beaver trapping,  mining,  logging, sediments

URL: http://www.platteriver.org/library/index.htm
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Author: Murray, T.B.
Year: 1964
Title: Chinook and steelhead historic spawning grounds, Shoshone Falls to Salmon River,
Snake River drainage
Reference Type: Report
City: Boise, ID
Institution: Idaho Power Company

Value of reference: The author uses multiple sources and personal observation to piece
together what the distribution and range of steelhead and Chinook salmon in the unobstructed,
pre-settlement middle Snake River (mouth of Salmon-lmnaha Rivers to Shoshone Falls) would
have been. Estimates of the river miles available as spawning habitat for these species before
major human impacts and dam building are given for each tributary, extending as far as the
Jarbidge  and Santa Rosa mountain ranges in northern Nevada.  Other pre-settlement
conditions are mentioned throughout, such as vegetation, historical conditions in each basin that
would have favored spawning and rearing of fingerling salmonids, human impacts that changed
migration potential in the Snake River drainage, and Native American fisheries.

The document gives a broad view of the fish population potential of the Snake River in pre-
settlement times. It summarizes pre-settlement spawning conditions in each tributary in the
basin for spring Chinook, steelhead, and fall Chinook.   Information is presented in a draft format
of text only.  The information is not referenced, and some statements are based on second-
hand knowledge.

Results relevant to EMAP: Prior to obstructed migration, the middle Snake River was a prime
producer of fingerling salmonids. Pre-settlement conditions favorable for spawning and rearing,
including the space available (in river miles) are summarized  for the following Snake  River
tributaries:  Boise, Owyhee,  Payette, Malheur, Weiser, Burnt, Powder, and Wildhorse Rivers
and Pine Creek.

On page  32 is a summary of the river miles historically available for spawning and rearing in
each sub-basin, totaling 2060 river miles.  By 1955, the availability and use of this production
potential  had been reduced by 90% due to over-fishing, habitat alterations  and blockage to fish
passage  caused by dams, agriculture,  logging, pollution, water diversions,  and climate changes.
In 1955, remnant runs were  spotty, and river habitat occupied by steelhead or Chinook salmon
totaled barely 200 miles on portions of Weiser and Wildhorse Rivers and Pine and Eagle
Creeks.

Geographic location: Idaho, Nevada, Snake River basin, ecoSO, eco12, EPA region 10, xeric
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Author: Musser, G.G.
Year: 1959
Title: Ecological Studies of the Flora and Fauna in Glen Canyon, Appendix E: Annotated check
list of aquatic insects of Glen Canyon
Reference Type: Report
City: Salt Lake City, UT
Institution: University of Utah
Pages: 207-221
Report Number: Anthropology Papers No. 40

Value of reference: Since historical macroinvertebrate data are very limited, this article is
sufficiently notable to include here, even though it was published in the mid 1900s. It is
considered the best comparable data for aquatic insects that exists for the geographic region.
Although the data are reported for an area now underwater, their historical presence in the
region is notable for reconstruction of insect distribution and community composition before dam
construction.

Results relevant to EMAP: In a 1958 survey of the Glen Canyon (before impoundment), 2315
individual aquatic insects were collected, including more than 91 species in 73 genera, 41
families, and eight orders. The bulk of the collection was from tributaries, while only 247 were
taken from the river.

This listing provides 1-8 lines of text description for each species collected regarding presence,
relative abundance, other locations  where present, habitat preferences, and other anecdotal
information.

Geographic location: Arizona, Colorado River basin, eco22, xeric, EPA region 9

Keywords: macroinvertebrates,  baseline data, species list
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Author: Muth, R. T.; Crist, L. W.; LaGory, K. E.; Hayse, J. W.; Bestgen, K. R.; Ryan, T. P.;
Lyons, J. P.; Valdez, R. A.
Year: 2000
Title: Flow and temperature recommendations for endangered fishes in the Green River
downstream of Flaming Gorge Dam
Reference Type: Report
Publisher: Upper Colorado Endangered Fish  Recovery Program
Report Number: Rpt. No. FG-53

Value of reference: This is a comprehensive  reference (344 pp.) for the changed conditions on
the Green River downstream of the Flaming Gorge dam, how they affect the native warmwater
fish populations (particularly the 3 major endangered species, humpback chub, Colorado
pikeminnow, and the razorback sucker), and suggested mitigations of the adverse effects to
ensure the continued existence of these fish species.

Results relevant to EMAP: The historic abundance and habitat needs of each of the species of
interest is covered in a separate chapter.  For example, critical habitat designated for Colorado
pikeminnow makes up only about 29% of the species' original range and occurs exclusively in
the upper Colorado River basin, and 600 to 650 adult Colorado pikeminnow occur today in the
Colorado River upstream of the Green River confluence.

Geographic location: Region 8, Utah, Green River, xeric, eco20

Keywords: fish, dams, water diversion, habitat degradation,  nonnative species, flow variability,
sediment, temperature

URL: http://www.ead.anl.gov/pub/doc/flaminggorgeflowrecs.pdf
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Author: Nehlsen, W.; Williams, J.E.; Lichatowich, J.A.
Year: 1991
Title: Pacific salmon at the crossroads: stocks at risk from California, Oregon, Idaho, and
Washington
Reference Type: Journal Article
Journal: Fisheries
Volume: 16
Issue: 2
Pages: 4-21

Value of reference: This is a landmark report of the status of salmon and steelhead on the
West Coast of the U.S.  It is extremely comprehensive and often cited.  It lists the population
status of 7 species (comprising 214 stocks), and the reasons for declines in individual bays and
tributaries throughout the region; it also mentions changes from historical conditions.

Few actual historical data are given; historical references reported are from varying years,
depending upon what is available, and the year is usually not specified.  For many of these
species, the declines that have occurred  even since the mid-1900s is so substantial, being
closely associated with hydropower development which intensified at that time, that the most
significant changes from an "historical" benchmark are captured in the period of the late 1900s.
The data reported are therefore significant and noteworthy.

Results relevant to EMAP: Since 1850s, development activities such as hydropower, fishing,
logging, mining, agriculture, and urban growth have caused extensive losses in salmon and
steelhead populations and habitats.

A few examples of the numerous summary statements provided in this document:  the Klamath
River population of spring and summer Chinook has undergone a 95% reduction from historical
population levels, due to dams, irrigation diversions, mining, timber harvest, and floods; many
native coho stocks on the southern Oregon coast have declined from historical levels of about
2000 spawners to fewer than  100 and are now dominated by hatchery programs; in the
Columbia River basin, historically large chum stocks in the lower river have declined to about
0.5% of their historic level; at  least 106 major populations of salmon and steelhead on the West
Coast have been extirpated, and over 200 stocks have become extinct in the Columbia River
basin, including 95 streams where Chinook have disappeared, 83 for steelhead, 17 for coho,
and 12 for sockeye (Oregon Trout, Personal communication by Nehlsen et al.) (see Table 2);
natural production in the Columbia River basin is now about 4-7% of pre-development levels,
which likely represents a significant loss of genetic diversity.

With the loss of so many populations prior to our knowledge of stock structure, the historic
richness of the salmon and steelhead resource of the West Coast will never be known; it is clear
that  what has survived is a small  proportion of what once existed.

Geographic location: mountains, xeric,  ecol, eco3, ecolO, eco11, eco15, eco16, eco17,
eco12, eco6, eco78, eco7, eco9, Pacific Northwest, Oregon, Washington, Idaho, California,
Columbia River basin, Coast Range, West Coast, EPA Region 9, EPA Region 10

Keywords: fish, salmon, status, habitat loss, agriculture, logging, dams, urban, nonnative
species, fishing

Abstract: The American Fisheries Society herein provides a list of depleted Pacific salmon,
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steelhead, and sea-run cutthroat stocks from California, Oregon, Idaho, and Washington, to
accompany the list of rare inland fishes reported by Williams et al. (1989).  The list includes 214
native naturally-spawning stocks: 101 at high risk of extinction,  58 at moderate risk of extinction,
54 of special concern, and one classified as threatened under the Endangered Species Act of
1973 and as endangered by the state of California. The decline in native salmon, steelhead,
and sea-run cutthroat populations has resulted from habitat loss and damage, and inadequate
passage and flows caused by hydropower, agriculture, logging, and other developments;
overfishing, primarily of weaker stocks in mixed-stock fisheries; and negative interactions with
other fishes, including nonnative hatchery salmon and steelhead.  While some attempts at
remedying these threats have been made, they have not been enough to prevent the broad
decline of stocks along the West Coast. A new paradigm that advanced habitat restoration and
ecosystem function rather than hatchery production is needed for many of these stocks to
survive and prosper into the next century.

Notes: Wlliams, J.E.  and others. 1989. Fishes of North America endangered, threatened, or of
special concern: 1989. Fisheries (Bethesda) 14(6):2-20.
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Author: Nesler, T.P.; VanBuren, R.; Stafford, J.A.; Jones, M.
Year: 1997
Title: Inventory and status of South Platte River native fishes in Colorado
Reference Type: Report
City: Fort Collins, CO
Institution: Colorado Division of Wildlife, Aquatic Wildlife Section

Value of reference: This report focuses primarily on current surveys of fish, but it also
addresses the available historical information,  utilizing Propst and Carlson 1986 (in this
bibliography) as a basis for reporting and is thus a good companion article to that paper
(although not a significant source of historical information on its own).  The added useful
information provided by this source is the mapped locations of  historical vs. current collections
in the basin (Figures 3-11). Although notable,  the historical distributions cannot realistically be
compared to modern distribution data because of a much lower sampling effort in the past.  The
article provides the list of native species, extirpated species, and  species that are now
considered common and at low risk of imperilment. It also provides a brief literature summary of
the historical river (page 80).

Results relevant to EMAP: The river channel of the South Platte is only 15% of its historical
dimensions due to agricultural use and water diversions.  Historically it was wide, shallow,
braided, and sparsely vegetated. After spring  runoff, the river was intermittent, often running
underground.  Today, irrigation return flows have created a perennial stream and raised water
table.

The historical composition of fish fauna and changes through time as a result of human impacts
have not been well-documented. This article reviews the historical literature, but the lack of
detail in historical survey literature prevents a meaningful comparison for most species.

The article's focus is on the 1992-94 survey results, but the species list, historical summary, and
maps are useful and will complement the historical information  presented by Propst and Carlson
1986-in this bibliography.

Geographic location:  Colorado, South Platte River basin, eco25, plains, EPA region  8

Keywords: fish, phab,  agriculture, dams, water diversion

Notes: Propst and Carlson. 1986. The distribution and status of warm water fishes in  the Platte
River drainage, Colorado. Southwestern Naturalist 31:149-67.
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Author: Northwest Power Planning Council
Year: 1986
Title: Compilation of Information on Salmon and Steelhead Losses in the Columbia River Basin
Reference Type: Report
City: Portland, OR
Institution: Columbia River Basin Fish and Wildlife Program

Value of reference: This is a valuable document of over 200 pages that uses several different
methods for estimating historical run sizes and losses of salmon and steelhead since pre-
settlement. It was developed with extensive public review and comment and is frequently cited
for the Pacific Northwest region.  Numerous tables of historical data.

It presents comprehensive information on historical and current run sizes of salmon and
steelhead in the Columbia River basin.  Data on historic fish runs have been gathered from
every available source ranging from actual recorded fish counts over time to the accounts of
Indian tribal elders and historical records from early settlers. Sources include historical,
anthropological, and archaeological data. Descriptions of current runs are based on adult fish
counts, redd (spawning nest) counts,  and harvest records.

Results relevant to EMAP: Salmon and steelhead runs in the Columbia River basin ranged
from about 10 to 16 million fish prior to a number of development activities by white settlers  in
the 1800s, whereas the current run size averages about 2.5 million fish, representing a loss of
at least 75%.

At one time, salmon and steelhead inhabited the entire Columbia River basin up to the Arrow
Lakes in  Canada and below Shoshone Falls on the Snake River. Since the mid-nineteenth
century, the estimated salmon and steelhead habitat in the entire basin has declined from about
13,000 miles of stream to only 9,000 miles, a 31% loss.

The greatest losses of fish  runs and habitat have occurred in the upper Columbia and upper
Snake river areas, where much of the habitat has been permanently damaged by the federally-
operated Chief Joseph and Grand Coulee dams in the mid-Columbia River area and
development in the Snake River Basin.

The document examines the impact on fish runs of a variety of development activities including
hydropower, fishing, irrigation, logging, mining, grazing, and agriculture.  The major impacts
caused by hydropower are blockage of fish habitat, alteration of fish habitat, and obstacles to
juvenile fish passing downstream and to adult fish returning upstream to  spawn.

Geographic location: Columbia River Basin, Oregon, Washington, Idaho, EPA Region 10,
eco11, ecolO,  eco16, eco4, ecol, eco3, eco9, mountains, xeric

Keywords: fish, salmon, steelhead, hydropower, dams, fishing, agriculture, logging, mining,
grazing
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Author: Olden, J.D.; Poff, N.L.; Bestgen, K.R.
Year: 2006
Title: Life-history strategies predict fish invasions and extirpations in the Colorado River Basin
Reference Type: Journal Article
Journal: Ecological Monographs
Volume: 76
Pages: 25-40

Value of reference: Much  of this  paper is theoretical and provides a basis for assessing risk to
native species from both biotic and abiotic drivers. It thereby illustrates the use of historical data
to predict future risk of extinction.  Of more direct use to EMAP is its summary of percent
changes in native and nonnative fish species in the lower Colorado River basin before and after
1980. This information constitutes Appendix D, which is on-line in the Ecological Archives
M076-002-A4 (http://esapubs.org/archive/mono/M076/002/appendix-D.htm).

The authors  use historical data from the SONFISHES data base (developed by W.L. Minckley
and others),  which  contains over 38,000 occurrence records for freshwater fishes from over 150
years of research.  Records include incidence, identity, and collection information for the
complete holdings of major regional museum collections, numerous smaller holdings, and
records from peer-reviewed and gray literature, and they are geo-referenced to within 1 km of
their collection site  in a GIS. This historical data base would likely be of value for other EMAP
applications  and data analyses (e.g., use of a different threshold year to define "historical"; or
excluding records from Mexico) and is available on-line at
http://desertfishes.Org//na/gis/index.html.

In this application, the historical period was defined as 1843-1980, and the modern period was
1981 to 1999.  The 1980 threshold corresponds with a major shift in sampling goals (see Pagan
et al. 2005)

Results relevant to EMAP: Table D1 of the on-line Appendix D lists 23 native fish species and
47 nonnative species of the lower Colorado River basin (including both U.S. and Mexican
reaches between Glen Canyon Dam and the Gulf of California) and the distributional changes
for each between the pre- and post-1980 threshold. Percent declines are given for native
species, while the spread (km/yr) is given for each nonnative species.  Declines range from
100% to -14% (negative declines being an increase); nonnative species spread ranges from 0.0
to 54.6 km/yr.

Geographic location: Colorado River basin, Colorado,  Utah, Arizona, EPA Region 8, EPA
Region 9, xeric, mountains, eco21, eco20, eco22, eco23, eco81, eco14

Keywords: fish, SONFISHES data base, nonnative species, prediction, extinction risk,  historical
occurrence data, species distribution, ranges, endangered fishes, functional niche, dams, river
regulation

Notes: For a related application, see Fagan et al. 2005 in this bibliography (different 2005
publication than the one listed below).

Two additional examples of the use of the SONFISHES data base to predict current risk of
extinction and need for management and listing at different spatial scales  can be found in:

Fagan, W.L., C. Aumann, C.M. Kennedy, and P.J. Unmack. 2005. Rarity, fragmentation, and
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the scale dependence of extinction risk in desert fishes. Ecology 86(1):34-41.

Olden, J.K., and N.L. Poff. 2005.  Long-term trends of native and non-native fish faunas in the
American Southwest.  Animal Biodiversity and Conservation 28(1):75-89.
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Author: Osmundson, D. B.; Burnham, K. P.
Year: 1998
Title: Status and trends of the endangered Colorado squawfish in the upper Colorado River
Reference Type: Journal Article
Journal: Transactions of the American Fisheries Society
Volume: 127
Issue: 6
Pages: 957-970

Value of reference: The article examines the factors that contribute to the episodic recruitment
of young pikeminnow in the upper Colorado river. Though the link to historic abundance of
pikeminnow  is not presented in a quantitative fashion, the paper does relate what would have
been historic hydrography and phab quality to successful pikeminnow reproduction.

Results relevant to EMAP: Colorado pikeminnow were once very abundant in the upper
Colorado River basin including the Green, Yampa, White, and  Uncompahgre tributaries. Today
pikeminnow  numbers are much  reduced. Adult survival  rates are fairly high (up to .87),
indicating that adult survival is not a major constraint on population increase, but successful
pikeminnow  reproduction is rare.

The results of this study show that high recruitment years follow extra high spring flows;
historically, before dams and irrigation diversions, high spring flows were a common, almost
yearly, phenomenon. High flows assist pikeminnow reproduction by flushing fine sediments from
cobble bars and reducing the  numbers of nonnative minnows.

