xvEPA
United States Environmental
Protection Agency
Office of Research and Development
Washington, DC 20460
September 2005
EPA 620/R-05/005
Environmental Monitoring and Assessment Program
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An Ecological Assessment of Western Streams and River"
Figure 1. Geographic range of EMAP West study. EMAP West included all
perennial streams and rivers, exclusive of the "Great Rivers" (lower sections of the
Columbia, Snake, Missouri, and Colorado Rivers) in a twelve state area.
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An Ecological Assessment of Western Streams ind Bfi
An Ecological Assessment
of Western Streams and Rivers
J. L Stoddard1, D.V. Peck1, S.G. Paulsen1, J. Van Sickle1, C.P. Hawkins2, AT. Herlihy3,
R.M. Hughes3, P.R. Kaufmann1, D.P. Larsen1, G. Lomnicky4, A.R. Olsen1, S.A.
Peterson1, P.L. Ringold1 , T.R. Whittier3
September, 2005
1 U.S. Environmental Protection Agency
Western Ecology Division
National Health and Environmental Effects Laboratory
Office of Research and Development
200 SW 35th Street
Corvallis, OR 97333
2 Western Center for Monitoring and Assessment of Freshwater Ecosystems
Department of Aquatic, Watershed, & Earth Resources
Utah State University
Logan, UT 84322
3 Department of Fish and Wildlife
Oregon State University
c/o U.S. Environmental Protection Agency
200 SW 35th Street
Corvallis, OR 97333
4 Dynamac Corp.
c/o U.S. Environmental Protection Agency
200 SW 35th Street
Corvallis, OR 97333
Recommended citation for this document:
Stoddard, J. L., D. V. Peck, S. G. Paulsen, J. Van Sickle, C. P. Hawkins, A. T. Herlihy,
R. M. Hughes, P. R. Kaufmann, D. P. Larsen, G. Lomnicky, A. R. Olsen, S. A.
Peterson, P. L. Ringold, and T. R. Whittier. 2005. An Ecological Assessment of
Western Streams and Rivers. EPA 620/R-05/005, U.S. Environmental Protection
Agency, Washington, DC.
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An Ecological Assessment of Western Streams ind Bfl
Acknowledgments
A project the size and scope of the one reported in this Assessment cannot be
completed without the cooperation of a large number of individuals and agencies. We
would particularly like to thank these organizations that cooperated in every stage of
design, data collection, data analysis and assessment:
U.S. EPA Region 8, Denver Colorado
U.S. EPA Region 9, San Francisco, California
U.S. EPA Region 10, Seattle, Washington
Arizona Game and Fish Department, Phoenix, Arizona
California Department of Fish and Game, Rancho Cordova, California
Colorado Division of Wildlife, Denver, Colorado
Idaho Department of Environmental Quality, Boise, Idaho
Montana Department of Environmental Quality, Helena, Montana
Nevada Division of Environmental Protection, Carson City, Nevada
North Dakota Department of Health, Bismarck, North Dakota
Oregon Department of Environmental Quality, Portland, Oregon
South Dakota Department of Game, Fish and Parks, Pierre, South Dakota
Utah Division of Water Quality, Salt Lake City, Utah
Washington Department of Ecology, Olympia, Washington
Wyoming Department of Environmental Quality, Sheridan, Wyoming
U.S. Geological Survey (Regional offices in: Tucson, Arizona; Rapid City, South Dakota;
Cheyenne, Wyoming; Bismarck, North Dakota)
The quality of this report was greatly improved by comments from J. David Allan
(University of Michigan) and Robin O'Malley (The Heinz Center).
The information in this document has been funded wholly or in part by the U.S.
Environmental Protection Agency under contract 68-D-01-005 to Dynamac Corporation,
cooperative agreement CR831682 to Oregon State University (Herlihy and Hughes),
and EPA STAR grant R-82863701 (Hawkins). It has been subjected 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.
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An Ecological Assessment of Western Streams incf
Executive Summary
In the 30 years since the passage of the Clean Water Act, Congress, the American
Public and other interested parties have been asking the U.S. Environmental Protection
Agency to describe the condition of the waters in the U.S. They want to know if there is
a problem, how big the problem is if there is one, and whether the problem is
widespread or occurs in hotspots. Additionally, they have been asking to understand
the types of human activities that are affecting streams and rivers, and which are likely
to be the most important. These are seemingly simple questions, and yet they have not
been answered in a reliable way in the past. This report presents the results of a unique
collaboration between the U.S. Environmental Protection Agency and twelve western
States, designed to answer these questions for the rivers and streams of the West.
Covering 42% of the land area, and 28% of the stream and river length in the lower 48
states, EMAP West is the largest monitoring and assessment effort designed to answer
the questions being asked of EPA that has been conducted to date. The States and
EPA collected biological, chemical and physical data at over 1340 perennial stream and
river locations to assess the ecological condition of western waters and the most
important factors affecting those conditions. Results provide clear pictures of the
biological quality of flowing waters across the West, within each of three climatic zones,
and in ten ecological regions. In partnership with the States and EPA Regions 8, 9, and
10, the EMAP program sent four-person teams to collect samples at sampling sites
chosen by an innovative statistical design that insures representative results.
This information fills an important gap in meeting requirements of the Clean Water Act.