Geographic location: Region 8, upper Colorado River basin, Colorado River, Green River,
Yampa River, Utah, Colorado, eco20, xeric

Keywords: Colorado squawfish, Colorado pikeminnow, upper Colorado River, endangered
species, extirpation,  recruitment, runoff, phab, fish,  nonnative fish, hydrologic variability,
sediment

Abstract: Status of the Colorado River population of the endangered Colorado squawfish
Ptychocheilus lucius (recently renamed the Colorado pikeminnow) was investigated by 1)
estimating adult numbers,  2) evaluating frequency of reproduction and recruitment, 3) identifying
trends via changes in size structure over time, and 4) examining historical accounts for clues to
former abundance. Adults and subadults were systematically captured from 278 km of river
during 1991-1994. Larvae and age 0 fish were systematically sampled in two reaches during
1986-1994. Estimated number of adults in the upper 98 km averaged 253 individuals; estimated
annual adult survival rate was 0.86. In the lower 181 km, estimates of subadults and adults
combined averaged 344 individuals. A sizable pulse of subadults 300-400 mm long found in the
lower reach in 1991 were from three year classes, 1985-1987. By 1992, these were distributed
throughout the river. Although catch rates of larger adults did not increase significantly in the
upper reach  during 1991-1994, catch rates offish less than 550 mm long increased fivefold.
Size frequency analysis of lower reach fish indicated the 1985-1987 cohorts were the largest
produced since before 1977, and no similarly strong year classes were produced subsequently.
Estimated years of origin of these recruiting fish coincided with years of higher than average
catch rates of larvae and age  0 fish in the upper reach and catch rates in subsequent years
were comparatively low. Very few individuals less than 450 mm long were found in the upper
reach during the past 15 years, suggesting that recruitment there is from colonization from the
lower reach. In contrast, significant numbers offish less than 400 mm in total length occurred in
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the upper reach during the mid-1970's. Abundance appears much lower than suggested in
historical accounts. Low adult numbers and sporadic pulses of recruitment may make this
population vulnerable to extirpation. Though adult survival rate is probably fairly constant,
recruitment is highly variable and may represent the most important demographic factor to
population persistence.
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Author: Patton, Timothy M.; Rahel, Frank J.; Hubert, Wayne A.
Year: 1997
Title: Using Historical Data to Assess Changes in Wyoming's Fish Fauna
Reference Type: Journal Article
Journal: Conservation Biology
Volume: 12
Issue: 5
Pages:  1120-1128

Value of reference: The article details methodology for comparing historic (1960) fish survey
data with recent (1990) fish survey data; even data with different sampling protocols.
Comparisons of recent and historic data for the purpose of assessing species trends are
frequently problematic due to differences in sampling designs, methodologies, and efficiencies.
Nevertheless, historic data can be a valuable source of information for trend assessments.

The article defines historic as "fish survey data from 1960". This would not be considered "pre-
settlement"; however, few data exist on fish populations in this  region that date back beyond the
early part of the 20th century.  A comparison of these different data sets is a place to start and a
helpful benchmark to monitor change.

Results relevant to EMAP: Findings include a general decline in species at the smaller spatial
scale (reach, stream, etc), with less evidence of decline overall at the drainage scale. "Although
this suggested that a drainage scale examination may be too coarse to detect changes in
distribution, changes at this scale may be the most important: species extirpated at such a large
scale represent the most serious declines and loss of evolutionary potential, and species
expanding into new drainages likely represent artificial introductions."

Among the declining native species, two habitat guilds are apparent. Species in the first guild
(flathead chubs, plains minnows, silvery minnows, river carpsuckers, and channel catfish) are
adapted to turbid rivers with silt and sand substrates historically common on the Great Plains.
Reservoirs and diversion dams have stabilized flows and  reduced  silt loads and likely have led
to declines among species in this guild.  Species in the second guild  (common shiners, finescale
dace, horneyhead chubs, lake chubs, and mountain suckers) tend to occupy small to medium-
sized streams with cool, clear water, and many require gravel substrates for spawning.  Land
management and irrigation practices have increased turbidity and siltation in many of these
streams.

Geographic location: Wyoming, Missouri River Drainage, eco17, eco18, eco25,  eco43,  plains,
mountains, xeric, EPA region 8

Keywords: historic fish survey, phab, fish,  land management, irrigation practices,  turbidity,
reservoirs, diversion dams, plains, mountains, declining species

Abstract: If conservation efforts are to be implemented before  a species becomes imperiled,
population declines must be identified before that species becomes extremely rare. Historic
survey data are more useful than recent data for detecting such declines. We compared 1960's
and 1990's fish survey data from 10 drainages in Wyoming (USA)  in  an effort to identify
declining species,  but these comparisons were problematic because of differences in sampling
designs, methodologies,  and efficiencies. We restricted our comparisons to locations common
to both surveys and to presence and absence data; we adjusted our data to account for the
more efficient sampling protocol of the 1990's  survey; and we examined data at four nested
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spatial scales: site, stream, sub-drainage, and drainage, based on data not adjusted for gear
bias, 12 our to 31 (39%) native species were collected in fewer locations during the 1990's
survey even though we used more efficient sampling gear. Based on data adjusted for gear
bias, the same 12 plus 4 additional native species (52%) showed declines. Fewer species
appeared to have changing distributions at the drainage scale than at the smaller scales, but
extirpations at the drainage scale represent the most serious declines. Despite the problems of
comparing historic and recent surveys, we were able to make minimum estimates of species
declines. Adjustment of data to account for gear bias allowed us to identify declines beyond a
minimum estimate.
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Author: Pearson, W.D.; Kramer, R.H.; Franklin, D.R.
Year: 1968
Title: Macroinvertebrates in the Green River below Flaming Gorge Dam, 1964-65 and 1967
Reference Type: Journal Article
Journal: Proceedings of the Utah Academy of Science, Arts, and Letters
Volume: 45
Pages: 148-167

Value of reference: This article reports conditions primarily in the mid-1900s, but since early
macroinvertebrate data are generally scarce, it represents some of the only baseline data
available for the basin. The Flaming Gorge Dam was closed in 1962.  The authors summarize
pre-1962 macroinvertebrate presence data from 5 sources (Table 3).  These  data are then
compared  to data collected after closure of the dam.

The article serves 2 functions: 1) it provides baseline macroinvertebrate data from the early
1960s for the Green River above Ouray, Utah; and 2) it allows a comparison  of pre- and post-
impoundment invertebrate communities for assessing the effects of the dam and changes in
water physical attributes on the invertebrate community. Most invertebrate data are reported by
genus or family. Table 3 reports presence data by taxon for pre- and post-impoundment
periods. Table 4 gives abundance data (mean number per square meter) on  rubble-gravel
substrates at the first collection site downstream from the dam, 1965 and 1967 (post-
impoundment).

Results relevant to EMAP: Seasonal variations in flow were reduced after closure of the dam;
summer, fall, and winter flows increased, and  spring flow decreased (data in Table 1). Winter
temperatures increased, while summer temperatures decreased, compared to pre-
impoundment years. Mean monthly pre-impoundment temperatures ranged from 0.5 to 21.0
degrees C at Greendale, while mean monthly  post-impoundment temperatures ranged from 2.0
to 12.5 degrees C.  At greater distances downstream from the dam, the river  physical condition
seemed to transition back to its pre-impoundment state.

Nine invertebrate forms reported from the area prior to the dam were not collected in the post-
impoundment study, while 10 groups not previously reported in the area were collected after
impoundment.  The latter group were not considered recent invaders,  but were assumed to
have been missed in previous sampling efforts.  The community at the sampling location directly
below the dam had a much lower species richness compared to pre-dam conditions. Species
composition was not noticeably altered below  the confluence of the Yampa River. Invertebrate
communities between the dam and the confluence of Vermillion Creek were altered, likely as a
response to lower summer water temperatures, which caused the near disappearance of one
species of Baetis from the first 9.5  km below the dam.

Mean number of individuals on rubble-gravel substrates ranged from 11 (several species) to
40,124 (Baetis sp.) per m2. Other abundance  data are given in Table 4.

Geographic location: Utah, Colorado Green  River basin, EPA region 8, eco20, xeric

Keywords: macroinvertebrates, phab, dams,  historical  data, baseline  data

Notes: For additional information about invertebrates above Flaming Gorge, see Binns, N.A.
1965. Effects of rotenone  treatment on the fauna of the Green River, WY.  Unpublished
Master's Thesis, Oregon State University, Corvallis, OR. 258 p.
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Author: Peters, E. J.; Schainost, S.
Year: 2005
Title: Historical changes in fish distribution and abundance in the Platte River in Nebraska
Reference Type: Book Section
Editor: Rinne, J. N.; Hughes, R. M.; Calamusso, B.
Book Title: Historical changes in large river fish assemblages of the Americas.
City: Bethesda, Maryland
Publisher: American Fisheries Society
Pages: 239-245

Value of reference: The historical changes stated in the title are inferred rather than clearly
stated due to a general lack of historical information and a presentation that only indirectly
addresses the historical changes in fish assemblages. Though the mainstem of the Platte is
mainly in Nebraska,  there is some discussion in the article of the forks of the Platte,  North and
South. The chapter was included even though the mainstem of the Platte is outside the EMAP
sampling region because there are few sources available about the fish assemblages of the
plains.

Results relevant to EMAP: Little is known of the fishes from the Platte River basin prior to the
time when diversions and damming had already altered flows. The earliest published fish
collections are those of Meek (1895) and Evermann and Cox (1896). Collection records in
Nebraska prior to 1945 documented 47 species from the Platte River of which one, the common
carp, was an introduced species. Today Platte River fish species number 100, most of them
introduced. In Table 1, p. 243, the authors show changes in ranks of percent frequency of
occurrence for fish species reported in collections from the Platte River before 1945 (pre-  large
scale fish introductions) and after 1985.

Two groups of fish species are declining for opposite reasons. Headwater or tributary species
that favor clear warm water and clean gravel substrate (10 species listed), such as brook
stickleback, central stoneroller, and johnny darter, are declining due to a shortage of habitat,
and are listed as species of concern in the plains states. The other declining group contains
species typical of large, turbid  rivers, such  as shovelnose sturgeon, flathead chub, and sauger.
Goldeye and sauger, for example, have been extirpated from the North and South Platte and
occur in small numbers in the lower Platte in Nebraska.  The lower Platte River retains the wide,
shifting sand bar habitats and  high turbidity characteristic of the pre-settlement river.

North Platte River - Reservoirs and diversion canals were  completed in the mid-1940's. The
river has been reduced from multiple channels to a single channel and sections are dewatered.
South Platte River -  River flow in Colorado is augmented from interbasin transfers of Colorado
River water. However, virtually all flow is diverted in Colorado and returned to the river as
sewage treatment water return flows downstream of the metropolitan areas along the front
range.

Geographic location: EPA Region 7, EPA Region 8, Nebraska, Colorado, Wyoming, Platte
River, North Platte River, South Platte River, eco25, eco21, high plains, southern Rockies

Keywords: fish, dams, water diversion, agriculture, pollution, nonnative species

Abstract: From its headwaters in the Rocky Mountains, the Platte River drains 230,362 km2 in
Colorado, Wyoming, and Nebraska. The Platte River is formed by the confluence of the North
Platte and South Platte near the city of North Platte, Nebraska, and receives additional flow
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from the Loup and Elkhorn rivers that drain the Sand Hills region of Nebraska. Water diversions
for mining and irrigation began in the 1840's in Colorado and Wyoming, and irrigation diversions
in Nebraska began in the 1850's. Construction of dams for control of river flows commenced on
the North Platte River in Wyoming in 1904. Additional dams and diversions in the North Platte,
South Platte, and Platte rivers have extensively modified natural flow patterns and caused
interruption of flows. Pollution from mining, industrial, municipal, and agricultural sources, and
introductions of 24 nonnative species have also taken their toll. Fishes of the basin were little
studied before changes in land use, pollution, and introduction of exotic species began. The
current fish fauna totals approximately 100 species from 20 families. Native species richness
declines westward, but some species find refugia in western headwaters streams. Declines in
26 native species have led to their being listed as species of concern by one or more basin
states.
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Author: Pilsbry, H.A.; Ferriss, J.H.
Year: 1911
Title: Mullusca of the southwestern states, V:  the Grand Canyon and northern Arizona
Reference Type: Journal Article
Journal: Proceedings of the Academy of Natural Sciences of Philadelphia
Volume: 63
Pages: 174-199

Value of reference: The article provides baseline information on the snails of the Grand
Canyon and the northern Arizona plateau, an area that had previously not been explored for
snails. It lists the species collected, organized by family, listing all collection stations and the
exact collection spot. Much of the document is taxonomic description of the species, but the
presence and distribution in the region would be the most valuable information for EMAP.

Collections were done by searching through sediment layers to find species that would likely be
seeking refuge from the arid climate. Since snails are not active most of the year, they might be
easier to miss in  an EMAP sampling visit.  Therefore this information is valuable as the most
complete listing of species found historically in the area.

Results relevant to EMAP: The annotated list of species found in the area begins on page 178
and is organized by species and locality where collected.  This baseline information can be used
for reconstruction of species richness or presence for this area.  It is difficult to discern from
descriptions  whether all collections sites are on a stream, but most seem to be associated with
a spring or seep, if not a tributary stream; many locations were high  in the canyon.

Geographic location: Arizona, Colorado River basin, EPA region 9, eco22, xeric

Keywords: macroinvertebrates,  snails, baseline data, historical data
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Author: Platts, W. S.; Gebhardt, K. A.; Jackson, W. L.
Year of Conference: 1985
Title: The effects of large storm events on basin-range riparian stream habitats
Reference Type: Conference Proceedings
Editor: Johnson, R. R.; Zieball, C. D.; Patton, D. R.; Ffolliott, P. F.; Hamre, R. H.
Conference Name: Riparian ecosystems and their management: Reconciling conflicting uses
Conference Location: Tucson, Arizona
Publisher: U.S. Forest Service General Technical Report RM-120
Pages: 30-34

Value of reference: The value of this reference is to document that woody debris was an
important component of stream channel structure even in aspen-dominated Northern Great
Basin riparian ecosystems.

Results relevant to EMAP: In the Jarbidge Mountains of northeastern Nevada, where there is
a concentration of EMAP sites, riparian zones historically were shaded by large aspen.
Decomposing aspen logs in streams provide evidence of this. However, due to heavy grazing
pressure (cattle eating young tree sprouts), the last generation of aspen has not been replaced.
The disappearance of wood in the channel allows floods to scour the alluvium and cause
accelerated erosion and incision of the stream channel.

Cutthroat trout were able to survive the floods in these streams. The authors conclude that
drought conditions may have more effect on cutthroat numbers than high water events. Where
streamside vegetation was abundant, flood impacts to fish populations were minimal.

Geographic location: Nevada, mountains, xeric, ecoSO, Great Basin, basin and range,
Jarbidge Mountains, EPA Region 9

Keywords:  fish, cutthroat trout, grazing, sediments, erosion, woody debris,  riparian vegetation,
phab
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Author: Propst, D.L.
Year: 1999
Title: Threatened and endangered fishes of New Mexico.
Reference Type: Report
City: Santa Fe, NM
Institution: New Mexico Department of Game and Fish
Report Number: Tech. Rpt. No. 1

Value of reference: Although New Mexico is not in the EMAP-West region, several major
drainages flow out of the state into Arizona and Colorado, and the corresponding fish species
occur in those neighboring states. The report focuses on the distribution of fish in New Mexico,
but makes numerous statements about species' total historical ranges and relative abundance
in portions of the basins outside of New Mexico.  In the second part of the report, 23 species are
profiled separately (although not all species were historically distributed in AZ or CO).  For each
profile, sections on listing status, distribution and current population status  include known
historical and current distribution throughout the species' ranges in all states and basins where
they occurred, as well as factors contributing to their decline.  This report would be valuable for
reconstructing historic ranges and comparing them with the current, reduced ranges.

The report includes an extensive bibliography, representing syntheses of numerous publications
for each species' profile. "Historical" does not necessarily equate to pre-settlement, but it
encompasses all of the known records of a species in its former distribution.

Results relevant to EMAP: Typical results are illustrated here, using Gila  chub  (the first
species  profile in the  report) as an example:

The Gila chub is a species of special concern in Arizona.  Historically,  it occurred in suitable and
rather specialized habitat throughout much of the Gila River drainage in southwestern New
Mexico and central and southeastern Arizona. Its preference historically was for cienega
habitats. In Arizona,  Gila chub persist in small headwater streams (many are springs or
cienegas) tributary to the San Pedro, Santa Clara, San Francisco, Gila, Verde, and Agua Fria
rivers. Although Gila chub still occur in a moderate number of localities within its historic range
in Arizona, its numbers  are low at many locations, and populations are considered unstable.

A variety of factors probably contributed to the decline of Gila chub, but loss of cienega habitats
by dewatering and channelization were probably the most detrimental.  Introduction of nonnative
piscivores also contributed to elimination of the chub from portions of its historic  range.

Geographic location: Arizona, Colorado, eco23,  eco26, eco20, eco21, eco22, EPA region 9,
EPA region 8, Arkansas River basin, Colorado River basin, Gila River basin, xeric, mountains,
plains

Keywords: fish, altered water flow regime, channelization, nonnative species, historical ranges
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Author: Propst, D.L; Carlson, C.A.
Year: 1986
Title: The distribution and status of warmwater fishes in the Platte River drainage, Colorado
Reference Type: Journal Article
Journal: The Southwestern Naturalist
Volume: 31
Issue: 2
Pages: 149-167

Value of reference: Fish data of the late 1970s are compared with historical data to assess
changes in community composition in the South Platte  drainage. There have been few
publications over time reporting on the warmwater ichthyofauna of the South Platte River and
none for the North Platte, and most previous studies have been geographically restricted.
Therefore, this article is of value for gathering and reporting compositional changes in the
historical community. Historical data included all  past reports of a species, dating as  far back as
1891.

Annotated species accounts from present-day sampling are given in various levels of detail,
including citations for studies in which a species was previously sampled, where the species is
currently found or not found, presence/absence or relative abundance compared to historical
reports,  whether the species is exotic, and reasons for  decline.

The species assemblage is grouped into 4 categories:  rare, common, uncommon, and
nonnative.  Each category is discussed, and reasons for decline or low numbers are given.
Species in each category are addressed singly or as a  group, and generalizations are made
regarding their status as compared to historical abundance.

Results relevant to EMAP: The native species composition of the  Platte River in Colorado has
never been diverse.  Thirty-one fish species were historically present in the South Platte The
lake  chub, hornyhead chub, and blacknose shiner have been extirpated.  Another three species
were not collected in the present study, and it is not apparent whether they are still present.

Current  distribution and abundance is a factor of historical distribution and status,  and habitat
alterations due to human impacts.  Extensive alterations in the basin are  due to water
diversions, dams, impoundments, ground water pumping, channelization, and  pollution.

Table 2  lists all fish species grouped by abundance category, excluding three reported
historically but not collected and three known to be extirpated, and including nine non-native
species.  Rare species (8 of 31  historical species) have been restricted historically and more
recently have experienced habitat reduction as a  result of human impacts.  Uncommon species
(6 of 31  historical species) were considerably more widespread  and common historically than
they  are presently; common species (11  of 31 historical species) have maintained their
populations largely because of wide environmental tolerances, but they have been affected by
habitat degradation or pollution in stressed reaches.

Geographic location: Colorado, South Platte River basin, eco25, EPA region 8, plains

Keywords: fish, water diversion, dams, ground water pumping,  channelization, pollution,
warmwater fishes
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Abstract: In a 2.5 year (1978-1980) study of the lotic warmwater fish communities of the Platte
River Basin, Colorado, 25 native and 9 non-native species were collected.  Three natives
(Nocomis biguttatus, Couesius plumbeus, and Notropis heterolepis) have been extirpated.
Salmo clarki stomins was not collected, nor were the provisional natives, Stizostedion vitreum
and Carpoides cyprinus.  Eleven native species were rare in the basin.  The rarity of each was
strongly correlated with their limited historic distributions,  rather special  habitat requirements,
and intolerance of environmental stresses. Six native species were historically more common
and widespread, but habitat deterioration associated with European settlement has caused their
decline. The remaining native species (8) were common  and widely distributed. The common
carp (Cyprinus carpio) was the only common non-native fish. Lack of suitable habitat is
believed responsible for the rarity of other non-native species.

Notes: See also Nesler et al. 1997 (in this bibliography) as a companion article which provides
maps of plotted collection locations from "historical" surveys in the South Platte drainage.
Nesler, T.P., R. VanBuren, J.A. Stafford, and M.  Jones. 1997. Inventory and status of South
Platte River native fishes  in Colorado.  Colorado Division  of Wildlife, Aquatic Wildlife Section,
Fort Collins, CO.
                                           161

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Author: Rahel, F.J.; Thel, L.A.
Year: 2004
Title: Flathead Chub (Platygobio gracilis): a technical conservation assessment
Reference Type: Electronic Source
Producer: USDA Forest Service, Rocky Mountain Region.
Access Year: 2006
Access Date: June 14

Value of reference: This is primarily a management document, but it contains information on
what is known of the historical distribution of the flathead chub.  It also reports on current listing
and population status, habitat requirements, and threats to the species.  Although a significant
portion of the chub's range is in Montana, this report does not address it because it is outside of
the Forest Service region 2 management jurisdiction.

Results relevant to EMAP: In Colorado, flathead chubs historically occurred in the Arkansas
River up to Salida, but specimens have not been collected recently upstream of a large
diversion on the Arkansas River near Florence, Colorado.  It is considered a species of special
concern in Colorado and as threatened in Kansas where it historically occurred in the large
rivers draining from Colorado. With only one exception, it has not been sampled in Kansas
since 1994.  In South Dakota, flathead chubs were common and characterized as the dominant
minnow species in the western tributary rivers and larger streams of the Missouri River. To the
north and east of the Missouri River, flathead chubs occurred only in the lower portions of larger
tributaries. Currently flathead chubs continue to be considered common in the rivers and larger
streams of western South Dakota.  Recent surveys found flathead chubs to be common in the
Moreau River, the Cheyenne River, and the Belle Fourche River. In Wyoming, flathead chubs
were historically present in the North Platte and Little Missouri rivers  but are now known to
occur only in very low numbers  in the North  Platte River and are likely much reduced in
numbers in the Little Missouri River. Currently, they are widely distributed in the rivers of the
northeast part of the state, including the Big Horn, Tongue,  Powder, Little Powder, Belle
Fourche, and Cheyenne river systems.

Loss of turbid conditions, adequate in-channel flow, and habitat connectivity associated with
water impoundment are major threats to this species.  The species remains widespread
throughout much of its historical range,  but it is unknown if remaining populations are stable or if
the species is continuing to decline. Competition with nonnative species also has a negative
effect on populations of the flathead chub.

Geographic location: South Dakota, Wyoming, Colorado,  Missouri River basin, Arkansas
River basin,  EPA Region 8, eco43, eco42, eco25, eco26, plains, Missouri River basin,  Arkansas
River basin,  Platte River basin

Keywords: fish, altered water flow regime, dams, nonnative species

URL: http://www.fs.fed.us/r2/projects/scp/assessments/flatheadchub.pdf
                                          162

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Author: Rees, D.E.; Carr, R.J.; Miller, W.J.
Year: 2005
Title: Plains minnow (Hybognathus placitus): a technical conservation assessment
Reference Type: Electronic Source
Producer: USDA Forest Service, Rocky Mountain Region
Access Year: 2006
Access Date: June 12

Value of reference: This report expands on Cross and Moss 1987 (also in this bibliography)
with  respect to a single species in the plains. The authors cite Cross and Moss frequently, but
their summary covers the broader region outside of Kansas, including states in EPA Region 8.
They note the absence of distributional data for plains minnow prior to settlement, and state that
it impossible to know the entire historical distribution of the species. However, trends since the
mid-20th century and human impacts in the region are discussed.  The status and decline of
plains minnow is summarized for the major basins draining the east side of the Rocky
Mountains.

Results relevant to EMAP: The plains minnow was historically distributed in suitable habitat
throughout the Arkansas River, Platte River, Kansas River, and Missouri River basins, including
the following states in the EMAP-West region: North and South Dakota, Montana, Wyoming,
and Colorado (they have been introduced into Utah). It maintains stable populations locally,  but
its range has been  restricted in South Dakota and Montana, while both its range and abundance
are in decline  in Montana, Wyoming, North Dakota, and Colorado.

It was once the most common fish of the Arkansas River system, but its abundance and
distribution have decreased substantially, and it now constitutes less  than 1% of the overall fish
population in that basin; it has possibly been extirpated from some drainages in Colorado.
Changes in the Missouri  River have led to a less severe decline of the species there, and
tributary populations in eastern Wyoming are currently stable.  The potential for further declines
in distribution  and abundance is high across the species' range.

An altered flow regime, groundwater pumping, and impoundments have reduced water quality
and altered the natural flood regime necessary to induce spawning. A loss of shifting channels
and gravel bars has resulted from water diversions, impoundments, land uses that alter flow
regimes, and groundwater mining, leading to degraded habitat and loss of natural disturbances
to which the plains  minnow is adapted.  The larger impact of these pressures has been the
fragmentation of metapopulations.  Competition with and predation by nonnative fish species is
an important potential impact, but it is not fully understood at present.

Geographic location: North Dakota, South Dakota, Montana, Wyoming, Colorado, EPA
Region 8, eco43, eco25,  eco26, eco42, plains, Missouri River basin, Arkansas River basin,
Platte River basin

Keywords: fish, nonnative species,  habitat degradation, habitat fragmentation, altered water
flow  regime, groundwater pumping, water diversion

URL: http://www.fs.fed.us/r2/proiects/scp/assessments/plainsminnow.pdf
                                         163

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Author: Rinne, J. N.
Year of Conference: 2004
Title: Forest and fishes: Effects of flows and foreigners on southwestern native fishes
Reference Type: Conference Proceedings
Editor: Scrimgeour, G. J.; Eisler, G.; McCulloch, B.; Silins, U.; Monita, M.
Conference Name: Forest Land-Fish Conference II: Ecosystem stewardship through
collaboration
Conference Location: Edmonton, Alberta
Pages:  119-124

Value of reference: The author reviews the historic and present day occurrence of the fishes of
Arizona as well as the chronology of alterations to the natural hydrology of the state.

Results relevant to EMAP: 75% of the riverine habitats in Arizona have been either lost or
altered between 1911 and 1970. Diversions on the Gila River constructed in 1928 dried the Gila
River to its confluence with the Salt River. Other major tributaries to the Gila, such as the San
Pedro,  San Simon and Santa Cruz Rivers have been dried due to groundwater pumping.

Six species of fish are now on the endangered or threatened list in Arizona. The Gila topminnow
was very common during early settlement times. Now it persists in fewer than a dozen isolated
springs in southern Arizona. The razorback sucker was once so abundant that it was pitchforked
from canals and used as fertilizer. The Colorado pikeminnow (formerly squawfish) and bonytail
chub persist today only as a result of restoration programs.

The paper includes tables that illustrate how flood flows favor native fishes and drought periods
(e.g., 1994-2003) result in increases in nonnative  species.

Geographic location: eco81, eco79, eco22, eco23, eco14, Arizona, Region 9, xeric,
mountains, Gila River, San Pedro River, Salt River

Keywords: fish, Colorado pikeminnow (squawfish), dams, habitat degradation, nonnative
species, hydrologic variability, water diversions

Abstract: Habitat alteration in physical (stream channel characteristics), chemical (nutrients,
temperature), or biological (introduced species) form can  have dramatic effects on native
southwestern USA fishes. Southwestern flow regimes, their alterations, and introduction of alien
species have had a dramatic, negative impact on  native southwestern fishes. The cumulative
and interactive impacts may result in various  responses by native fish assemblages. Managers
should  not expect the same result when one or more factors are in operation that may affect an
aquatic ecosystem in the southwestern USA. Ultimately, consideration of temporal-spatial
influences, natural factors, interactions of factors,  and sound monitoring or research activities
will determine which factors most influence southwestern fish assemblages in respective
situations.

Notes: A related paper that includes a description of the historic hydrologic variability (i.e., rivers
turbid during spring runoff, clear during base flow, and intermittent in lower reaches during
drought), and a map of the hydrology of Arizona showing 20th Century changes:
Rinne, J. N., and J. A. Stefferud. 1999. Single versus multiple species management: Native
fishes in Arizona. Forest Ecology and Management 114:357-365.
                                          164

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Author: Rinne, J. N.; Simms, J. R.; Blasius, H.
Year: 2005
Title: Changes in hydrology and fish fauna in the Gila River, Arizona-New Mexico epitaph for a
native fish fauna?
Reference Type: Book Section
Editor: Rinne, J. N.; Hughes, R. M.; Calamusso, B.
Book Title: Historical changes in large river fish assemblages of the Americas.
City: Bethesda, Maryland
Publisher: American Fisheries Society
Pages: 127-137

Value of reference: This book chapter summarizes earlier articles and gathers results from the
gray literature about the Gila River and its tributaries concerning historic hydrology and native
fish species and their present day status.

Results relevant to EMAP: Historically, the Gila River between Florence and Phoenix, Arizona
was about a kilometer wide, scattered with beaver ponds, shaded by cottonwood gallery forest,
and "teeming with fishes." The Gila was described as a large, essentially permanent stream of
clear to sea green water with a well-defined channel flanked by numerous cottonwoods and a
dense growth of willows and cane. In 1848 Emory described the river as "wide and rich" and
alive with geese and ducks. By  1920 this same area was described by Ross (1923) as "desolate
wastes of sand and silt."

Twenty fish species were native to the Gila River basin (listed in Table 1 on p. 130). Four of
these species (Monkey Spring chub, Santa Cruz pupfish, Colorado pikeminnow, razorback
sucker) have been extirpated, 8 species are endangered (includes pikeminnow and razorback
sucker), two species are  threatened, and two species are state listed species of concern. The
pikeminnow and razorback sucker once ran in spawning schools up the Gila and Salt  rivers.
Razorback suckers were once removed from canals in the Phoenix valley with pitchforks
because they were so numerous they blocked the water flow. The last pikeminnow was taken in
the Gila basin in 1950. The razorback sucker has been reintroduced, but is not self sustaining.
Gila trout persist naturally in a few headwater streams in New Mexico. Nonnative fish  (40
species) dominate the Gila River today, particularly in the lower reaches where there are no
native fish present.

Geographic location: Arizona, Gila River, EPA Region 9, eco23, eco79, eco81, xeric

Keywords: dams, water  diversion, nonnative species, historical, hydrology, fish, xeric

Abstract: The Gila River originates in southwestern New Mexico and  courses its way  for over
700 km to the west before emptying into the main-stem Colorado River near Yuma, Arizona.
Historically, this river was a major watercourse across the Sonora Desert of Arizona. At present,
main-stem dams and numerous diversions have markedly altered the historic hydrology of the
river. Seventeen native species once occupied the main stem of this large southwest desert
river. More than twice that number (40) of nonnative fish species have been introduced into the
waters of the Gila over the past century. Currently, less than half of the native fauna is present
in the main stem and then primarily in the upper three reaches of the river. The majority of the
species (70%) are federally listed  as threatened, endangered, or sensitive. The combination of
hydrological alteration and accompanying introductions of nonnative, principally sport  fishes has
basically extirpated the native fauna in all  but the uppermost reaches of the Gila River main
stem.
                                         165

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Author: Robison, R.S.
Year: 1957
Title: The Yakima River-historical and present Indian fishery
Reference Type: Report
City: Seattle, WA
Institution: Washington Department of Fisheries
Pages: 13

Value of reference: Report provides rough estimates of pre-settlement salmonid abundance
and catches by Native Americans in the Yakima River basin. The earliest estimates are for the
period prior to 1848, which is significant because the Yakima Valley was developed very early
for agriculture, and this represents probably the best estimate of a true pre-settlement salmon
population. These estimates provide baseline data for numbers of salmonids that the basin was
capable of supporting before major impacts destroyed or prevented access to spawning habitat.

Results relevant to EMAP: The dominant native fish species of the Yakima River were Chinook
salmon, sockeye salmon, coho salmon, steelhead trout, cutthroat trout, dolly varden trout,
whitefish, squawfish and suckers. Salmon ran up to Keechellus Lake in the headwaters of the
Yakima River in the Cascade Mountains.  Based  on the estimated number of pre-settlement
Indian families and average consumption per family, the author estimates that the total Yakima
River catch was 160,000 salmon annually prior to settlement. He further states that the actual
run to the river and its tributaries could easily have been 3 times the catch or 480-500 thousand
salmon.

From 1847 to 1875, harvest by Native Americans apparently dropped from  160,000 to 20,000
salmon annually. From 1875-1906, runs were still declining, but greater fishing effort kept the
catches at 20,000 annually. The catch dropped to a low of 1000 by 1930

Streambed assessments in the 1950s led  to the conclusion that available habitat in the basin
could support at least 500,000 spawning salmon  each year.  The construction of irrigation
diversion dams, beginning in 1850, created migration barriers, and diversion ditches led salmon
into orchards where they died.  Other early impacts were log drives, mining, and over-fishing.
(Note:  The report does not address impacts occurring downstream in the Columbia River,
which could have impacted runs if their timing coincided.)

Geographic location: Yakima River basin, Washington, EPA region 10, mountains, xeric,
ecolO

Keywords: fish, water diversion, dams, mining, logging, fishing
                                         166

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Author: Roemhild, G.
Year: 1982
Title: The Trichoptera of Montana and ecological notes
Reference Type: Journal Article
Journal: Northwest Science
Volume: 56
Issue:  1
Pages: 8-13

Value of reference: The diversity of aquatic macroinvertebrates is poorly represented in early
literature. Although this synthesis report of Trichoptera distribution in Montana was made more
than a  century after settlement, it can be used to gauge the level of knowledge of the diversity of
this order prior to 1980. Following five years of surveys, the author collected 78 species
reported from Montana for the first time (54% increase in recorded diversity). The author also
identifies portions of the region where more work was needed to adequately describe the
Trichoptera fauna, including the southwestern, southeastern, and northeastern portions of the
state. While this is a recent work, it helps to characterize some of the challenges of using
anecdotal historical macroinvertebrate data for reconstructing reference conditions. References
such as this help to highlight the limits of what can be gleaned regarding macroinvertebrate
diversity and geographic distributions from historic literature prior to systematic collection
activities.

Results relevant to EMAP: Between 1970 and  1980, the number of recorded species of
Trichoptera from Montana increased from 100 (Newell 1970) to 222 (122% increase in recorded
species diversity), resulting from a series of systematic surveys. This reference provides useful
baseline data for Trichoptera distribution in Montana up to that date, since the notes concerning
ecological preferences and distribution are drawn from a number of previous publications. The
author collected 204 of 222 species (92%) known to exist in Montana during the late 1970s and
1980, including 78 species that had not previously been reported.  During the same general
timeframe, others collected specimens of many of the remaining 18 species known to exist in
the state, but not collected by the author. Geographic distribution,  altitudinal distribution, habitat
affinity, water temperature preference, and relative abundance information are provided that
may be helpful for reconstructing potential historical distributions for each species.

Geographic location: Regions, RegionIO, Plains, Mountains, Montana, North Dakota, Idaho,
Oregon, Eco15, Eco16, Eco17, Eco18, Eco41, Eco42, Eco43

Keywords: macroinvertebrates; Trichoptera; historical data

Abstract: The known Montana Trichoptera is comprised of 14 families, 69 genera, and 222
species. Seventy-eight species are reported from Montana for the first  time. One hundred sixty-
seven species (77 % of the total) are known to occur on both sides of the continental divide, 22
species (10 %) occur on the east side only, and 29 species (13 %) occur only west of the divide.

Notes: Newell, R. L. 1970. Checklist of some aquatic insects from Montana. Proc. Mont. Acad.
Sci. 30:45-56.
                                          167

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Author: Rucks, M.J.
Year: 1984
Title: Composition and trend of riparian vegetation on five perennial streams in southeastern
Arizona
Reference Type: Book Section
Editor: Warner, R.E.; Hendrix, K.M.
Book Title: California Riparian Systems: Ecology, Conservation, and Productive Management.
City: Berkeley, California
Publisher: University of California Press
Pages: 97-107

Value of reference: Though the sample size is small, the more highly disturbed streams are
compared to a reference stream where grazing had been excluded since 1973. There is no
historical data used in the study, and there is an assumption that the broadleaf community was
once more prevalent along Arizona streams. It is also unclear whether the streams/rivers are
similar in size and discharge. They were selected because they all occur on BLM lands. The
value of this article is in the observation that riparian vegetation on Arizona streams that is
subject to  prolonged disturbance evolves away from a broadleaf community toward a so-called
riparian scrub community.