The purpose of the assessment is fourfold:
^ Report on the ecological condition of all perennial flowing streams and rivers with
the exception of those considered "Great Rivers," (the lower Columbia, Snake,
Missouri and Colorado Rivers).
<£*< Describe the ecological condition of western streams and rivers with direct
measures of plants, fish, and other aquatic life. Assessments of stream quality
have historically relied solely on chemical analysis or sometimes on the status of
game fish.
<^< Identify and rank the relative importance of chemical, physical and biological
disturbances affecting stream and river condition.
^< Encourage states to include these design and measurement tools as a portion of
their State monitoring programs, so that future condition assessments will be
ecologically and statistically comparable both regionally and nationally.
The results of these surveys show that only 51% of the stream and river length in the
West could be considered in least-disturbed condition. Of the three climatic areas of the
West, the mountains appear to be in the best shape with 56% of the length of flowing
waters in least-disturbed condition. The plains and xeric regions present the most
concerns with close to 50% of the length of streams and rivers in the most-disturbed
conditions (42% and 46%, respectively).
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An Ecological Assessment of Western Streams and River"
Mountains
Plains
West-wide Biological Condition
EMAP West Climatic and Ecological Regions'
Mountains
r I Soulhwestern Mounlains
1 I Northern Rockies
CD Southern Rockies
I. J Pacific Northwesl
Plains
I I Cultivated Northern Plains
13] Rangeland Plains
Xeric
I Northern Xeric Basins
^1 Southern Xeric Basins
HH Eastern Xenc Plateaus
S3 Xeric California Lowlands
'Based on Omemtk ievel lit EcOfegtons,
January T999
Xeric
The results also reveal what is most likely responsible for diminishing biological quality
in flowing waters across the West. Disturbance of shoreline (or riparian) habitat was the
most widespread stressor observed across the West, and in each of the three major
regions. Excess mercury in fish was widespread across the xeric and plains areas but
not the mountains. Non-native vertebrates, primarily fish, were very common across the
entire West. Evaluation of the stressors most likely responsible for poor condition in the
West is best understood by looking at both the extent of each stressor (i.e., how
widespread it is) and the relative risk posed to aquatic biota when a specific stressor is
present. High nitrogen concentrations are found in just over one-quarter of western
streams, and fish assemblages are almost four times as likely to be in poor condition
when nitrogen exceeds a critical threshold as when nitrogen is below these critical
values. Excess salinity also poses a high relative risk to fish when it occurs, but is
present in only 5% of the stream resource. From a management point of view, the
highest priority stressors to address are those that are both common, and that pose
high risk to biota.
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An Ecological Assessment of Western Streams and River"
Riparian Disturbance
Streambed Stability
Riparian Vegetation
Habitat Complexity
Nitrogen
Phosphorus
Mercury in Fish
Salinity
Non-native Vertebrates
Non-native Crayfish
Asian Clam
Relative Extent
of Aquatic Stressors
Relative Risk
to Fish Biotic Integrity
0% 10% 20% 30% 40% 50%
% of Stream Length in
Most Disturbed Condition
1234
Relative Risk Factor
We trust that this report will be useful for land managers, decision makers and citizens
throughout the region. Readers who wish to know more about the technical background
are directed to the scientific journals where the methodologies and supporting
information already have been published and to the appendices of this report.
Finally, we firmly believe that knowledge of the current quality of our flowing waters that
this report describes is among the first steps in deciding rational management plans and
priorities. We believe that the results of this assessment, and others like it in the future,
will let the public know, as the USA Today put it: "whether to celebrate environmental
successes, tackle new threats or end efforts that throw money down a drain".
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An Ecological Assessment of Western Streams ind Bfl
Foreword
This report presents an ecological assessment of non-tidal streams and rivers across
twelve states of the western U.S. (Figure 1). It is based on the results of a unique and
experimental monitoring program implemented through the U.S. EPA's Environmental
Monitoring and Assessment Program (EMAP) during the years 2000-2004. We present
these results in a way that we hope both environmental resource managers and the
general public find useful, with two major objectives in mind: (1) to document, in as clear
and unbiased a manner as possible, the overall condition of the vast network of streams
and rivers of the western U.S.; and (2) to demonstrate the utility and flexibility of an
EMAP-like approach to environmental monitoring and assessment at this regional scale.
Our approach in collecting the data for this assessment has two key characteristics.
First, it focuses as much as possible on direct measures of biological indicators, and on
the chemical and physical properties of streams and rivers that are most likely to have
effects on biological communities. Second, it uses an innovative statistical design that
insures that the results are representative of the region, and allows us to extend this
statistical certainty in the results to subregions of the West (e.g., to major ecological
regions) where desired.
The assessment is divided into two major categories. We first document the ecological
condition of streams and rivers in the West, through the use of direct measures of their
resident biological assemblages: aquatic vertebrates (e.g., fish and amphibians); and
benthic macroinvertebrates (e.g., larval insects, snails, mussels, worms and
crustaceans). We then assess the relative importance of potential stressors on those
assemblages, based on direct measures of their chemical, biological and physical
habitat. We present the results in this way in order to inform readers about where the
major aquatic ecological issues occur in the region, what the most important threats to
the aquatic ecological condition are, and how much risk these stressors pose to aquatic
ecosystems.