Results relevant to EMAP: The reference stream where grazing had been excluded was the
only one of the five streams to have a good representation of broadleaf tree seedlings (Fremont
cottonwood, Arizona sycamore, Arizona walnut, velvet ash) in the 1-3 inch size class. Other
sample sites may have had mature broadleaf species represented, but the seedling size class in
each case was absent or heavily browsed by cattle.

The author recorded the % of broadleaf trees in the seedling size class and the % of seedlings
browsed by cattle. For example, at Bonita Creek, 1.5% of willows were in the seedling size-
class, and 67% of these were browsed.

The author concludes by saying that three of the five streams show a trend toward replacement
of the broadleaf riparian community by riparian scrub (such as saltcedar, burro brush, and
mesquite).

Geographic location: Arizona, xeric, EPA Region 9, eco79, eco23, Aravaipa  Creek, Gila River,
San Francisco River

Keywords: riparian vegetation, phab, grazing

Abstract:  Composition and trend of 78 km (49 mi) of riparian vegetation on five watercourses
was determined. Aravaipa Creek has been excluded from cattle since 1973 and was the only
study area with a dominant broadleaf riparian community and a trend towards  maintaining this
community.
                                         168

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Author: Rumble, M.M.; Sieg, C.H.; Uresk, D.W.; Javersak, J.
Year: 1998
Title: Native woodlands and birds of South Dakota: past and present
Reference Type: Report
City: Fort Collins, CO
Institution: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station
Pages: 11
Report Number: Research Paper No. 8

Value of reference: The authors use historical and present bird community and General Land
Office Surveys,  historical photos, and early journal excerpts to reconstruct the general character
of pre-settlement riparian areas along the Missouri River and its tributaries in South Dakota.
The intent was to test the hypothesis that woodlands were expanding and the bird community
was changing as a result, a process which had been hypothesized for the Platte River in
eastern Colorado (Knopf 1986). This paper does not attempt to determine change in the
amount of woodlands between pre-settlement and the present; it simply reported an historical
condition based on several pieces of evidence. It includes a section describing woodlands
along the Missouri River and larger tributary streams in pre-settlement times.

Results relevant to EMAP: Extensive native woodlands occurred in the valleys of the Missouri
River and its tributaries in central and western South Dakota in the 1870s and 1880s.  Canyons
were filled with deciduous trees, including cottonwood, green ash, willow, oak, and wild plum. In
many places the under story was very thick. Many large pieces of driftwood were left by
torrents and floods that scoured the floodplain and exposed roots.  Early 20th century
photographs of mature trees indicate that trees were established well before settlement.

Geographic location: South Dakota, Missouri River basin, eco43, EPA region 8, plains

Keywords: phab, historical data, GLO notes, historical photographs

Notes: Knopf, F.L. 1986. Changing landscapes and the cosmopolitism of the eastern Colorado
avifauna. Wildlife Society Bulletin 14:132-142.
                                         169

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Author: Samson, Fred B.; Knopf, Fritz L; Ostlie, Wayne R.
Year: 1998
Title: Status and Trends of the Nation's Biological Resources: Regional Trends of Biological
Resources-Grasslands
Reference Type: Electronic Source
Producer: Northern Prairie Wildlife Research Center Online
Access Year: 2005
Access Date: July 2005
Last Update Date: January 21, 2000

Value of reference: This chapter highlights the status and trends of the main bodies of North
American grasslands; the tall-grass prairie, the mixed-grass prairie, and the short-grass prairie.
It features the animals and plants dependent on native grassland and attempt to provide insight
into the relationship between remaining native grassland and biological resources by reviewing
available, current information and by describing threats.

Great Plains stream ecology is closely connected to the land use practices now common to the
region.  This source outlines the changes in grassland habitats and how in turn these changes
affect streams.  Impoundments and irrigation practices have altered the sediment content and
stream flow.  This in turn has contributed to changes in fish populations.  Decades of intensive
agricultural development and modified flow regimes are held responsible for declines in the
fishes endemic to the small streams and turbid rivers of the Great Plains (Cross and Moss
1987-in this bibliography).

Results relevant to EMAP: A good overview of prairie ecosystems in North America. This is a
comprehensive  source that documents changes to the prairie ecosystem since settlement and
the development of agriculture. The article describes the flora, fauna, soil characteristics, and
overall ecology of the various regions (short grass to tall grass prairies) of the Great Plains.

Chapters include; prairie past and present (prairie grasses, land resources and management,
prairie insects and animals), prairie integrity and legacies, resource and research needs, and
literature cited.

This reference is a good all-around source that catalogs the ecosystem structure, the biotic
community, and the changes that have occurred since agricultural development. This source
also contains an extensive bibliography.

Geographic location: Great Plains, plains, EPA region 6, EPA region 7, EPA region 8, Kansas,
Nebraska, Oklahoma, Texas, New Mexico, Colorado, North Dakota, South Dakota, Wyoming,
Montana, eco25, High Plains, eco26, Southwestern Tablelands. eco27, Central Great Plains,
eco44, Nebraska Sand Hills, eco43, Northwestern Great Plains

Keywords: phab, fish, native species, turbidity, fish communities, altered water flow regime,
grasslands, prairie insects, prairie animals, historic condition, plains rivers, impoundments,
agriculture

URL: http://www.npwrc.usgs.gov/resource/2000/grlands/grlands.htm
                                          170

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Author: Say, T.
Year: 1825
Title: Descriptions of new hemipterous insects collected in the expedition to the Rocky
Mountains, performed by order of Mr. Calhoun, Secretary of War, under command of major
Long
Reference Type: Journal Article
Journal: Journal of the Academy of Natural Sciences Philadelphia
Volume: 4
Issue: 2
Pages: 307-345

Value of reference: This  reference provides an example of the qualitative characteristics of the
earliest macroinvertebrate collection literature in western North America. Although Say was a
zoologist, and the descriptions of collected Hemiptera specimens are provided in  detail,
important collection information is lacking.  Dates and specific collection locations are  usually
not provided, although they may be recorded on museum specimens.  Distribution information is
very generalized, such as "inhabits North America", "inhabits Missouri", "inhabits Arkansas near
Rocky Mountains".

Results relevant to EMAP: The earliest macroinvertebrate collection data in western North
America provides some anecdotal information  regarding species encountered during
expeditions. The collection was made in a very non-systematic fashion; information on collection
date was not recorded (although this information may be available in the museum records) , and
location information is very coarse. In this case, only a few of the specimens collected are
aquatic. The relevance of this reference to EMAP is that it establishes coarse  baseline data and
elucidates the limitations of what can and cannot be reconstructed of aquatic macroinvertebrate
communities prior to European settlement.

Geographic location: EPA Region?, EPA Regions, Mountains, Plains, Rocky Mountains

Keywords: macroinvertebrates;  Hemiptera; baseline conditions
                                         171

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Author: Schalk, R.F.
Year: 1986
Title: Estimating salmon and steelhead usage in the Columbia basin before 1850: the
anthropological perspective.
Reference Type: Journal Article
Journal: Northwest Environmental Journal
Volume: 2
Issue: 2
Pages: 1-30

Value of reference: Evidence of salmonid declines were reported as early as 1882; thus many
"historical" population data do not reflect an approximate pre-settlement condition.  In this
article, salmon runs are estimated for a very early time period, producing probably the best
supported approximations of pre-settlement salmon runs for the Columbia basin (also see
Meengs and Lackey 2005-in this  bibliography-who used similar approaches for calculating
historical coastal runs).  Estimates are based on native American fish catches, consumption,
population data, and catch efficiency. The catch estimate adjusts earlier estimates by Hewes
(1973) and Craig and Hacker (1940)-both cited below-by accounting for variation in
consumption rates among tribes, inclusion of a migration calorie loss factor, and an inedible
waste loss factor.  Catches are converted into total run size by dividing by an catch efficiency
rate.

This reference illustrates the use of anthropological data for determining the former importance
of salmon and steelhead to the Indian tribes of the Columbia  basin, estimating the magnitude of
the aboriginal salmon and steelhead catch in the early 19th century, and translating to total fish.
It provides a baseline historical datum for gauging the magnitude of total losses and for broad
application in managing and sustaining current populations.

Results relevant to EMAP: The annual salmonid catch by Indians in the early 19th century was
estimated to be 41,754,800 pounds, which is almost twice as large as previous estimates, but
which is considered a minimal  catch,  capable of sustaining human populations, even in years of
low salmon production.

This translates into a total run size range estimate of 9 to 12.6 million fish per year, which
compares well with the low end of the estimate by the Northwest Power Planning Council
(NWPPC 1986, in this bibliography), yet is consistent with the conclusion that it is a minimum
estimate, not including fish catches for uses other than human consumption, e.g., dog food, fuel.

Geographic location: Oregon, Washington,  Idaho, EPA region 10, eco3,  eco4, eco11, ecolO,
eco9, 3co15, eco12, eco16, mountains, xeric, Columbia River basin

Keywords: fish, salmon, steelhead, pre-settlement population estimate, anthropological data,
native American fish catch

Notes: Craig, J.A. and R.L. Hacker. 1940. The history and development of the fisheries of the
Columbia River. Bulletin of the Bureau of Fisheries 49:133-216.

Hewes, G.W. 1973. Indian fisheries productivity in pre-contact times in the Pacific salmon area.
Northwest Anthropological Research Notes 7(2):133-155.
                                          172

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Author: Scheurer, Julie A.; Bestgen, Kevin R.; Fausch, Kurt D.
Year: 2003
Title: Resolving Taxonomy and Historic Distribution for Conservation of Rare Great Plains
Fishes: Hybognathus (Teleostei: Cyprinidae) in Eastern Colorado Basins
Reference Type: Journal Article
Journal: Copeia
Volume: 3
Issue: 1
Pages: 1-12

Value of reference: This article highlights the difficulty in establishing historic fish distribution
and numbers. "Few early collections exist and most of these were made after habitats were
already altered, some native species were extirpated and nonnative species ere introduced."
For example, fish collections are known from only 12 locations before 1900 in the Great Plains
portion of eastern Colorado (Fausch and Bestgen,  1997), yet diversion of water for irrigation
was well  developed by the 1860's. As a result, the historic distributions of fishes described only
in early reports are not fully known. A  second main problem is that identification of some taxa is
difficult, resulting in inaccurate field surveys.

The goal of the research was to develop a technique to distinguish H. hankinsoni from H.
placitus in western Great Plains watersheds where they are sympatric.  The model is then used
to accurately identify all available museum specimens of Hybognathis, this allowed for
clarification of historic distributions of H. hankinsoni and H. placitus.

This study helps document the importance of museum collections and the correct species
identification for the determination historic conditions and establish changes in distribution and
habitat over time.

Results relevant to EMAP: The different morphologies of H. hankinsoni and H. placitus are
consistent with adaptations for their preferred habitats. H. hankinsoni prefers small, clear
streams with low velocity. In contrast, H. placitus prefer medium to large plains streams with
more turbid environments.

Correct identification of these two species helped establish what the historic stream
environment was like in the area of collection.  In addition, better identification of museum
specimens provides a more accurate conclusion about historic distributions and range of
species within the stream system.  Based on the finding of this study, the current distribution  for
these two species is believed to be contracting from the western edge of their former range.
Article also contains an extensive bibliography.

Geographic location: Colorado, eco25, Great Plains, plains,  EPA region  8, Platte River,
Republican River, Smoky Hill River

Keywords: native fish,  historical distribution, fish, early collections, taxonomy

Abstract: Similar morphology and confused historical taxonomy of Hybognathus hankinsoni
(brassy minnow) and Hybognathus placitus (plains minnow) have made determination of their
historic distributions and conservation status unclear in eastern Colorado basins. We developed
logistic regression models from morphometric measurements to predict species identity of
Hybognathus collections from Colorado and adjacent counties (n = 1154 specimens in  134 lots).
A model based on orbit diameter, standard  length, and eye position correctly predicted  98% of
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the specimens examined and 100% of the museum lots. Hybognathus hankinsoni have larger
eyes centered on a horizontal line through the tip of the snout, whereas H. placitus have smaller
eyes centered above the tip of the snout. The two species were historically sympatric in the
Platte, Republican, and Smoky Hill River basins, whereas H. placitus was allopatric in the
Arkansas River basin. The taxonomic characters defined here will allow accurate identification
of future collections to determine the status of these native fishes.

URL: http://www.bioone.org/bioone/?reguest=get-abstract&issn=0045-
8511&volume=003&issue=1&page=0001
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Author: Scott, L. B.; Marquiss, S. K.
Year: 1984
Title: An historical overview of the Sacramento River
Reference Type: Book Section
Editor: Warner, R. E.; Hendrix, K. M.
Book Title: California Riparian Systems: Energy, Conservation, and Productive Management.
City: Berkeley, California
Publisher: University of California Press
Pages: 51-67

Value of reference: This article contains a useful description of the early (1850's) effects of
hydraulic mining.

This paper summarizes an analysis of two aspects of the history of the Sacramento River: the
fluvial process; and man's development of the floodplain over the last 130 years. The analysis
was made to trace the origins of problems - seepage, loss of riparian vegetation, and limited
public access - occurring in the riparian zone, and to establish a perspective from which to study
these problems. Significant historical aspects of these problems must be considered in a
comprehensive study of the river.

Results relevant to EMAP: Thirty five years of hydraulic mining created an estimated
equivalent of 100 years of sediment delivered from the Sacramento Basin into San Francisco
Bay-three times the average delivery  under natural conditions.  It is estimated that the
elevations of the Sacramento, Feather, Yuba, Bear, and American Rivers rose as much as 6 m
(20 ft). The higher streambeds led to a series of floods in the 1860's and 70's  and finally an act
of the legislature banning hydraulic mining. The floods literally buried farms under many feet of
mud and debris.

Graph on p. 55 of changes in bed elevation of the Sacramento and Yuba rivers from 1850 to
1950.

Geographic location: California, Central Valley, Sacramento River, eco7, eco6, EPA Region 9,
xeric, mountains

Keywords: riparian vegetation, phab, xeric,  mountains, sediment, water diversions, dams,
mining, agriculture
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Author: Sedell, J. R.; Froggatt, J.L.
Year: 1984
Title: Importance of streamside forests to large rivers: The isolation of the Willamette River,
Oregon, U.S.A., from its floodplain by snagging and streamside forest removal
Reference Type: Journal Article
Journal: Verh. Internat. Verein. Limnol.
Volume: 22
Pages: 1828-1834

Value of reference: The authors provide a well documented example of changes in
morphological characteristics, general physical habitat, and riparian conditions within the 10th
largest river in the continental U.S., dramatically altered by agricultural activities and snagging
over the last 150 years. The links to locations of original source material for reconstructing river
channel characteristics and riparian  forests at the time of settlement (1850's) may be of use for
tracking down historical material for  other watersheds and regions.

Human disturbance types and associated changes in stream and riparian conditions are clearly
documented, with quantitative estimates made that can be compared against current conditions.

Although the authors discuss the implications of the habitat changes in terms of possible
generalized changes in aquatic macroinvertebrate and fish community characteristics, the
primary value of the paper lies in its  detailed documentation of changes  in physical habitat and
riparian conditions.

Results relevant to EMAP: Channel complexity and riparian gallery forest composition
changed dramatically since settlement began in earnest in the 1850's (see Fig. 2). Between
1870 and 1950, more than 65,000 snags and streamside trees were removed from 114 km of
river to aid navigation. Channel simplification began when channels and sloughs were closed off
with wing dams by 1872.

By 1983, surface water volume, coarse and fine organic inputs had decreased to 25 percent of
their historic levels in the upper portion of the watershed. Gallery forests, which had extended
1.5 - 3.5 km on either side of the river, were reduced to narrow, discontinuous ribbon,
immediately adjacent to the main channels and primary tributaries.

Conversion to agriculture was the primary factor responsible for loss of  riparian woodlands.
Secondary and tertiary channels, which functioned as 3rd- or 4th-order streams in 1854 had all
but disappeared by 1946, when the  river was confined primarily to a single channel. The authors
speculate that the functional feeding groups of invertebrate and fish communities would have
been more like lower order streams  in these lost channels.  Most of the channel changes
occurred prior to the construction of dams for flood control.

Geographic location: EPA  RegionIO; Oregon; Willamette Valley; Mountains;
Willamette River Basin, eco3, mountains

Keywords: phab;  fish; macroinvertebrates; snag removal; agriculture; dams; habitat loss;
change detection
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Author: Sedell, J.R.; Luchessa, K.J.
Year of Conference: 1981
Title: Using the historical record as an aid to salmonid habitat enhancement
Reference Type: Conference Proceedings
Editor: Armantrout, N.B.
Conference Name: Symposium on Acquisition and Utilization of Aquatic Habitat Inventory
Information
Conference Location: Portland, Oregon
Publisher: American Fisheries Society, Bethesda, Maryland (1982)
Pages: 210-223

Value of reference: This paper discusses historical conditions in numerous basins of
Washington and Oregon and is therefore more of a general observation of prevailing conditions
in multiple basins, as compared to the historical condition. It presents an historical perspective
that the authors suggest can help provide a needed rationale for rehabilitation of wild salmonid
stocks, including creation of new habitat,  restoring damaged habitat, and protecting good
habitat.

The basic  premise is that historical information can assist in our understanding of how far many
river systems deviate from a pre-settlement condition (i.e., optimum habitat requirements for
salmonids), specifically with respect to habitat complexity created  by large wood and debris
dams.

Results relevant to EMAP: Historically, streams in lowlands of the Willamette Valley and Puget
Sound consisted of a network of sloughs, islands, beaver ponds, and drift dams with no main
channel. Using historical documentation, the authors found that debris dams in many basins of
western Oregon and Washington were once very common, often damming 20% or more of a
stream's length. In  many lowlands, a high degree of interaction of the stream with its flood plain
was common.  For example, over a quarter of the area of the Skagit River lowlands were beaver
marsh, sloughs, and wet grass meadows.

Large volumes of wood  influenced both low and high gradient channels; many  rivers were
completely blocked by drift jams for 100-1500 m  in the mid 1800s. The historical record shows
that even in big rivers, large wood contributed to  in-channel structure. Salmon were once
abundant under these conditions. For example, using published material for the Siuslaw River,
estimated  runs in the 1890s would have been about 27,500 Chinook and 218,750 coho salmon.
However, the habitat is no longer present to support those run sizes, even though they are
being set as goals.

Channelization and clearing of large wood and debris to facilitate river transport began in the
mid 1800s and continued into the 20th century to  create easier access to spawning areas.
Management alternatives to debris clearing in high-gradient reaches is discussed and supported
by the historical record and current literature findings.

Geographic location: Washington, Oregon, EPA region 10, ecol, eco2, eco3, numerous
basins, mountains

Keywords: phab, large wood, debris dams, anadromous fish, logging, channelization, habitat
degradation
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Abstract: Historically, wild anadromous fish stocks evolved with stream systems that were
obstructed by fallen trees, beaver dams, and vegetation growing in and beside the channels.
River systems as large as 7th order had large numbers of fallen trees in their channels and
often were obstructed by drift jams that were up to 1500 m long. The main river channels
contained abundant gravels and fine sediments. Habitat complexity was great because of scour
around boulders and fallen trees, and the presence of numerous and extensive stable side
channels and sloughs. These pristine streams interacted intensively with their flood plains.
Historical records document over 100 years of "diligent" stream and river cleanup. Primary
activities included removal of boulders, large woody debris, and other obstructions from
channels. We believe that historical documentation of the ways unmanaged streams interacted
with the streamside forest allows us to know how far we have deviated from the optimum habitat
requirements for various salmonids. Until we understand the structure of undisturbed habitats
that wild stocks  develop within, and the sequence of changes that have occurred in those
habitats, our present protection  and enhancement efforts will lack both a rational context and
effective direction.
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Author: Sedell, J. R.; Reeves, G. H.; Hauer, F. R.; Stanford, J. A.; Hawkins, C. P.
Year: 1990
Title: Role of refugia in recovery from disturbances: Modern fragmented and disconnected river
systems
Reference Type: Journal Article
Journal: Environmental Management
Volume: 14
Pages: 711-724

Value of reference: The reference does not describe reference condition per se (except for a
short description of changes on the Willamette River (see Results below), but it does give a
useful table of attributes of refugia at various spatial scales. These attributes are the same as
those natural features composing a reference stream reach, segment, or watershed.  The
authors see this classification system as being applicable to both the conservation of existing
minimally disturbed systems as well as the recognition of isolated natural features within
disturbed systems.

Results relevant to EMAP: The authors compile a list of stream refugia attributes at various
spatial scales (channel unit, reach, segment, watershed).

Between 1854 and 1967 the Willamette River, Oregon, became increasingly isolated from its
floodplain as a result of channelization and agricultural modification of riparian forests. In 1854,
the riparian forest was in contact with >250 km of river edge on oxbow lakes and cutoff sloughs.
By 1967 the  length of river edge had been systematically decreased to 64 km, a reduction of
74%. Much of the change in riparian forest interaction was completed by 1910 owing to snag
removal and river navigation improvements (revetments).

The implication of these changes are that the ability of alluvial reaches to provide refugia, retain
sediments and organic materials and to determine the quantity of organic inputs has been
greatly reduced.

Geographic location: Willamette River, Oregon, EPA Region 10, eco3, mountains

Keywords: phab, riparian vegetation, river ecosystems, refugia, groundwater, reference
condition, human disturbance

Abstract: Habitats or environmental factors that convey spatial and temporal resistance to biotic
communities that have been impacted by biophysical disturbances may be called refugia. Most
refugia in rivers are characterized by extensive coupling of the main  channel with adjacent
streamside forests, floodplain features, and groundwater. These habitats operate at different
spatial scales, from localized particles to channel units such as pools and riffles, to reaches and
longer sections, and at the basin level. A spatial  hierarchy of different physical components of a
drainage network is proposed to provide a context for different refugia. Examples of refugia
operating at different spatial scales,  such as pools, large woody debris, floodplains, below
dams, and catchment basins are discussed. We hope that the geomorphic context proposed for
examining refugia habitats will assist in the conservation of pristine areas and attributes of river
systems and also allow a better understanding of rehabilitation needs in rivers that have been
extensively altered.
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Author: Shaffer, H. Bradley; Fisher, Robert N.; Davidson, Carlos
Year: 1998
Title: The role of natural history collections in documenting  species declines.
Reference Type: Journal Article
Journal: Trends in Ecology and Evolution
Volume: 13
Issue:  1
Pages: 27-30

Value of reference: This article summarizes ways in which museum collections and related
data repositories have been used as a source of historical information in documenting changes
in the presence or absence of species.  Although museum data often represent an imperfect
match to current sampling programs, they can still provide the critical information necessary to
identify declines, and should comprise one of the standard databases in conservation  biology.

Results relevant to EMAP: Museum and other historic locality archives offer a rich source of
material for the analysis of species declines; however, assessments of changes in abundance
over time are very problematic, and should be interpreted with great caution.

Judiciously using museum collections as a source of historical data, changes in the
presence/absence of individual species and communities can successfully be evaluated across
a wide range of plant and animal taxa in habitats ranging from single-species temperate habitats
to complex tropical systems.

This article is a helpful tool and includes a good bibliography.

Geographic location: Article not specific to one geographic area, however  the article does list
several studies from California (e.g., Fisher, R.N and Shaffer, H.B., 1996,  The decline of
amphibians in California's great central valley, Conservation Biology 10, 1387-1397, in this
bibliography) as examples of studies using museum specimens or other archival records as
historical data to document species decline.

Keywords: historic condition, phab, museum collections, fish, amphibians, species decline

Abstract: Efforts to document the decline of extant populations require  a historical record of
previous occurrences. Natural history museums contain such information for most regions of the
world, at least at a coarse spatial  scale. Museum collections have been successfully used to
analyze declines in a wide range of plants and animals,  at spatial scales ranging from  single
localities to large biotic and political regions. Natural history museum collections, when properly
analyzed, can be an invaluable tool in documenting changes in biodiversity during the past
century.
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Author: Sheldon, A.L.
Year: 1979
Title: Stonefly (Plecoptera) records from the basin ranges of Nevada and Utah
Reference Type: Journal Article
Journal: The Great Basin Naturalist
Volume: 39
Issue: 3
Pages: 289-292

Value of reference: Since macroinvertebrate information is limited, this record of the
distribution of Plecoptera in streams on Nevada's mountain ranges in the 1979 may have value
to EMAP if combined with other papers such as Stewart et al. (1974) on distribution and past
dispersal of southwestern  U.S. Plecoptera.

Distributional records are given for 40 stonefly species on 15 isolated mountain ranges mostly in
Nevada (1 included in Utah).
Stewart, K.W., R.W. Baumann, and B.P. Stark. 1974. The distribution and past dispersal of
southwestern United States Plecoptera. Transactions of the American Entomological Society
99:507-546.

Results relevant to EMAP: This list of Plecoptera species sampled in 1979 may be compared
with species sampled 25 yrs later for EMAP.

Stonefly (Plecoptera) species are listed by family with a record of mountain range and county
where collected.

Geographic location: EPA Region 9, central basin and range, Nevada, Utah, eco13, xeric

Keywords: macroinvertebrates, animal taxonomy and  geography, entomology, stonefly,
Plecoptera
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Author: Shepard, B.B.; Sanborn, B.; Ulmer, L; Lee, D.C.
Year: 1997
Title: Status and risk of extinction for westslope cutthroat trout in the upper Missouri River
basin, Montana
Reference Type: Journal Article
Journal: North American Journal of Fisheries Management
Volume: 17
Pages: 1158-1172

Value of reference: Although this article focuses on calculating probabilities and risk of
extinction of westslope cutthroat trout in multiple basins in Montana, it does contain some
historical information about distribution  in the upper Missouri River, including Figure 1: map
showing sub-basins in Montana believed to have supported westslope cutthroat trout at the time
of European settlement (Behnke 1992,  this bibliography).  The authors examined evidence from
the historical record to estimate the length  of streams and rivers once occupied by the trout.
144 sub-basins on federal lands were assessed and rated according to the estimated extinction
risk for westslope cutthroat as: very high, high, and moderate.

Results relevant to EMAP: There is some disagreement in the historical record as to the
historical range of the trout.  For this analyses, the authors assumed that it originally occupied
the entire Missouri River drainage down to, and including, the Musselshell River and the upper
Milk River basin,  but not the upper Sun River basin

The abundance and distribution of westslope cutthroat trout have declined substantially
throughout their historical range.  Trout that are at least 90% genetically pure (based on
allozyme electrophoresis) now occupy less than 5% of the original 93,000 km of stream habitat
they historically occupied in the upper Missouri River basin in Montana. Remaining populations
are restricted to isolated headwater habitats,  many of which are impacted. Factors suggested
as contributing to decline were grazing, mining, fishing, genetic introgression, and competition
with nonnative species.

Each current population of the trout occupied relatively small habitat fragments in headwaters
(<35 km of continuous stream length), and each was isolated either physically or biologically.
Most (71%) of the 144 populations assessed had a very high predicted risk of extinction; 19%
had a high risk, and 10% had a moderate risk.  The conclusion was that westslope cutthroat
trout populations inhabiting federal lands within the upper Missouri  basin are at serious risk of
extinction under current conditions.

Geographic location: Montana, upper Missouri River basin, eco43, eco42, eco17, EPA region
8, mountains

Keywords: fish, westslope cutthroat trout,  habitat fragmentation, nonnative species, grazing,
mining, fishing, genetic introgression

Abstract: Westslope cutthroat trout Oncorhynchus clarki lewisi now occupy less than 5% of the
subspecies'  historical range within the upper Missouri River drainage in Montana. We assessed
the risk of extinction for 144 known populations inhabiting streams within federally managed
lands in the upper Missouri River basin using a Bayesian viability assessment procedure that
estimates probability of persistence  based  on subjective evaluation of population survival and
reproductive rates as influenced by environmental conditions. We first customized this model
using estimates of demographic parameters from the literature and field data. Each population
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was classified into one of three risk groups based on their Bayesian probability of persistence
over 100 years (p100). Most (71%) of the 144 populations had a very high predicted risk of
extinction (p100 < 50%), 19% exhibited a high risk (50% < p100 <80%), and 10% had a
moderate risk (80 < p100 < 95%). Higher average predictions of plop were consistently
associated with populations inhabiting watersheds with lower levels of management activities.
Analysis of variance and a matrix of information divergence measures indicated that livestock
grazing, mineral development, angling, and the presence of nonnative fish had the greatest
association with both estimated population parameters and persistence probabilities. Of 26
major sub-basins within the upper Missouri River drainage, 16 support at least one known
westslope cutthroat trout population on federal lands, and 14 of these 16 support at least one
population with an estimated p100 value of 0.5 or greater. Results of our analysis have led to
action by citizens of Montana,  prompting state and federal managers to develop  a conservation
and restoration program for this subspecies in the upper Missouri River basin.
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Author: Silkensen, G.
Year: 1993
Title: South Platte River observations: Historical clues to the evolution of a river's ecology
Reference Type: Book Section
Editor: Woodring, R. C.
Book Title:  Defining ecological and sociological integrity for the South Platte River basin.
City: Fort Collins, Colorado
Publisher: Colorado Water Resources Research Institute
Pages: 41-53
Series Title: Information Series No. 72

Value of reference: The author compiles multiple views of the pre-settlement South Platte
River written by the  first explorers to the region.

Results relevant to EMAP: In the mid-19th Century large stretches of the South Platte River
valley in northeastern Colorado were treeless, and described by phrases such as "a miserable
country" of "alkali soils" and "unvaried sterility". The earliest observations of the South Platte
reveal a river which  could be a raging torrent one year, and a dry sand bed the next.  P. 42.

Today the hydrography is evened out by diversion of water from the upper Colorado  River; an
average total of nearly 400,000 acre-feet/year of water is imported into the South Platte basin.
This is approximately 30% of the South Platte's annual native runoff. Nearly 95% of this water
originates in the Colorado River basin. The North Platte basin supplies most of the balance. P.
51

Short descriptions of observations made during expeditions in 1820 and 1842, addressing
variability in amount of riparian vegetation on tributaries and relative to the Rocky Mountains, as
well as two descriptions of the confluence of the North and South Platte (pages 43 and 44), are
included.

Geographic location: Colorado, EPA Region 8, xeric, eco25, eco26, South Platte River

Keywords: riparian  vegetation, phab, hydrology, runoff, agriculture

Abstract: The South Platte River begins high in the Colorado Rockies, emerging from the
foothills of the front range southwest of Denver. From here the river flows  in a general
northeasterly direction across Colorado's high plains before leaving the state and entering
Nebraska. During the 19th Century, that portion of the river which traverses the high  plains was
explored  by both Stephen H. Long and Charles C. Fremont. The river also became one of the
primary routes (the Denver Road) to the Colorado gold fields during the 1859 Pikes Peak gold
rush, and later for pioneers, settlers, and the railroads.  Eventually the river's water was stored
and used to irrigate  crops in the South Platte valley. Throughout Colorado history, the river has
been both praised and cursed. Early descriptions have ranged from "treeless"," sandy",
"barren",  to " a beautiful river in whom the thirsty finds a true friend." Many 19th Century
explorers, gold-seeking fifty-niners, pioneers, and farmers encountered the South Platte River
and described it in detail. These descriptions, albeit unintentionally, often provide clues to the
ecological nature of the South Platte River as it began to evolve during the last half of the 19th
Century.
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Author: Skinner, J. E.
Year: 1962
Title: An historical review of the fish and wildlife resources of the San Francisco Bay area
Reference Type: Report
City: Sacramento, CA
Institution: The Resources Agency of California and California Department of Fish and Game
Pages: 57-71
Report Number: Water Projects Branch Report No.1

Value of reference: The reference provides a view of the extent of the fishing effort on the
Sacramento-San Joaquin River system during the years of commercial fishing and salmon
canneries. Although the river system was considered degraded in the late 1800s, the salmon
catch data provide a good benchmark for assessing salmon losses since then.

Results relevant to EMAP: A table in Appendix C-2 and a bar graph show the salmon catch
data for the gillnet fishery on the lower Sacramento-San Joaquin River for the years 1864-1957.
The numbers do not include the portion of the catch consumed locally or that were caught
above the  city of Sacramento. The gillnet catch peaked at over 10,000,000 pounds in 1880 and
1910; and  it exceeded 1,000,000 pounds every year until 1910, after which the catch amounts
became more variable.

The Wakeman report in 1870 surveyed the fisheries of the tributaries of San Francisco Bay and
described the disturbed condition of streams due to the logging operations, saw mills, and flour
mills located on them. The inference from his description is that the coastal streams had once
been very  productive of silver salmon  (Oncorhynchus kisutch) and steelhead trout (Salmo
gairdnerii), but at the time of the 1870 survey they were already degraded.

Map IV Fold out map in  back of book.  Historical  salmon migration routes and probable
distribution.
Appendix F comprises two tables: a "List of selected freshwater fishes of the San Francisco Bay
area" and "Some initial introductions of freshwater food and game fishes now  occurring in the
San  Francisco Bay area". The majority of the introductions occurred in the late 1800's,
beginning  in 1872 with eastern brook trout (Salvelinus fontinalis). Of the anadromous fishes,
silver salmon were limited to coastal streams until 1956 when they were introduced into the
Sacramento River system.

Geographic location:  California, San Francisco Bay basin, Sacramento River, San Joaquin
River, eco6,  eco7, Central Valley, EPA Region 9, xeric

Keywords: fish, Chinook salmon, silver salmon, fishing, urban, logging, dams, nonnative
species
                                         185

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Author: Stalnaker, C.B.; Holden, P.B.
Year: 1973
Title: Changes in native fish distribution in the Green River system, Utah-Colorado
Reference Type: Journal Article
Journal: Proceedings of the Utah Academy of Science, Arts, and Letters
Volume: 50
Pages: 25-32

Value of reference: This article provides descriptive summaries of the historical distribution and
relative abundance of seven indigenous species common to the main tributaries of the upper
Colorado basin and reports fish distribution following impoundment by the Flaming Gorge dam.
It cites publications dating from the 1890s to the early 1960s (pre-impoundment), documenting
declines before closure of the dam. It then reports changes in abundance and distribution in the
mid-1960s following  closure of the dam and in 1973. It thus provides several historical points of
reference for tracking the changes in populations of these 7 species (Colorado squawfish,
roundtail chub, bonytail chub, humpback chub, humpback sucker, bluehead sucker,
flannelmouth sucker).

Results relevant to EMAP: Minckley and Deacon (1968; in this bibliography) document the
decrease in native fishes in the lower Colorado  River basin. Subsequently, the upper Colorado
River basin was the last available habitat for the large river endemic fishes.  All species were
historically reported to be common to abundant  in the upper Colorado basin except the
humpback chub. Prior to closure of the dam, declines were already being reported for some of
these species, but the roundtail chub, bonytail chub, bluehead sucker, and flannelmouth  sucker
still seemed to be doing well at least in some portions of their range.

After closure of the Flaming Gorge dam, stream physical habitat in the first 65 miles
downstream (above the mouth of the Yampa River) changed drastically.  None of the 7 native
species investigated were still reproducing, and  all species  except the flannelmouth sucker,
bluehead sucker, and roundtail chub were eliminated from that area.  Growth rates of the
bonytail chub, roundtail chub, and Colorado squawfish had decreased greatly. Introduced
rainbow and brown trout had replaced the large  native fishes in that stretch of river. The
humpback chub, Colorado squawfish, bonytail chub, and humpback sucker were considered
rare and possibly endangered at the time of publication (1973).