This report is written for the public, for environmental managers, and for decision-
makers. Much of the technical background for the report has already been published in
the scientific literature, and we refer sparingly throughout the report to these
publications (denoted by superscript numbers in the text). The key publications that
support the elements of this assessment are listed in Appendix A at the back of the
report. Readers who wish to learn more about the design, specific indicators, or other
elements of the assessment are encouraged to consult this list and read the technical
papers upon which this assessment is based.
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An Ecological Assessment of Western Streams ind Bfl
Purpose
This Ecological Assessment of Western Streams and Rivers has four purposes:
<^< Report on the ecological condition of all perennial flowing waters smaller than the
"Great Rivers" of the western U.S.;
<^< Focus on direct measures of biological assemblages in assessing ecological
condition;
<^< Identify and rank the relative importance of potential stressors affecting stream
and river condition, using supplemental measures of chemical, physical and
biological habitat;
£"< Influence how States design their monitoring programs, and how they assess
and report on the condition of streams and rivers.
The U.S. EPA Environmental Monitoring and Assessment Program (EMAP) assembled
crews in the years 2000 through 2004 to collect over 1500 samples on 1340 perennial
streams throughout the western U.S. This project, known as EMAP West, included both
wadeable streams and non-wadeable rivers, and sampled sites that were either
randomly chosen to be representative of the entire population of flowing waters in the
West, or hand picked to represent the best possible condition ("reference sites"). This
ambitious project was carried out in partnership with twelve western states (Arizona,
California, Colorado, Idaho, Montana, Nevada, North Dakota, Oregon, South Dakota,
Utah, Washington and Wyoming), the U.S. Geological Survey (USGS), multiple
universities, and Environmental Protection Agency (EPA) Regions 8, 9 and 10. All of the
crews were trained to use identical sampling methods to facilitate comparisons across
the region, and all of the data were subject to strict quality assurance procedures (see
Appendix B).
Introduction
Most historic assessments of stream quality have focused on describing the chemical
quality of streams and, occasionally, on sport fisheries impacts. As we have made
progress in controlling chemical problems, it has become obvious that the primary
ecological concern is actually the condition of the plant and animal communities that
inhabit these streams and rivers.
In this assessment we have tried to address this concern not by ignoring physical and
chemical measurements, but by shifting the focus to direct measurements of the biota
(e.g., fish and other vertebrates, and stream invertebrates) themselves. In this
assessment, ecological condition is defined by biological indicators. The biological
organisms in a stream integrate the many physical and chemical stressors and forces,
including other biota (invasive and/or non-native species), that are acting in, and on, the
stream ecosystem. Stream and river condition can be determined by assessing
appropriate biological indicators (see Indicators of Ecological Condition, below), or
combinations of these indicators called indices. Information on the ecological condition
of streams and rivers is supplemented by measurements of other stream
characteristics, especially those physical, chemical, or other biological factors that might
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An Ecological Assessment of Western Streams and River"
I I Upper Missouri River Basin
CD Northern California Coastal Drainage
Southern California Coastal Drainage
Wenatchee River Basin
I I Deschutes/John Day River Basins
Figure 2. EMAP West study area with five special interest areas highlighted.
Also shown is location of 965 probability sites sampled and used for reporting
on ecological condition.
influence or affect stream condition. These stream characteristics allow us to assess the
factors that might have a negative effect on the ecological condition of streams (i.e.,
stressors).
EMAP West
EMAP West was a five-year effort to collect stream and river data across the twelve-
state area represented by the portions of EPA Regions 8, 9 and 10, located in the
conterminous United States (Figure 1). The methods employed were consistent across
the region, and across stream sizes. They were developed to allow one four-person
crew to collect the maximum amount of data on vertebrate, macroinvertebrate and algal
assemblages, physical and chemical habitat, invasive riparian plant species, and major
toxic contaminants in fish tissue, in a one day visit to each site1' . The sites were
chosen according to a probability design, where each site has a known probability of
being selected for sampling, and collectively the sites are statistically representative of
the population of flowing waters in the region. EMAP's probability design uses the same
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An Ecological Assessment of Western Streams incf
philosophy as a Gallup Poll (or other opinion polls), and brings the statistical rigor of
sample surveys to the science of environmental assessment. Within the EMAP West
region, several special interest areas were identified for additional site selection (Figure
2). The higher density probability design in these areas will allow us to make future,
stand-alone, assessments of each area (the Upper Missouri River Basin, the
Wenatchee Basin of Washington, the John Day and Deschutes River Basins in Oregon,
the Northern California coast, and the Southern California coast), as well as each of the
12 western states. In this Assessment we present results at three different levels of
geographic resolution—West-wide, in three major climatic regions (Mountains, Xeric
and Plains) and in 10 ecological regions of the West (see Reporting Units for EMAP
West, below). These results make up the bulk of this Assessment. Interested readers
are urged to consult the references in Appendix A for additional information on
probability designs3"5. The specific details of the EMAP West design, as well as detailed
information on data, indicators and analyses used in this report, can be found in the
EMAP West Statistical Summary6.