Geographic location: Utah, Colorado, Green River basin,  EPA region 8, xeric, eco18, eco20,
eco21

Keywords: fish, nonnative  species, dams, habitat fragmentation
                                         186

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Author: Starnes, W.C.
Year: 1995
Title: Colorado River Basin Fishes
Reference Type:  Electronic Source
Producer:  U.S. Department of Interior, National Biological Service
Access Year: 2005
Access Date: May 18

Value of reference: Web site summarizes the changes in fish species richness between the
1800s and  present, including the increase in nonnative species.  Tributaries and sections of the
river are listed along with the species richness in the 1800s and the changes in richness that
occurred throughout the 20th century, notably the introduction of numerous species, creating
higher species richness (sometimes more than double the historical levels) but lower native
species diversity (Table 2). Gives list of native fish taxa of the river basin,  including status of
jeopardized species (Table 1). Summary also discusses the use of baseline data describing
unaltered native fauna and determining, to the extent possible, the true extent of diversity of
native fish.

Results relevant  to EMAP: Historically, the lower basin (downstream of the Arizona/Utah
border)  had the greatest diversity of taxa (44), while the upper basin contained 14 species; the
number of native species has drastically declined since the 1800s in every portion of the basin,
while the number  of introduced species has increased, and in many cases, far surpassed the
native richness (Table 2).

Presently, 40 of the 49 native species are  considered either possibly or actually jeopardized or
are extinct (see Table 1 for status by species). Impacts to fish include impoundments, irrigation
diversions,  diking, channelization, pollutants, habitat destruction, grazing, dewatering, and
competition with nonnative species (at least 72 nonnative fish taxa have been introduced to the
CO River system); genetic integrity is compromised by hybridization between native and
nonnative species.

The situation complicates the use of biodiversity as an indicator of ecological integrity of the
ecosystem.

Geographic location: Colorado River basin, xeric, eco20, eco22, eco14, eco81 eco23,
Colorado, Utah, Arizona, EPA Region 8, EPA Region 9

Keywords: fish, dams, agriculture, water diversion, diking, channelization, pollutants, habitat
destruction, grazing, dewatering, nonnative species, species diversity

URL: http://biology.usgs.gov/s+t/noframe/e063.htm
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Author: Steedman, R. J.; Whillans, T. H.; Behm, A. P.; Bray, K. E.; Cullis, K. I.; Holland, M. M.;
Stoddart, S. J.; White, R. J.
Year: 1996
Title: Use of historical information for conservation and restoration of Great Lakes aquatic
habitat
Reference Type: Journal Article
Journal: Canadian Journal of Fisheries and Aquatic Sciences
Volume: 53
Issue: Suppl. 1
Pages: 415-423

Value of reference: Though the specific information applies to the Great Lakes, the conceptual
background and application of the approach to management is universal. The section "Why is it
important to consider historical information?" is among the most thorough presentations of the
utility of historical information encountered.

Results relevant to EMAP: Why is it important to consider  historical information?
(Section headings)
1. Those who ignore history are doomed to repeat the worst of it.
2. Historical information is frequently required during the specification of targets for ecosystem
restoration.
3. Historical information can be used to modify values and beliefs as they relate to habitat.
4. By its very nature, information about natural ecosystem processes needs to be interpreted in
a context that is long term and retrospective.
5. Humans are not very good at perceiving slow processes or rare events without the help of
scientists or historians.
6. In culture, religion, and science, humans have often preferred to seek out and preserve
stability in the natural world and to filter human perceptions through models grounded on
stability or steady-state dynamics.
7. Human perceptions and expectations are influenced by the highly modified and simplified
state of most contemporary landscapes.
8. The present is the history of the future.

Geographic location: Not applicable

Keywords: historic fish abundance, historical information, retrospective analysis, aquatic habitat
management

Abstract: We provide a rationale and methodological overview for historical (retrospective)
study of Great Lakes aquatic habitats and biota. Historical information has significant potential
to direct aquatic habitat management in the Great Lakes, particularly in setting restoration goals.
Although the use of historical information has been opportunistic (it is limited by the preservation
of information in specific forms) and generally of low resolution(it is generally semiquantitative at
best), the products of these analyses have been compelling (they have changed attitudes and
expectations of people) and surprising (many of the conclusions of historical analysis were not
predictable from other sources).
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Author: Suckley, G.
Year: 1860
Title: Report upon the fishes collected on the survey
Reference Type: Book Section
Editor: U.S. War Department
Book Title: Reports of Explorations and Surveys to ascertain the most practicable and
economical route for a railroad from the Mississippi  River to the Pacific Ocean, made under the
direction of the Secretary of War, in 1853-4.
City: Washington, D.C.
Publisher: Government Printing Office
Volume: 12
Pages: 307-368

Value of reference: This is an original early source that describes the massive numbers of
various species of salmon in river basins of the Pacific Northwest in the mid-19th century. It
offers first-hand descriptions and drawings of the species encountered.  Notes on abundance,
general  distribution,  and migration distances to inland rivers and streams are spread throughout
the document. It is somewhat laborious to sift through to glean pertinent information, but it is
worthwhile in  its documentation of true pre-settlement conditions. Taxonomy may be difficult to
pair with modern names, but should be possible for a fish biologist with the descriptions and
drawings included in the document. Most is descriptive information, but it provides a good
perspective, which could be very useful as a supplement to later, more quantitative summaries
in reconstructing historical conditions.

Results relevant to EMAP: A range of descriptive information can be extracted from this
document, including fish distribution, general abundance, species present, distance ascended
upriver to spawn, habits, descriptions, early Native American fishing and usage, and other
natural history anecdotes. A variety of baseline information can be extracted that may not be
reported in later documentation. The reference should be consulted for details. The information
is relevant for any historical  reconstruction of pre-settlement conditions.

Geographic location: Pacific Northwest, Oregon, Washington, Columbia River basin, Puget
Sound, EPA Region 10, ecol, eco2, eco3, eco4, eco9, ecolO, eco11, mountains, xeric

Keywords: fish, historical data, primary source, baseline information

URL: http://www.cprr.org/Museum/Pacific  RR  Surveys/
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Author: Swift, C. C.; Haglund, T. R.; Ruiz, M.; Fisher, R. N.
Year: 1993
Title: The status and distribution of the freshwater fishes of southern California
Reference Type: Journal Article
Journal: Bulletin of the Southern California Academy of Sciences
Volume: 92
Issue: 3
Pages: 101-167

Value of reference: This is one of the few references encountered that cover the fishes of
southern California. The article describes native and exotic species, their ranges, and changes
in their status (qualitative) between early settlement times and the present.

Results relevant to EMAP: In southern California 38 native freshwater fish taxa have been
extirpated or severely reduced  in number since European settlement.
Coastal areas were once well watered with an extensive stream system, springs, and marshes.
After settlement, channel modifications and lowering of the water table altered stream habitats
toward more desert-like conditions. The lowland areas are so highly modified today (e.g.,
concrete-lined channels) that they are practically uninhabitable for resident species and those
that migrate between the headwater areas and the coast. 40% of the freshwater fishes of the
Los Angeles basin  were extirpated after the second World War following the completion of a
large flood control project.
The article includes detailed distribution maps for selected species that separate records into
pre-1970 and post-1970.

Geographic location: xeric, eco6, eco8, southern California, Los Angeles basin, Region 6

Keywords: fish, distribution, habitat degradation, water diversion, channelization, dams,
nonnative species,  urban, pollution

Abstract: The fresh and low salinity waters of southern California include the Owens, Mohave,
Colorado, and coastal  drainages south of Monterey Bay to the Mexican border. The youthful
topography presents a strong dichotomy between steep rocky streams abruptly meeting
relatively flat deserts or coastal plains. Little or no intermediate, foothill habitat exists. Thirty-
eight native freshwater and 23 estuarine fishes have been recorded from this area.  In addition,
at least 100 species have been introduced, with widely varying success.  Since the late 1940's
and 1950's the native fishes of the Owens, Colorado, and Mohave drainages have been in
jeopardy or extirpated  in California. At the same time, the lowland fishes in coastal drainages
still remain in a few isolated areas, but are so reduced that special protection is needed. Only
one estuarine species, Eucyclogobius newberryi, is threatened. Some tropical estuarine species
of extreme southern California were last collected 50 to 80 years ago, and are very rare or
extirpated here. If the remaining elements of the fish fauna are to survive, immediate action is
needed to preserve the remaining habitat and to restore areas within the native range.
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Author: Tabor, V.M.
Year: 1998
Title: Endangered and threatened wildlife and plants: Final rule to list the Topeka shiner as
endangered
Reference Type: Report
City: Manhattan, KS
Institution: U.S. Department of Interior, Fish and Wildlife Service
Report Number: Federal Register: 69008-69021, 50 CRF Part 17

Value of reference: This document provides justification and background for listing the Topeka
shiner as an endangered species.  It provides a summary of the species' historical distribution in
6 states, including one-South Dakota-in the EMAP-West region. The reasons for decline of
the species are summarized in detail.

Results relevant to EMAP: The Topeka shiner was historically widespread and abundant
throughout low order tributary streams in portions of 6 states of the central prairie region.
Stream basins within the range historically occupied by Topeka shiners within the EMAP-West
region include the Big Sioux, Vermillion, and James basins in South Dakota. The species
occupied open pools in small streams with cool, clear water.  Many such streams reportedly
existed throughout the species' geographic range.

The number of known occurrences of Topeka shiner populations has been reduced by
approximately 80%, with 50% of this decline occurring within the last 25 years.  It now inhabits
less than 10% of its original geographic range. The species now primarily exists as isolated and
fragmented populations. Some recent capture sites in each of the historical basins in South
Dakota, including a few new localities, are given in the document. The species has been
extirpated in many of its historical river basins, primarily in Kansas, Missouri, Iowa,  and
Nebraska.

Intensive agricultural development and grazing,  leading to increased sedimentation and
eutrophication, has the greatest impact on the Topeka shiner.  Other impacts include the
maintenance of altered waterways, dewatering of streams, tributary impoundment, and
channelization.

Geographic location: South Dakota, EPA region 8, eco34, eco42, eco46, plains, Big Sioux
basin, Vermillion basin, James basin

Keywords: fish, endangered status, agriculture, grazing, water diversion, dams, channelization,
habitat degradation
                                         191

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Author: Taft, Oriane W.; Haig, Susan M.
Year: 2003
Title: Historical wetlands in Oregon's Willamette Valley: implications for restoration of winter
waterbird habitat
Reference Type: Journal Article
Journal: Wetlands
Volume: 23
Issue: 1
Pages: 51-64

Value of reference: This reference is a good synthesis of the pre-settlement condition and
extent of the Wllamette River, associated wetlands, oxbows, marshes, etc. and how land use
practices have extensively altered the habitat to bring it to its current condition. The study used
a combination of primary sources: expedition journals, explore/naturalist logs, missionary
writings, early settler-farmer diaries, promotionists' reports, and government documents;
Secondary sources include habitat maps, geomorphology studies, anthropological research,
and prior work on the historical Wllamette River and its floodplain to compile a view of the "pre-
settlement" habitat of the Wllamette Valley.

Results relevant to EMAP: This report investigated the historical Wllamette Valley at the time
of Euro-American settlement (ca. 1840) and attempts to determine the pre-settlement  spatial
extent of the river and wetlands in the valley.

This is a good source for establishment of pre-settlement habitat condition of the Wllamette
Valley and the river/ wetlands structure. It also helps document habitat change after agricultural
development in the valley.

Paper presents a good historical overview and changes to the Wllamette River system due to
land use practices and development; includes an extensive bibliography.

Geographic location: Oregon, Wllamette River, Wllamette Valley, Pacific Northwest, EPA
region 10, eco3

Keywords: phab, agricultural landscape, fire, historical wetlands, Kalapuya, land use,
shorebirds, pre-settlement condition, wading birds, waterfowl, wetland loss, wetland prairie

Abstract:  Before agricultural expansion in the 19th century, river valleys of North America
supported expanses of wetland habitat. In  restoring these landscapes, it is important to
understand their historical condition and biological function. Synthesizing historical primary
accounts (from explorers, travelers, settlers, and farmers) with  contemporary knowledge of
these wetland systems, we developed a profile of the wetlands and their use by non-breeding
waterbirds (e.g., waterfowl, wading birds, and shorebirds) within the Wllamette Valley, Oregon,
ca. 1840. We found evidence for three  types of wetlands used  by non-breeding waterbirds in
fall, winter, and spring: emergent wetlands, riverine wetlands, and wetland prairie. The most
extensive wetland type was wetland prairie, which functioned as fall/winter habitat for
waterbirds, but only while native Kalapuyans managed the region with fire. Since the mid-1800s,
four species, in particular, have decreased their use of the Willamette Valley: trumpeter swan
(Cygnus buccinator),  snow goose (Chen caerulescens), sandhill crane (Grus canadensis), and
long-billed curlew (Numenius americanus). Information suggests that ca. 1840, waterbirds and
their habitats were more abundant in the Wllamette Valley than today. Restoration of the
Wllamette Valley landscape is warranted,  and today's agricultural wetlands-former wetland
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prairie-hold highest restoration potential.

URL: http://www.bioone.org/bioone/?request=get-abstract&issn=0277-
5212&volume=023&issue= 1 &page=0051
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Author: Tait, C. K.; Li, J. L; Lamberti, G. A.; Pearsons, T. N.; Li, H. W.
Year: 1994
Title: Relationships between riparian cover and the community structure of high desert streams
Reference Type: Journal Article
Journal: Journal of the North American Benthological Society
Volume: 13
Issue: 1
Pages: 45-56

Value of reference: Tait et al. recreate studies done in western Oregon and Washington in the
semiarid Blue Mountains of eastern Oregon to examine how the absence of riparian canopy
affects fish and macroinvertebrate communities. Though the mention of pre-settlement
conditions is brief, the assumption is that there was once much more riparian vegetation present
along Blue Mountain streams, that agriculture and grazing have greatly reduced the amount of
vegetation and shading along those streams, and that stream communities have been
dramatically altered as a result.

Results relevant to EMAP: The hypothesis of the study is that extensive destruction of riparian
stream cover by human activity has affected the structure of Blue Mountain streams by
increasing incident radiation and altering water temperature regimes. Canopy removal in
coolwater streams often has been associated with increased salmonid abundance or biomass in
western Washington and Oregon. In this study, densities of steelhead trout (Oncorhynchus
mykiss) and sculpin (Coitus sp.) decreased significantly with greater incident radiation and
higher stream temperatures.

Sites with considerable upstream vegetative cover, maintained cooler summer temperatures
than unshaded reaches or canopied sites with limited extent of upstream riparian vegetation.
Water temperatures in open reaches at study sites often exceeded 30 degrees C, well beyond
the normal range of tolerance for salmonids and cottids. Study sites with high light levels were
dominated by the large caddisfly larvae Dicosmoecus, that feeds on thick beds of filamentous
algae. This armored caddisfly escapes predation by the warmwater fish populating the open
study reaches and sequesters a significant portion of the energy entering the stream that would
otherwise be transferred to predators.

"Warm water species offish, such as redside shiners, bridgelip suckers, northern squawfish,
and chiselmouth chub, were positively related to solar input (r = 0.82, p = 0.025), but unrelated
to temperature (r = 0.63, p = 0.13)." These warmwater species would normally not enter
tributaries  of the size  sampled in this  study. "In contrast, cool-adapted rainbow trout and Paiute
sculpin showed a strong  negative correlation (r = -0.97, p =  0.0004) with temperature and a
negative but insignificant correlation (r = -0.47, p = 0.29) with incident light."

Geographic location: xeric, mountains, eastern Oregon, John Day River basin, eco11, EPA
Region 10

Keywords: riparian vegetation, macroinvertebrates, periphyton, fish, salmonids, sculpins,
cyprinids, open canopy, stream ecology, benthic community structure, trophic interactions,
agriculture, grazing

Abstract: Many studies on cool, forested streams have shown that removal of riparian canopy
leads to higher incident radiation, blooms in algal and macroinvertebrate populations, and
concomitant increases in salmonid abundance. In warm, high-elevation desert streams,
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however, an open canopy may not increase salmonid density. Our seven study reaches on 3rd
order tributaries of the John Day River in eastern Oregon included riparian areas ranging from
denuded, heavily grazed stream banks to intact conifer forest. Average summer solar inputs to
these sites varied from 165 to 2230 megajoules/sq m, and stream temperatures were influenced
by the density and extent of canopy. Densities of steelhead trout (Oncorhynchus mykiss) and
sculpin (Coitus spp.) decreased significantly with greater incident radiation and higher stream
temperatures, although many warmwater cyprinids increased in abundance in unshaded sites.
Periphyton standing crop (g ash-free dry mass/m2) closely tracked solar inputs and was, in turn,
strongly positively correlated with biomasses of total invertebrates and of grazers. Collector,
shredder, and predator biomasses, and numerical abundances of all invertebrate groups,  did
not change with canopy density. The abundances of chironomids and baetids were unrelated to
increases in  light or algal resources, in contrast to studies in Cascades and Coast Range
streams where irruptions of these taxa occurred in canopy openings. In our streams the large-
bodied caddisfly Dicosmoecus accounted for the higher total invertebrate biomass observed in
exposed sites. These insects composed 55-96% of the total biomass in open reaches, but only
0-1.4% in the three most shaded sites. Increases in total invertebrate biomass with increasing
light levels or periphyton were not observed when Dicosmoecus were removed from the
analysis. Dicosmoecus are consumed infrequently by juvenile trout or other small fish species
common in John Day tributaries; consequently,  extensive openings in the canopy appear to
produce few advantages to upper trophic levels in these streams.
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Author: Thurow, R.F.; Lee, D.C.; Rieman, B.E.
Year: 1997
Title: Distribution and status of seven native salmonids in the interior Columbia River basin and
portions of the Klamath River and Great Basins
Reference Type: Journal Article
Journal: North American Journal of Fisheries Management
Volume: 17
Issue: 4
Pages: 1094-1110

Value of reference: This paper presents individual and composite distributions and status of
seven native salmonids:  bull trout, westslope cutthroat trout, Yellowstone cutthroat trout,
redband trout, steelhead, ocean type Chinook salmon and stream type Chinook salmon.  It
describes their potential historical range, loss of historical range, and factors that have
influenced current distribution and status.  This is a detailed summary of seven salmonids,
which are addressed similarly but in less detail in a broader summary by Lee and others 1997
(this bibliography).