The EMAP West Region
The region covered by EMAP West comprises almost 42% of the land area of the
conterminous United States. It is roughly half federal land (primarily managed by the
U.S. Forest Service and Bureau of Land Management) and half private, with 7% under
tribal jurisdiction. It is a topographically and climatically varied region, including the
western Great Plains, the Rocky Mountains and the Continental Divide, the rainforests
of the Olympic Peninsula, the rugged peaks of the Sierra Nevada, and the intensely arid
climates of the Sonoran and Mohave Deserts. Wthin this diverse geographic region are
the headwaters (and main stems) of the Missouri, the Arkansas, the Rio Grande, the
Snake, and the Colorado Rivers. Rapid population growth has been, and continues to
be, a consistent theme in the West, as do competing uses for the water. The EMAP
West region includes some of the most rapidly growing metropolitan areas of the
country: Denver and the front range of the Rockies, Salt Lake City and the Wasatch
Front, Phoenix, Las Vegas, the San Diego to Los Angeles corridor, Portland and
Seattle. In spite of this history of rapid growth, water has always been a scarce and
precious resource in the West. The rivers of the West have been valued for their scenic
beauty (e.g., the Grand Canyon of the Colorado River), their biological resources (e.g.,
salmon of the Pacific Northwest), and their capacity to generate vast quantities of
electrical power and irrigation water.
Reporting Units for EMAP West
We report here at three levels of geographic resolution:
(1) the Executive Summary and the main body of the report present results for all of
the EMAP West region (referred to as "West-wide");
(2) the main body of the report focuses on three major climatic regions (Mountains,
Plains and Xeric), in addition to the West-wide results; and
(3) results for ten aggregated ecological regions (or ecoregions, areas that have
similar soils, vegetation, climate, and physical geography) are presented briefly in
Appendix C.
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An Ecological Assessment of Western Streams and River
Mountain
Climatic Region
Plains Climatic Region
Cultivated Northern Plains
Southwestern Mountains
EMAP West Climatic and Ecological Regions'
Mountains
: ' Southwestern Mountains
i I Northern Rockies
( I Southern Rockies
CD Pacific Northwest
Xeric
I I Northern Xeric Basins
[ " Southern Xenc Basins
I 1 Eastern Xeric Plateaus
r~l Xeric California Lowlands
Plains
I 5 Cultivated Northern Plains
CD Rangeland Plains
•Basod on Qmemtti Ltvet III Ecorcgions.
January T9S9
Xeric California
Northern Xeric Basins Eastern Xeric Plateaus~~Southern Xeric Basins
Xeric Climatic Region
Figure 3. Location of three climatic regions (Mountains, Plains and Xeric) and ten
aggregated ecological regions used as reporting units in this assessment.
Photographs are of typical probability sites sampled as part of EMAP West in each
ecological region.
Both the climatic regions and ecoregions we report on here are aggregations of
Omernik ecoregions7. As a result of their similar characteristics, one expects the water
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An Ecological Assessment of Western Streams incf
resources within a particular climatic or ecological region to have similar characteristics,
similar stresses and similar responses to those stresses. An ecoregion perspective
highlights the differences, for example, between mountain areas with the steep slopes,
shallow soils, and cooler climate, and valley areas that are relatively flat, have deep
soils, and warmer temperatures; ecoregions permit us to have different expectations for
flowing waters in these very different areas. Typically, management practices within an
ecoregion are applicable to many flowing waters with similar problems, because the
characteristics of the streams in the ecoregion are similar. The climatic and ecological
regions used for EMAP West are illustrated in Figure 3, with photographs of probability
sites sampled for this assessment. Interested readers are directed toward the
references in Appendix A for further information on Omernik ecoregions and their
characteristics.
What is an Ecological Assessment?
When we speak of assessing the ecological condition of streams and rivers of the
western United States, we are focused on evaluating two critical components of aquatic
ecosystems: the condition of their biota, and the relative importance of human-caused
stressors.
The ecological condition of streams and rivers is represented by the condition of their
biotic communities—the living components of aquatic ecosystems that integrate the
many forms of human disturbance and stream modifications that we are interested in
assessing. Often these components are assessed in terms of their biotic integrity, one
of the main characteristics of aquatic systems that the Clean Water Act aims to protect.
Biotic Integrity is defined as "the capability of supporting and maintaining a balanced,
integrated, adaptive community of organisms having a species composition, diversity,
and functional organization comparable to that of the natural habitat of the region"8 9.
Stressors, or the pressures that human beings exert on aquatic systems through their
use of the surrounding environment, are the chemical, physical and biological
components of the ecosystem that have the potential to degrade biotic integrity. Some
obvious chemical stressors are toxic compounds, excess nutrients (nitrogen and
phosphorus) or acidity from acidic deposition or mining. Most physical stressors are
created when we modify the physical habitat of a stream network—excess
sedimentation, bank erosion, loss of streamside trees and vegetation can all degrade
biotic integrity, and may result from human activities in watersheds. Biological stressors
are characteristics of the biota themselves that can influence biotic integrity; examples
are non-native or invasive species (either in the streams and rivers themselves, or in the
riparian areas adjacent to them). One of the key components of an ecological
assessment is a measure of how important (e.g., how common) each of these stressors
is in a region, and how severely they affect biotic integrity.