Results relevant to EMAP: Results are summarized for each species and for the area as a
whole with respect to all species combined.  Tabular (Table 1) and mapped results of historical
and current distributions and predicted strong populations (Figures 2-7).

Known or predicted occurrence as a percentage of subwatersheds in the historical range: Bull
trout-6%; Yellowstone cutthroat trout-66%; westslope cutthroat trout~85%; redband trout-64%
(combined occupancy by sympatric and allopatric forms); steelhead-46%; Chinook salmon
stream type~28%; Chinook salmon ocean type~29%.

Although some of the taxa remain in most of their potential range, declines in abundance,
reductions in distribution, and fragmentation into smaller patches are apparent for all species
examined. Four of seven taxa are present in less than 50% of their historical range.  Less than
38% of subwatersheds supported two or more taxa. Less than 0.01% supported strong
populations of three  salmonids and only 3% supported two.

A literature review of the human impacts that have contributed to declines (provided in the
discussion) addresses introduction of nonnative species, habitat degradation, habitat
fragmentation and inaccessibility caused by dams, overfishing, and genetic dilution in hatchery
programs.

Geographic location: Oregon, Washington, Idaho,  EPA region 10, Columbia River basin,
Klamath River basin, ecoSO, eco9, eco11, ecolO, eco15, eco16, eco12, mountains, xeric

Keywords: fish, salmonids, habitat degradation, nonnative species, dams, fishing, hatchery
programs

Abstract: We summarized presence, absence, current status, and potential historical
distribution of seven native salmonid taxa - bull trout Salvelinus confluentus, Yellowstone
cutthroat trout Oncorhynchus clarki bouvieri, westslope cutthroat trout O. c. lewisi, redband trout
and steelhead O. mykiss gairdneri, stream type (age-1 migrant) Chinook salmon O.
tshawytscha, and ocean type (age-0 migrant) Chinook salmon  - in the interior Columbia River
basin and portions of the Klamath River and Great basins. Potential historical range was defined
as the likely distribution in the study area prior to European settlement. Data were compiled
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from existing sources and surveys completed by more than 150 biologists. Within the potential
range of potamodromous salmonids, status was unknown in 38-69% of the area, and the
distribution of anadromous salmonids was unknown in 12-15%. We developed models to
quantitatively explore relationships among fish status and distribution, the biophysical
environment,  and land management, and used the models to predict the presence of taxa in
unsampled areas. The composition,  distribution, and status of fishes within the study area is
very different than it was historically. Although several of the salmonid taxa are distributed
throughout most of their potential range, declines in abundance and distribution and
fragmentation into smaller patches are apparent for all forms. None of the salmonid taxa have
known or predicted strong populations in more than 22% of their potential ranges, with the
exception of Yellowstone cutthroat trout. Both forms of Chinook salmon are absent from more
than 70% and steelhead from more than 50% of their potential ranges, and all are approaching
extirpation in portions of their remaining ranges.  If current distributions of the taxa are useful
indicators, many aquatic systems are remnants of what were larger and more complex, diverse,
and connected systems. Because much of the ecosystem has been altered, areas supporting
strong populations or multiple species will be critical for conservation management. Moreover,
restoration of a broader matrix of productive habitats also will be necessary to allow fuller
expression of phenotypic and genotypic diversity in native salmonids.

Notes: Lee and others 1997 (this bibliography) present an extensive assessment of changes in
status of 46 fish species in the interior Columbia basin and portions of Klamath and Great
basins.

Rieman and others 1997 describe bull trout in more detail:
Rieman, B.E., D.C. Lee, and R.F. Thurow.  1997. Distribution, status, and likely future trends of
bull trout within the Columbia River and Klamath River basins.  North American Journal of
Fisheries Management 17:1111-1125.
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Author: U.S. Department of Agriculture, Forest Service.
Year: 1996
Title: Status of the interior Columbia basin: summary of scientific findings
Reference Type: Report
City: Portland, OR
Institution: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station
and U.S. Department of the Interior, Bureau of Land Management
Pages: 144
Report Number: Gen. Tech. Rpt. PNW-GTR-385

Value of reference: Though the results of the assessment are general and presented for the
entire region, there are several useful maps and tables that summarize historical and present
day distributions of key salmonids in the Columbia Basin.

Results relevant to EMAP: A Basin-wide analysis of riparian vegetation found a widespread
decline in shrublands in the riparian zones. In the overstory, cottonwood and aspen have also
declined significantly in the last 100 years.

Map of historic salmonid distribution in the Columbia Basin for six species of salmon and map of
current key salmonid presence.

Table of Historical and Occupied Range and Habitat Status for key salmonids within the Basin
assessment area.

Geographic location: Columbia Basin, ecolO, eco15, eco16, eco12, eco11, ecoSO, Oregon,
Idaho, Washington, northern Great Basin, Blue Mountains, Columbia Plateau, EPA Region 10,
mountains, xeric

Keywords: fish, ecosystem assessment, ecosystem management, ecosystem integrity, risk
analysis, salmonids, historical, riparian vegetation

Abstract: The Status of the Interior Columbia Basin  is a summary of the scientific findings from
the Interior Columbia Basin Ecosystem Management Project.  The Interior Columbia Basin
includes some 145 million  acres within the northwestern United States. Over 75 million acres of
this area are managed by the Forest Service or the Bureau of Land Management. A framework
for ecosystem management is described that assumes the broad purpose is to maintain the
integrity of ecosystems over time and space. An integrated scientific assessment links
landscape, aquatic, terrestrial, social,  and economic characterizations to describe the
biophysical and social systems. Ecosystem conditions within the  Basin have changed
substantially within the last 100 years. The status of ecosystems  is described in terms of current
conditions and trends under three broadly defined management options. The scientific
information brought forward will be used in decision making, and  may potentially amend Forest
Service and Bureau of Land Management plans within the Basin. The information highlighted
here represents an integrated view of biophysical and socioeconomic elements at a scale never
before attempted. The risks and opportunities are characterized in the broad context of the
Basin for managers and the public to  use as a foundation for discussion about future
management.

URL: http://www.fs.fed.us/pnw/pubs/summarv/gtr  385a.pdf
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Author: U.S. Department of Interior
Year: 1994
Title: Endangered and Threatened Wildlife and Plants: Designation of Critical Habitat for the
Threatened Spikedace (Meda fulgida)
Reference Type: Report
Publisher: Federal Register
Volume: 59
Issue: 45
Pages: 10906-10915

Value of reference: This is a policy document, but it briefly summarizes the historical and
present range, habitat needs, and status of the spikedace as background for designating critical
habitat.

Results relevant to EMAP: The spikedace is found in moderate to large perennial streams
where it inhabits shallow riffles with sand, gravel, and rubble substrates and moderate to swift
currents. Recurrent flooding is important to maintain habitat and the species' competitive edge
over nonnative fish species.

The spikedace was first collect in 1851 from the San Pedro river in Arizona. Historically it was
common throughout much of the Verde, Agua Fria, Salt,  San Pedro, San Francisco, and Gila
(upstream from Phoenix) River systems in both main stem and moderate gradient perennial
tributaries up to 1900 m elevation.

Due to habitat destruction and competition and predation by nonnative fish, its range and
abundance have been severely reduced, and it is now restricted to only 9% of its historic range
of 2600 km of stream.

Geographic location: Arizona, xeric, mountains, eco22, eco23, eco79, eco81, EPA region 9,
Verde River, San Pedro River, Gila River, Salt River, San Francisco River, Agua Fria

Keywords: fish, nonnative species, habitat degradation,  flooding, flow alteration
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Author: U.S. Department of Interior
Year: 1994
Title: Endangered and Threatened Wildlife and Plants; Designation of Critical Habitat for the
Threatened Loach Minnow (Tiaroga cobitis)
Reference Type: Report
Publisher: Federal Register
Volume: 59
Issue: 45
Pages: 10898-10906

Value of reference: This is a policy document, but it briefly summarizes the historical and
present range, habitat needs, and status of the loach minnow as background for designating
critical habitat.

Results relevant to EMAP: The loach minnow was first collected in 1851 from the San Pedro
River in Arizona. Historically, it was locally common throughout much of the Verde, Salt, San
Pedro, San Francisco, and Gila (upstream from Phoenix) River systems in suitable habitat in
both main  stem and tributaries up to 2200 m elevation. The historical range was estimated as
2600 km of river.

This species needs recurrent flooding to maintain a substrate free of embedded sediments and
to maintain conditions that allow it to better compete with nonnative fish species.  Due to flow
alterations, habitat destruction, and competition and predation by nonnative fish species, its
range and abundance have been severely reduced, and it is  now restricted to only 17% of its
historic range.  It is included o the State lists of threatened and endangered species in Arizona
and New Mexico.

Geographic location: Arizona, San Pedro River, Blue River, White River, Verde River, Gila
River, EPA region 9, eco22, eco23, eco79, eco81, xeric, mountains

Keywords: fish, nonnative species, habitat degradation, flooding, flow alteration
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Author: U.S. Geological Survey
Year: 2004
Title: Pre-settlement wildlife and habitat of Montana: An overview ( Pre-settlement Habitat and
Wildlife literature)
Reference Type: Electronic Source
Producer: U.S. Geological Survey; Northern Prairie Wildlife Research Center
Access Year: 2005
Access Date: June 24

Value of reference: A bibliography of books, papers, and documents pertaining to pre-
settlement habitat and wildlife of Montana and adjacent lands.  References cover the Great
Plains and include information on the following: Natural history, exploration, history of
settlement, ecology, species inventories, expedition accounts, etc.

Results relevant to EMAP: A good source to locate available pre-settlement literature and
references. This web site includes listings of many early exploration accounts and
observations, which may  be the only source for pre-settlement conditions of the Great Plains.
Stream conditions and species inventories may be limited, however some baseline information
can be gleaned from some of these references.

Geographic location: Montana, North Dakota, South Dakota, Wyoming, Colorado, Iowa, Great
plains, mountains, plains,  eco25, eco21, eco43, eco17, eco42, eco41, eco15, eco44, eco27,
EPA region 7, EPA region 8

Keywords: phab, pre-settlement, literature survey, early expeditions, species inventories, fish,
ecology, historic condition

URL: http://www.npwrc.usgs.gov/resource/literatr/presettl/books.htm
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Author: Valdez, R.A.; Muth, R.T.
Year of Conference: 2005
Title: Ecology and conservation of native fishes in the upper Colorado River basin
Reference Type: Conference Proceedings
Editor: Rinne, J.N.; Hughes,  R.M.; Calamusso, B.
Conference Name: Historical Changes in Large River Fish Assemblages of the Americas
Conference Location: Bethesda, MD
Publisher: American Fisheries Society
Volume: 45
Pages: 157-204

Value of reference: Although the focus of this chapter is on current status and ecology of the
fishes (see Table 1), the section 'Current Status and Ecology' includes summaries of the
historical status and distribution for the following species: Colorado Pikeminnow, Humpback
Chub, Bonytail, Razorback Sucker, Roundtail Chub, Flannelmouth Sucker, Bluehead Sucker,
Mountain Sucker, and Colorado River Cutthroat Trout.

The relative abundance in different parts of a river and its tributaries is described in text format,
with references to many of the original historical ichthyological reports, some of which are cited
in this bibliography.

A section on 'threats to native fishes' is also included, describing the primary causes of decline
of the native fish species.

Results relevant to EMAP: Historical distribution and abundance is described for a number of
species, for example: "The Colorado pikeminnow...was once widespread and abundant in warm
main-stem rivers and tributaries...Wild populations of Colorado pikeminnow are presently found
only in the upper basin in about 25% of historic range basin-wide"; "Razorback sucker was
historically common to abundant in most warm regions of the Colorado River system during the
19th and 20th centuries....the species now exists naturally  in only a few locations"; "Roundtail
chub in the upper basin remains as 15 populations in about 55% of its historic habitat...[it] was
once common in 5 tributary rivers  where it is now nearly eliminated."

Threats to native fishes are discussed: flow regulation and diversion, degraded water quality.
nonnative  fish, and physical habitat destruction, alteration,  and fragmentation.

Geographic location: Colorado River basin, Colorado, Wyoming, Utah, EPA region 8, xeric,
mountains, eco20, eco22, eco23,  eco21, eco18, eco19

Keywords: fish, historical status and distribution, water diversion, dams, nonnative fish, habitat
degradation and fragmentation
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Author: Van Steeter, M. M.; Pitlick, J.
Year: 1998
Title: Geomorphology and endangered fish habitats of the upper Colorado River. 1. Historic
changes in stream flow, sediment load, and channel morphology
Reference Type: Journal Article
Journal: Water Resources Research
Volume: 34
Issue: 2
Pages: 287-302

Value of reference: The authors examine the changes in channel morphology and sediment
load of a segment of the upper Colorado River near Grand Junction, Colorado between 1900
and 1995 and relate it to the habitat requirements of a native fish, the Colorado squawfish.

Results relevant to EMAP: Flow records were divided into a predevelopment period (1900-
1949) and compared to a post-development period (1950-1995) since most of the reservoirs
were built upstream after 1950. Dams, irrigation withdrawals, and interbasin transfers have
significantly altered the natural flow regimes of the upper Colorado and Gunnison rivers. Peak
discharges in reaches used by endangered native fishes are 29-40% lower than they were in
the past. Reservoirs affect the way runoff is distributed throughout the year; yearly average
discharge is similar to that in the past, but the spring peak flows are much reduced.

Sediment loads are similar to those in the past; however, since high flows are less common, the
rivers have lost their capacity to carry the sediment. In the last 40 years or so, there is a
tendency for sediment to build up in the channel,  causing it to become narrower and less
complex.

The rivers' declining ability to carry sediment affects native fish because the substrate is not
regularly cleaned of silt and sand by peak flows. This has limited the reproductive success of
the Colorado squawfish. The silting of the channel also favors nonnative (competitive) fish such
as the channel catfish. There has also been significant habitat loss for native fish as
backwaters, bars, and islands have been reduced. Analysis of aerial photographs indicates that
between 1937 and 1993 the main channel of the  Colorado River has narrowed by an average of
20 m and about 1/4 of the area formed by side channels and backwaters has  been lost.

Geographic location: eco20, Region 8, Colorado, upper Colorado River, Gunnison River, xeric

Keywords: fish, Colorado squawfish, sediment, dams, habitat degradation, nonnative species,
phab, channel geomorphology, historic change, hydrologic variability, peak discharge

Abstract: The hydrologic,  geomorphic, and ecologic effects of reservoir operation are thought to
be key factors in the decline of native fishes in the upper Colorado River basin. The present
paper examines the extent to which changes in stream flow and sediment loads have affected
alluvial reaches of the Colorado River near Grand Junction, Colorado. The analysis shows that
since 1950, annual  peak discharges of the Colorado River and its major tributary, the Gunnison
River, have decreased by 29-38%. The total volume of runoff delivered to the study area has
not changed  significantly over the period of record, but the annual hydrograph has been
modified greatly by  reductions in peak flows and augmentation of base flows.  Annual
suspended sediment loads of the Colorado River and Gunnison River have likewise decreased.
This was particularly apparent during the period from 1964 to 1978, when annual sediment
loads were 40-65% less than the long-term average. Analysis of aerial photographs indicates
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that between 1937 and 1993 the main channel of the Colorado River has narrowed by an
average of 20 m and about 1/4 of the area formed by side channels and backwaters has been
lost.
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Author: Varley, J. D.; Gresswell, R. E.
Year: 1988
Title: Ecology, status, and management of the Yellowstone cutthroat trout
Reference Type: Book Section
Editor: Gresswell, R. E.
Book Title: Status and management of interior stocks of cutthroat trout.
City: Bethesda, Maryland
Publisher: American Fisheries Society
Pages: 13-24

Value of reference: The authors compare historical and present Yellowstone cutthroat trout
distribution and discuss the factors implicated in its decline.

Results relevant to EMAP: Yellowstone cutthroat trout once inhabited about 24,000 km of
stream in Montana, Wyoming, Idaho, and a corner of Utah. Today they exist in an estimated
2400 km of stream in and around Yellowstone and Grand Teton National Parks.

The Yellowstone cutthroat trout presently occurs mainly in headwater streams, but historically,
the fish had a greater elevational distribution. Its historic elevational range extended from 275 m
to 3200 m. The fish were common in large rivers such as the Snake River above Shoshone
Falls and the main stem Yellowstone River at Miles City, Montana.

Yellowstone cutthroat declines are attributed mainly to stream dewatering, grazing-related
riparian vegetation loss, and the introduction of nonnative species.

Geographic location: Region 8, Montana, Wyoming, Idaho, Utah, Yellowstone River basin,
Snake River basin, mountains, eco17, eco43, eco12

Keywords: fish, cutthroat trout, distribution, grazing, riparian vegetation, habitat degradation,
nonnative species, water diversion

Abstract: The Yellowstone cutthroat trout Salmo clarki bouvieri is the most abundant and widely
dispersed subspecies of inland cutthroat trout. The historic range of the subspecies included the
Yellowstone River drainage in Montana and Wyoming and portions of the Snake River drainage
in Wyoming, Idaho, Nevada, Utah, and perhaps Washington. Introductions of nonnative fishes,
environmental degradation, and human exploitation have severely reduced this range.  The
subspecies is estimated to presently exist in a genetically pure form in about 85% of the historic
lake  habitat but only in about 10% of the estimated original stream range. Additionally,
Yellowstone cutthroat trout populations have been established outside the historic range in at
least seven western states and two Canadian provinces. High landing rates and angler success,
coupled with the fish's relatively large mean length, make the Yellowstone cutthroat trout a
valuable recreational resource; however, vulnerability to angling has often led to overharvest of
wild stocks. Current management of the Yellowstone subspecies includes wild trout programs
for native and introduced populations and maintenance stocking from hatchery brood stocks.
Genetic integrity, habitat management, and special angling regulations are important elements
that influence the success of these programs. The status of the Yellowstone cutthroat trout is
encouraging, but future management must emphasize protection of the full range of genetic
diversity.
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Author: Warren, G.K.
Year: 1856
Title: Explorations in the Dacota Country, in the year 1855
Reference Type: Report
City: Washington, D.C.
Institution: U.S. Senate
Report Number: Executive Document No. 76, 34th Congress, 1st Session.