Indicators of Ecological Condition
We estimate the ecological condition of streams and rivers by analyzing the composition
and relative abundance of key biotic assemblages—in the case of EMAP West, we
focus on aquatic vertebrates (fish and amphibians) and macroinvertebrates (larval
insects, crustaceans, worms and mollusks). The Clean Water Act explicitly aims "to
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An Ecological Assessment of Western Streams incf
restore and maintain the chemical, physical, and biological integrity of the Nation's
waters". Our assessment of ecological condition is focused on biological integrity,
because of the inherent capacity of biological organisms and assemblages to integrate
the chemical and physical stressors that affect them over time. Our measures of biotic
integrity include two examples of a widely used indicator of condition called the Index of
Biotic Integrity, or IBI. The IBI is a multi-metric index—the total score is the sum of
scores for a variety of individual measures, or metrics, that make up the key
characteristics of biotic integrity (e.g., taxonomic richness, habitat and trophic
composition, sensitivity to human disturbance, and other aspects of the biota that reflect
"naturalness"). Originally developed for fish in Midwestern streams, the IBI has been
modified numerous times for other regions, taxonomic groups, and ecosystems10' 11.
Some of the details of IBI development for this assessment are given in the following
paragraphs. In addition to assessing ecological condition on the basis of biotic integrity,
we employ another commonly used measure to report on the health of
macroinvertebrate assemblages—the Observed/Expected, or 0/E, index. 0/E is a
measure of how many kinds of macroinvertebrates are expected to occur at a site, but
are not actually found at that site. Our 0/E index is also described below.
Aquatic Vertebrate IBI
The IBI we use to assess aquatic vertebrates includes metrics chosen to represent
these key characteristics of biological integrity: taxonomic richness (number of species);
taxonomic composition (e.g., is the assemblage dominated by trout or minnows); habitat
use (e.g., bottom-dwelling vs. water-column species); life history (e.g., are migrating
species present); reproductive strategies (e.g., are there species present that require
clean gravels to spawn); pollution tolerance; feeding groups (e.g., fish-eating vs. insect-
eating); and the presence of non-native species. For each of the three climatic regions
of the West (Figure 3), we chose one metric from each of these classes of
characteristics, and scored them against regional expectations of what value was
possible for each stream (based on reference conditions—see "Setting Expectations"
below). The resulting IBI combines all of the metrics in each region into an index whose
values range from 0 to 100, with 100 denoting the best possible condition. The process
we used to develop the IBI for aquatic vertebrates in EMAP West is described in some
detail in the EMAP West Statistical Summary6.
Macroinvertebrate IBI
The characteristics of the macroinvertebrate assemblages used to measure biotic
integrity were: taxonomic richness (number of taxa); taxonomic composition (e.g., is the
assemblage dominated by non-insects); taxonomic diversity; feeding groups (e.g., are
there shredders, scrapers or predators present); habits (e.g., are there burrowing,
clinging or climbing taxa present); and pollution tolerance. Different specific metrics
were chosen in each of these categories, in each of the three climatic regions of the
West (Figure 3). Each metric was scored against our expectations of what value was
possible for each stream (based on reference conditions—see "Setting Expectations"
below), and then combined to create an overall IBI, whose values range from 0 to 100.
A detailed discussion of the process we used to develop a macroinvertebrate IBI can be
found in the EMAP West Statistical Summary6.
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An Ecological Assessment of Western Streams and River"
Macro!nvertebrate O/E
In addition to biotic integrity, the loss of key taxa can be used as a measure of
ecological condition12"15. For EMAP West, we developed an O/E index, described in
detail in the EMAP West Statistical Summary6, that is simply the number of
macroinvertebrate taxa observed at a site divided by the number of taxa expected to
occur (based on the reference site approach described in Setting Expectations, below).
The values range from 0 (none of the expected taxa present) to slightly greater than 1
(more taxa than expected present). This index is a direct measure of how many taxa are
missing at a site—a value of 0.5 indicates that half of the macroinvertebrate taxa we
expected to find at a site were missing.
Aquatic Indicators of Stress
As human beings utilize the landscape, their
actions can produce effects that are stressful to
aquatic ecosystems. These aquatic stresses
can be chemical, physical, or in some cases,
biological. In this assessment we have
selected a short list of stressors from each of
these categories. These are not intended to be
all-inclusive, and in fact some stressors that
are likely to be important are not included here
because we have no current way to assess
them at the site scale (e.g., water withdrawals
for irrigation). We hope that future
assessments of stream and river condition in
the West will include a more comprehensive
list of stressors from each of these categories.
The use of land for cattle grazing can supply
both nutrients and excess sediments to
streams in the West, but is not itself
considered a stressor
We emphasize that the highlighted stressor indicators are direct measures of stress in
the stream or adjacent riparian areas. They are not landuse or land cover alterations
such as row crops, mining or grazing. While any form of human landuse can be a
source of one or more stressors to streams, we choose to focus on the stressors
themselves, rather than on their sources.
Chemical Stressors
We report here on four indicators of chemical stress:
• Total phosphorus concentration—phosphorus is a nutrient, and is usually
considered to be the most likely nutrient limiting algal growth in freshwaters
throughout the U.S. It is a common ingredient in fertilizers, and high concentrations
may be associated with agricultural and urban landuse.
• Total nitrogen concentration—nitrogen is another nutrient, and is particularly
important as contributor to coastal and estuarine algal blooms. Sources include
fertilizers, wastewater, animal wastes, and atmospheric deposition.
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An Ecological Assessment of Western Streams and River
Excessive nutrients, like phosphorus and
nitrogen, can lead to algal blooms, and other
biotic effects
» Salinity—excessive salinity occurs
in areas with high evaporative losses
of water, and can be exacerbated by
repeated use of water for irrigation,
or by water withdrawals (by slowing
transit time of flowing waters). Both
electrical conductivity and total
dissolved solids (IDS) can be used
as measures of salinity; for EMAP
West, we have chosen to use
conductivity.
» Mercury in Fish Tissue—Sources
of mercury in the environment
include some types of mining
(especially gold mining), coal
combustion, the burning of industrial and residential waste, herbicides, fungicides,
and pulp, paper and textile effluents. Because it is a fairly common contaminant in
coal and solid waste, airborne mercury is very widespread, and is a common
contaminant in rain and snow across most of the U.S. Once it reaches lakes and
streams, mercury can be converted to toxic methylmercury by bacteria, and begin to
accumulate in algae, invertebrates and vertebrates. Higher trophic levels (e.g.,
piscivorous [fish-eating] fish) and long-lived species tend to accumulate higher
concentrations of methylmercury. For EMAP West, we sampled large piscivorous
fish, large non-piscivorous fish and small fish, and measured whole-body mercury
concentrations in each group. If mercury concentrations exceeded the levels
established for the protection of wildlife (see Appendix D) in any of the three fish
groups sampled at a site, that site was considered to be stressed by mercury.
Physical Habitat Stressors
Although there are many aspects of stream and river habitats that can become stressful
to aquatic organisms when altered or modified, we focus here on four specific aspects
of physical habitat:
fa Streambed stability—streams and rivers adjust their channel shape and
streambed particle size in response to the supply of water and sediments from
their drainage areas. One measure of this interplay between sediment supply
and transport is relative bed stability (RBS). The measure of RBS that we use in
this assessment is a ratio comparing the particle size of observed sediments to
the size sediment each stream can move or scour during its flood stage, based
on the size, slope and other physical characteristics of the stream channel16. The
RBS ratio differs naturally among regions, depending upon landscape
characteristics that include geology, topography, hydrology, natural vegetation,
and natural disturbance history. Values of the RBS Index can be either
substantially lower (finer, more unstable streambeds) or higher (coarser, more
stable streambeds) than those expected based on the range found in least-
disturbed reference sites—both high and low values are considered to be
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An Ecological Assessment of Western Streams and River"
Low Relative Bed Stability (RBS) is
characterized by the accumulation of larger
than expected quantities of very fine silt and
sediment in streams.
indicators of ecological stress. Excess
fine sediments can destabilize
streambeds when the supply of
sediments from the landscape
exceeds the ability of the stream to
move them downstream. This
imbalance results from numerous
human uses of the landscape,
including agriculture, road building,
construction and grazing. Lower than
expected streambed stability may
result either from high inputs of fine
sediments (from erosion) or increases
in flood magnitude or frequency
(hydrologic alteration). When low RBS
results from fine sediment inputs,
stressful ecological conditions can
develop because fine sediments begin filling in the habitat spaces between
stream cobbles and boulders. The instability (low RBS) resulting from hydrologic
alteration can be a precursor to channel incision and arroyo formation. Perhaps
less well recognized, streams that have higher than expected streambed stability
can also be considered stressed—very high bed stability is typified by hard,
armored streambeds, such as those often found below dams where fine
sediment flows are interrupted, or within channels where banks are highly altered
(e.g., paved or lined with rip-rap).
Habitat complexity—the most diverse fish and macroinvertebrate assemblages
are found in streams and rivers that have complex forms of habitat: large wood,
boulders, undercut banks, tree roots, etc. Human use of streams and riparian
areas often results in the simplification of this habitat, with potential effects on
biotic integrity. For this assessment, we use a measure that sums the amount of
in-stream habitat consisting of undercut banks, boulders, large pieces of wood,
brush, and cover from overhanging vegetation within a meter of the water
surface16, all of which are quantified by EMAP field crews.
Riparian Vegetation—the presence of a complex, multi-layered vegetation
corridor along streams and rivers is a measure of how well the stream network is
buffered against sources of stress in the watershed. Intact riparian areas can
help reduce nutrient and sediment runoff from the surrounding landscape,
prevent bank erosion, provide shade to reduce water temperature, and provide
leaf litter and large wood that serve as food and habitat for stream organisms.
The presence of canopy trees in the riparian corridor indicates longevity; the
presence of smaller woody vegetation typically indicates that riparian vegetation
is reproducing, and suggests the potential for future sustainability of the riparian
corridor. For this assessment we use a measure of riparian vegetation complexity
that sums the amount of woody cover provided by three layers of riparian
vegetation: the ground layer, woody shrubs, and canopy trees
16
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An Ecological Assessment of Western Streams and River
Healthy and intact riparian corridors
provide important services to streams-
preventing or reducing the impact of
landuse in the watershed
disturbance observed in the stream,
the banks, throughout the reach).
^« Riparian Disturbance—the vulnerability
of the stream network to potentially
detrimental human activities increases
with the proximity of those activities to
the streams themselves. For this
assessment, we use a direct measure of
riparian human disturbance that tallies
eleven specific forms of human activities
and disturbances (e.g., roads, landfills,
pipes, buildings, mining, channel
revetment, cattle, row crop agriculture,
silviculture) along the stream reach, and
weights them according to how close to
the stream channel they are observed16.