Value of reference: This primary source provides physical descriptions of several river basins
in the plains, including the Missouri, Little Missouri, Platte, Rapid, White, Big Shyenne, Big
Sioux, Vermillion, and James. Appendix A gives accounts of the explorations of these areas in
journal format, including additional habitat descriptions of stream widths, bank height, sediment
composition, and riparian vegetation.  Appendix B provides detailed descriptions of a smaller
area under consideration for a military reserve in the vicinity of eastern Wyoming and western
South Dakota. Appendix E is a geological summary, but also provides descriptions of riparian
vegetation along rivers and streams, including the dominant trees, shrubs, and herbaceous
riparian plants of the region, and a portion about travel through the  badlands. This is a good
source for early descriptions of riparian areas and landscapes of the plains region.

Results relevant to EMAP: Accounts describe the region encompassing  southeast Wyoming,
southern South Dakota, and northern Nebraska, including numerous descriptions of riparian
habitats and stream physical characteristics throughout the exploration route. The majority of
accounts mention the presence of grasses and woody plants such as cottonwood, willow, ash,
oak, elm, boxelder, and wild plum. In  places along streams where only grass was found, the
accounts often include a mention of nearby wooded areas, upstream or downstream.  Stream
sediment type, width, depth, bank height, presence of fish (occasional mention) are also
included in descriptions.

In several locations of the exploration route, the author notes that trees (primarily
cottonwood)were once more plentiful (based on signs of trees being cut),  but they had been cut
down for use by the "Indians".

Geographic location: Wyoming, South Dakota, plains, EPA Region 8, Missouri River basin,
Little Missouri River basin, Platte River basin, Rapid River basin, White River basin,  Big
Shyenne River basin, Big Sioux River basin,  Vermillion River basin, and James River basin,
eco43, eco17, eco42, eco46

Keywords: phab, riparian vegetation,  primary source, historical accounts, explorations
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Author: West, Elliott; Ruark, Greg
Year: 2004
Title: A long, long time ago ... Historical evidence of riparian forests in the Great Plains and how
that knowledge can aid with restoration and management
Reference Type: Journal Article
Journal: Journal of Soil and Water Conservation
Volume: 59
Issue: 5
Pages: 105-110

Value of reference: This article presents a differing point of view regarding the historical
presence of large woody riparian areas along larger Great Plains streams and waterways.  The
author suggests that early historic accounts of the streams suggest that the original vegetation
included large wooded riparian zones and that current thought (streams without woody
vegetation) is based on post-settlement accounts which were after the woody vegetation had
been removed by the increased demand on the resource due to the push for settlement and
westward expansion.

This article points out the importance of finding pre-settlement accounts and surveys when
determining "natural" conditions. The author points out that much of the current historical
baseline used to determine "normal conditions"  is based on accounts that date back to the early
20th century.  In those reports trees were largely absent or thinly represented along water
courses. No one should conclude from these records, that the absence of timber was natural.
Rather the lack of trees was the consequence of some of the most rapid changes that the
region has ever known.

Results relevant to EMAP: Many of the larger  streams of the Great Plains had a more
extensive riparian woodland than had been commonly assumed. Riparian vegetation
experienced substantial change during the mid to late 1800's due to human impacts. By 1900
most of the trees and other woody vegetation along the rivers and streams in the Great Plains
had been cut and removed by Indians, gold seekers, soldiers,  railroad crews and settlers.
These riparian zones were once heavily forested with wide bands of trees but are now occupied
primarily by herbaceous plants or cropland.

Looking at historical accounts from the pre- or early  1800's point to a  more abundant woody
riparian cover. This article highlights the importance of true pre-settlement reports and
descriptions to determine "historic or reference condition", particularly in the Plains, which was
altered early and dramatically.

Geographic location: Great  Plains, Nebraska,  Kansas, Colorado, Wyoming, eco25, eco27,
eco43, plains, Platte River, North and South Platte rivers, Arkansas River, Solomon River,
Republican River, EPA Region 7, EPA Region 8

Keywords: phab, riparian zone, trees, human impact
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Author: Wissmar, R. C.; Smith, J. E.; Mclntosh, B. A.; Li, H. W.; Reeves, G. H.; Sedell, J. R.
Year: 1994
Title: A history of resource use and disturbance in riverine basins of eastern Oregon and
Washington (early 1800's-1990's)
Reference Type: Journal Article
Journal: Northwest Science
Volume: 68
Issue:  Special Issue
Pages: 1-35

Value of reference: A comprehensive look at the settlement and cumulative disturbance history
of six river basins in eastern Oregon and Washington (the Okanogan, Methow, Yakima,  Little
Naches, John Day River, and Grand Ronde Rivers) and how 150 years of human use has
affected fish populations and instream and riparian habitats. This paper is a companion to
Mclntosh et al. 1994 (in this bibliography), but it delves into the chronology of historical resource
use in greater detail.

Results relevant to EMAP: Wssmar et al. also discuss impacts to fish populations that are not
as evident as those that are commonly reported, such as the effects of early diversions,
ditching, and dredging for mining operations,  changes to the pattern of snow accumulation and
an earlier snowmelt caused by clear cutting, and fish response to high temperatures from a loss
of shading in eastern Oregon streams.

Earlier peak flows in the Upper Grande Ronde River may influence the survival of salmon
smolts because fish outmigration is timed largely to peak flows. Early peak flows could force
smolts to outmigrate too early and lower fish survival. The hydrograph of the John Day basin
has changed significantly due partly to vegetative changes, with base flows increasing in all
managed watersheds and remaining the same in wilderness areas. Prior to settlement, the John
Day River basin supported substantial runs of spring and fall Chinook salmon and steelhead and
resident fish such as bull trout (Salvelinus confluentus). Currently salmon runs are suppressed,
with fall Chinook being nearly extinct (escapements < 100 fish), while spring Chinook runs range
from 2000 - 5000 and steelhead from 15,000  - 40,000 fish.

Turbidity in some parts of the basin, such as Cottonwood Creek, a tributary to the North  Fork,  is
notoriously high after storm events. The resulting siltation of stream beds decreases aquatic
insect production and degrades spawning gravels. Lack of thermal cover also affects fish food
availability. Exposed reaches with high solar radiation  produce algae which changes the types
of invertebrate prey base. Severe increases in water temperatures both summer and winter are
critical  limiting factors for salmonids over many portions of the John Day River basin.

Geographic location: ecolO, eco11, Columbia Plateau, Blue Mountains, North Cascades,
Eastern Cascades Slopes and Foothills, eco77, eco9,  Oregon, Washington, mountains, xeric,
EPA Region 10

Keywords: historical, fish, salmonids, human disturbance, temperature, sediments, logging,
mining, grazing, dams, roads, water diversions

Abstract: A historical  review of human activities influencing streams and riparian ecosystems in
eastern Washington and Oregon shows that cumulative effects of resource uses and
management over the past two centuries are  altering the health of many river basins. Past
practices such as livestock grazing and forest harvest  near riparian areas and streams became
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collectively significant over long time periods and are continuing today. Case histories for the
Okanogan and Methow River basins (north central Washington), the Naches River (eastern
Cascade Mountains), and the Grande Ronde and John Day River basins (eastern and north
central Oregon) provide chronologies of events that shaped the present-day landscapes and
socio-economic conditions of the region. Historic cumulative effects on stream and riparian
ecosystems include livestock grazing and mining from the 1860's until about 1910. Timber
harvest, roads, fire management, dams, irrigation, and fisheries increased in importance during
the 20th Century. Management histories show minimal actions for reducing damage to stream
and riparian ecosystems. Managers commonly perpetuate the notion that streams and riparian
areas are difficult to manage because little is known about how these ecosystems function.
Many agencies strive to develop procedures for treating the symptoms of degraded ecosystems
while giving little consideration to the causes. Other agencies  and public groups concerned with
conflicting issues like water allocations and minimum instream flows for fish usually disagree
with plans for resolving these issues. The continuous dissent by these parties only adds to the
plight offish as available water and habitats continue to  decline. Alternatively, new basin-wide
management strategies of federal and environmental organizations offer hope for improving the
ecosystem biodiversity and population levels offish and wildlife. Priorities include the protection,
restoration, and monitoring of habitats and networks that connect stream and riparian
ecosystems in degraded and intact watersheds. Intact watersheds (e.g., roadless and
wilderness areas) function as critical habitats and refuge areas for fish and wildlife of adjoining
ecosystems.
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Editor: Yarrow, H. C.; Henshaw, H. W.; Cope, E. D.
Year: 1875
Title: Reports upon the zoological collections obtained from portions of Nevada, Utah,
California, Colorado, New Mexico, and Arizona during the years 1871, 1872, 1873, and 1874
Reference Type: Edited  Book
Series Title: Geographical and geological explorations and surveys west of the 100th meridian
in charge of first lieutenant George M. Wheeler
City: Washington, D. C.
Publisher: Government Printing Office
Volume: 5
Number of Volumes: 6
Number of Pages: 1021

Value of reference: This tome describes biota (fish) collected on a series of survey
explorations  made between 1871 and 1874 in 6 western states. The landscape descriptions in
the mammals and birds chapters give glimpses of riparian vegetation. The chapter on fish
(retained as hard copy) is valuable because it describes non-commercial cyprinids and suckers
(including  some line drawings).

Results relevant to EMAP: The descriptions of riparian growth along streams flowing through
foothills and low mountains (at elevations as low as 2700 ft.) in arid regions (San Luis Valley,
Colorado;  Gila River, Arizona,  smaller streams in Arizona) are notable in their continual mention
of tall cottonwoods and heavy brush, so thick at times to "render progress at all times difficult,
and occasionally well nigh impossible."

Streams issuing from the base of the mountain normally disappeared in the "thirsty sands of the
plains below", but even on the  dry flats, the luxuriant vegetation which enclosed the banks did
not disappear until the stream sank beneath the sand.

The chapter on fish collected during the surveys lists species encountered and location,
descriptions of individual  fish with some body measurements, some general indications of
abundance, and occasional anecdotes of fishing for subsistence or market.

Geographic location: Nevada, Utah, California, Colorado, New Mexico, Arizona, mountains,
xeric, eco19, eco13, eco21, eco23, Provo River, San Pedro River, Gila River, EPA Region 8,
EPA Region  9

Keywords: fish, riparian vegetation, phab, historical survey
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Author: Yoshiyama, R.M.; Fisher, R.W.; Moyle, P.B.
Year: 1998
Title: Historical abundance and decline of Chinook salmon in the central valley region of
California
Reference Type: Journal Article
Journal: North American Journal of Fisheries Management
Volume: 18
Pages: 487-521

Value of reference: This research reconstructs historical Chinook salmon estimates (numbers
and pounds) in two major drainages-San Joaquin and Sacramento Rivers, and discusses
declines that may have begun as early as the 1850s, the factors causing those declines, and
the general changes in ranges of the four major Chinook runs over the last 70 years. It brings
together many historical and current references and thus is a very thorough synthesis article
that covers the history and status of Chinook salmon in the Central Valley. Paper also
discusses  the differential impacts on the 4 runs (spring, winter, fall, late-fall).

Results relevant to EMAP: The Central Valley system contained a productive Chinook
resource before the 20th century; historical Chinook runs for the Central Valley were estimated
between 1 and 2 million spawners per year in the late 1800s, which was reduced by
approximately 50-90% by the late 1900s (see Table 5).

Harvest records estimate takings in 1856 at 450,000 fish (nearly 4000 per day); at an average
weight of about fifteen pounds each, this amounts to 6,750,000 pounds (includes spring,
summer, and winter run catches). Catches during 1875-1910 were  often 5-10 million pounds
annually, averaging at least 7,180,000 Ib and exceeding 10 million pounds in 1880,  1883, 1909,
and 1910 (see Table 2).

A decrease in the abundance of salmon in the Sacramento River was noticed as early as 1851
beginning  with widespread mining. Factors causing declines over time are overfishing,
destruction of habitat by hydraulic mining, dredge mining, railroad construction, logging,
construction  of dams, water diversions, and establishment of hatchery programs.

Geographic location: eco6, eco7, California, Central Valley, xeric,  San Joaquin River,
Sacramento  River,  EPA Region 9

Keywords: fish, historical fish catch, historical fishery, fishing, mining, dams, water  diversion,
hatchery egg collecting

Abstract:  The Central Valley drainage of California formerly produced immense numbers of
Chinook salmon Oncorhynchus tshawytscha.  Four seasonal  runs occur in  this system-fall, late-
fall, winter, and spring runs.  Differences in life history timing  and spatial distribution enabled the
four runs to use the drainage to the fullest possible extent and once made  it one of the richest
regions in  the world for Chinook salmon production.  Native American fishers within the central
valley drainage harvested Chinook salmon at estimated levels that reached 8.5 million pounds or
more annually.  Native harvests, therefore,  were roughly comparable to the peak commercial
harvests taken later by Euro-American fishers, but whether or not native fishing depressed the
productive capacities of the salmon populations to any substantial degree is not known. The
commercial Chinook salmon fishery in CA started about 1850 in the  San Francisco Bay and
Sacramento-San Juaquin Delta region,  where it formed the nucleus of the first major fishery
conducted by Euro-American immigrants in the state. This fishery was one of the important
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early industries that supported the Euro-American settlement of the Central Valley region.  The
salmon fishery remained centered there until the early 1900s, when ocean salmon fishing began
to expand and eventually came to dominate the fishery. Annual catches by the early
Sacramento-San Juaquin in-river fishery commonly reached 4-10 million pounds and generally
were higher than the total statewide catches made during the most recent several decades.
The historical abundances of Central Valley Chinook salmon before large-scale commercial
exploitation and depletion of the runs cannot be determined with certainty. However, on the
basis of early commercial catch records, the maximal production levels of the central valley
Chinook salmon stocks in aggregate may be conservatively estimated to have reached
approximately 1-2 million spawners annually. Although substantial investment has been made
by the state of California in managing the Chinook salmon resource since the early years of the
commercial fishery, Chinook salmon have declined over the decades  to small fractions of their
previous numbers. The decline of the central valley Chinook salmon  resource was caused by
several factors: overfishing, blockage and degradation of streams by  mining activities, and
reduction of salmon habitat and stream flows by dams and water diversions.  Differences
between the four Chinook salmon runs in life history timing and habitat requirements partly
account for their different population histories; the winter run is now threatened with extinction,
the spring run recently has approached  a similarly imperiled state, and the late-fall run has been
at moderately low population levels for the past two decades. Only the fall run, in aggregate,
can be regarded as secure, but it too has undergone substantial reductions in abundance. Fall-
run spawner numbers were especially low in the San Juaquin River basin in recent years, and in
Sacramento River basin  streams their numbers have been heavily influenced by production of
hatchery fish.
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Author: Young, M.K.
Year: 2003
Title: Yellowstone Cutthroat Trout
Reference Type: Electronic Source
Producer: American Fisheries Society, Montana Chapter
Access Year: 2005
Access Date: May 18
Last Update Date: April 18, 2005

Value of reference: Summary addresses a subspecies of cutthroat trout, historically wide-
ranging and found in numerous basins in several states. The focus here is on the fish species
of Montana, but historical accounts are given for the species entire range in the West.
Estimates of percent range reductions are given by state, although these are complicated
because the species is stocked and is actually now found in more waters than it was historically.
Concerns about the genetic homogenization of various subspecies of cutthroat trout and among
populations within the Yellowstone cutthroat trout subspecies due to introductions are
discussed.

Results relevant to EMAP: Historically, Yellowstone cutthroat trout were believed to have
occupied much of the Yellowstone River basin, including portions of the Clarks Fork of the
Yellowstone River,  Bighorn River, and Tongue River basins in Montana and Wyoming, and
parts of the Snake River basin in Wyoming,  Idaho, Utah, and Nevada (Behnke 1992 (in this
bibliography)—Figure 1  shows the potential  historical range in Montana).

They have undergone substantial declines in distribution and abundance throughout their range.
Populations in Utah and Nevada are limited  to 102 basins; in Idaho, the trout occupied 43% of
the historical range, in Wyoming 42% and in Montana, 32% (although more recent estimates
suggest that only 10% of the historically occupied fluvial habitat in Montana still contains
genetically pure populations).

The greatest threat is competition with nonnative fish-brown trout, brook trout, lake trout-while
a related concern is the widespread stocking of non-indigenous populations of YC-trout
throughout the historical range, which tends to genetically homogenize populations; habitat
issues are of lesser importance, but examples of the detrimental effects of habitat degradation,
loss, and fragmentation on Yellowstone cutthroat trout are numerous-dewatering for irrigation,
dams, reservoirs, channelization, grazing, logging, mining, road-building.

Geographic location: Montana, mountains, eco 15, eco17, eco42, eco43, EPA Region 8,
Yellowstone River basin, Bighorn River basin, Tongue River basin, Snake River basin

Keywords: fish, historical distribution, agriculture, logging, dams, channelization, mining, roads,
nonnative species,  fishing

Notes: Other species of concern in Montana are listed on the website and can be accessed
electronically via the link provided in this entry.  However, few present historical estimates or
ranges.

URL: http://www.fisheries.org/AFSmontana/SSCpages/yellowstone cutthroat trout.htm
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