The index generally varies from 0 (no
observed disturbance) to 6 (4 types of
throughout the reach; or 6 types observed on
Biological Stressors
Although most of the factors that we can clearly identify as stressors to streams and
rivers are either chemical or physical, there are aspects of the biological assemblages
themselves that we might consider stresses. Biological assemblages can be stressed
by the presence of non-native species, which can either prey on, or compete with,
native species. When non-native species become established in either vertebrate or
invertebrate assemblages, their presence conflicts with the definition of biotic integrity
that the Clean Water Act is designed to protect ("having a species composition,
diversity, and functional organization comparable to that of the natural habitat of the
region"). In many cases, non-native species have been intentionally introduced. Brown
trout and brook trout, for example, are common inhabitants of streams in higher
elevation areas of the Mountain and Xeric climatic
regions, where they have been stocked as game
fish. To the extent that non-native game fish and
amphibians compete with, and potentially exclude,
native fish, however, they might be considered a
threat to biotic integrity.
• Non-native Vertebrate Species—Whether to
consider non-native vertebrates (fish and
amphibians) as stressors may be as much a
societal issue as a scientific one. As an
illustration of this, consider that the most
commonly occurring non-native vertebrate
species in Western streams are brown trout,
brook trout, rainbow trout, common carp,
smallmouth bass, green sunfish and largemouth The bullfrog (Rana catesbeiana) is a
bass (in order of the number of stream
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An Ecological Assessment of Western Streams and River"
kilometers where they are found, but considered non-native). With the exception of
common carp, these species are all game fish, introduced intentionally by state fish
and game agencies in order to encourage sport fishing. A real dilemma develops
when we consider that the presence of game fish, despite their being intentionally
introduced, conflicts with the definition of biotic integrity that the Clean Water Act is
designed to protect. We report here on the presence of non-native fish and
amphibians as an indicator of potential stress, primarily to provide information about
how widespread they are in the West. Additional information on other kinds of
vertebrate species considered to be non-native in parts or all of the West can be
found in the EMAP West Statistical Summary6.
• Non-native Crayfish Species—Although EMAP West sampling was not designed
to sample crayfish effectively, both native and non-native crayfish species were
found in the macroinvertebrate (i.e., sampled by kick-net) and aquatic vertebrate
(i.e., sampled by electro-fishing) samples. By comparing the species list found with
records on non-native distribution, we determined the presence of three non-native
crayfish species in the EMAP West database: Orconectes virilis (a Canadian and
northern U.S. species that has moved into the Southwest), Pacifastacus leniusculus
leniusculus (native to the Northwest, but now moving into the Southwest), and
Procambarus clarkii (a Southeastern and Mexican species that has colonized much
of the West). In this Assessment, we report on the presence or absence of non-
native crayfish (any of the above-listed species), rather than their abundance,
because we cannot guarantee that they were
sampled quantitatively. Details of crayfish
data collection and interpretation can be
found in the EMAP West Statistical
Summary6.
Asian Clam—The Asian clam (Corbicula
fluminea) is primarily an economic concern
because it fouls water intake pipes. It may
also have ecological effects, but the
demonstration of these has been elusive. It is
known to compete with native clam species,
and may also compete with other filter-
feeding benthic invertebrates. Corbicula is
considered to an invasive species and if
present at all, it has the capacity to be very
abundant. EMAP West macroinvertebrate
samples frequently contain Asian clam, but
we are not confident that they are sampled
report on their presence or absence in this
The Louisiana (or red swamp)
crayfish (Procambarus clarkii) is an
invasive species from the
Southeastern U.S. and Mexico, now
found in all of the West with the
exception of the Plains
quantitatively. For this reason, we
Assessment.
Setting Expectations
In order to assess current ecological condition, we need to be able to compare what we
measure today to some estimate of what we would expect our measurements to look
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An Ecological Assessment of Western Streams incf
like in a less-disturbed world. Setting reasonable expectations for each of our indicators
is one of the greatest challenges to making an assessment of ecological condition.
Should we take a historical perspective, and try to compare our current conditions to
estimates of pre-Columbian conditions, or to pre-industrial conditions, or to conditions at
some other point in history? Or should we accept that some level of anthropogenic
disturbance is a given, and simply use the best of today's conditions as the yardstick
against which everything else is assessed?
These questions, and their answers, all relate to the concept of reference condition17'18;
what do we use as a reference, or yardstick, to assess today's condition? Because of
the difficulty of estimating historical conditions for many of our indicators, EMAP West
uses "Least-Disturbed Condition" as our reference. Least Disturbed Condition is found
in conjunction with the best available physical, chemical and biological habitat
conditions given today's state of the landscape. It is described by evaluating data
collected at sites selected according to a set of explicit criteria defining what is "best" (or
least disturbed by human activities). These criteria vary from region to region, and were
developed iteratively with the goal of identifying the least amount of ambient human
disturbance in each climatic region of the West. If done correctly, reference criteria
describe the sites whose condition is "the best of what's left" in the West.
To develop biological indicators for EMAP West, we use the chemical and physical data
we collected at each site (e.g., nutrients, chloride, turbidity, excess fine sediments,
riparian condition, etc.) to determine whether any given site is in Least Disturbed
Condition for its ecoregion. Note that we deliberately do not use data on landuse in the
watersheds for this purpose—sites in agricultural areas (for example) may well be
considered Least Disturbed, provided that they exhibit chemical and physical conditions
that are among the best for the region. Nor do we use data on the biological
assemblages themselves, since these are the primary components of the stream and
river ecosystems for which we need estimates of Least Disturbed Condition, and to use
them would constitute circular reasoning. For each of the stressor indicators, a similar
process (identifying Least Disturbed sites according to specific criteria, but excluding the
specific stressors themselves from the criteria identifying the sites) was used. Interested
readers can find more detailed information about how we determined Least Disturbed
Condition in the EMAP West Statistical Summary6 and in Appendix D.
We then use a reference site approach18' 19 to set expectations—the Least Disturbed
sites in each region are sampled using identical methods to the sites we are trying to
assess. The range of conditions found in these "reference sites" describes a distribution
of values, and extremes of this distribution are used as thresholds to distinguish sites in
relatively good condition from those that are clearly not. One common approach is to
examine the range of values (e.g., for a particular IBI) in all of the reference sites in a
region, and to use the 5th percentile of this distribution to separate the most disturbed
sites from moderately disturbed sites; similarly, the 25th percentile of the reference
distribution can be used to distinguish between moderately disturbed sites and those in
Least Disturbed Condition20'21. Details on how we set thresholds for this Assessment
can be found in Appendix D at the back of this report.
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An Ecological Assessment of Western Streams and River"
Extent of Resource
The sampling frame used to select the sites for sampling in EMAP West is based on the
perennial stream network contained in EPA's River Reach file (known as RF3). RF3 is a
digitized version of 1:100,000 scale USGS topographic maps, showing both perennial
and non-perennial streams. The total length of the RF3 stream network in the EMAP
West region that is labeled perennial is 628,625 km. A significant proportion of this total
(207,770 km, or 33%; Figure 4) was found through site evaluation and sampling to be
either non-perennial, or non-target in some other way (e.g., wetlands, reservoirs,
irrigation canals). This is an important finding for the States of the West, who are
required to report on the condition of all perennial streams under their jurisdiction; west-
wide, the total perennial stream resource is overestimated by one-third in RF3. The
level of overestimation varies greatly from one climatic region to another—more than
half (55%) of the RF3 stream length in the Xeric region was non-target, as was 33% in
the Plains, and 24% in the Mountains.
The remaining "target stream length" (420,855 km) represents the portion of the
sampling frame that meets our criteria for inclusion in this Assessment (i.e., perennial
streams and rivers). Part of the target stream length (73,967 km, or 18%) was not
Sampled Perennial Length
Access Denied
I I Inaccessible
Non-target
West-wide
Mountains
Plains
Xeric
0 50 100 150 200 250 300 350
Stream Length (km x 1000)
Figure 4. Stream length estimates (with 95% confidence intervals) for key
categories of streams in EMAP West, including target sampled (all accessible
perennial streams and rivers), and non-target (non-perennial streams, or non-
streams).
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An Ecological Assessment of Western Streams incf
accessible to sampling because crews were denied access by landowners (Figure 4).
Again, this proportion varied from one climatic region to another (16% in the Mountains;
18% in the Plains; 26% in the Xeric). An additional portion of the target stream length
(42,344 km, or 11%) was physically inaccessible due to physical barriers or other
unsafe local conditions (Figure 4). The unsampled portion of the stream resource in the
West cannot be assessed for condition—no inferences should be made that apply the
results of this Assessment to the unsampled portion of the stream population. The
remainder of the sampling frame constitutes the assessed length of stream for this
Assessment-304,544 km, representing 48% of the original frame length, and 72% of
the target stream length (Figure 4).
Ecological Condition
Results for the indicators of ecological condition (aquatic vertebrate IBI,
macroinvertebrate IBI and macroinvertebrate 0/E Index) are shown for all of the EMAP
West region, and for the three climatic regions, in Figure 5. Additional results at the ten
ecoregion level are shown in Appendix C. The same format is used to display the
results for chemical (Figure 6), physical (Figure 7) and biological habitat (Figure 8)
indicators. In all of these figures the order of the climatic regions (Plains, Xeric and
Mountains) follows the results for the vertebrate IBI, with the first region (Plains) having
the highest percentage of stream length in most-disturbed condition for this indicator.
Readers with an interest in any given climatic region should be able to scan across
pages to compare and contrast the ecological and stressor condition for that region.
West-wide, results suggest that roughly half of the stream length is in least disturbed
condition, while approximately one-quarter is in most disturbed condition, but results
vary according to which assemblage and which index is being assessed. More
important, results vary greatly by region.
Aquatic Vertebrate Biotic Integrity
In the case of aquatic vertebrates, 18% of the stream length in the West would be
considered to be in most-disturbed condition, while 44% was in least-disturbed
condition. Approximately 9% of the stream length west-wide consisted of small streams
where no fish or amphibians were collected—these streams are considered to be
'unassessed' because we cannot assume that their lack of aquatic vertebrates was due
to anything other than natural causes (i.e., small size).
One of the biggest issues for assessing vertebrate (particularly fish) data in the West is
the large numbers of streams where the presence of threatened and/or endangered fish
species limits the amount of sampling that can be conducted. West-wide, 12% of stream
length could not be sampled because crews were denied sampling permits by the
agencies responsible for protecting threatened and endangered fish species. One could
interpret the sum of stream lengths in most-disturbed condition (18%) and where
permits were denied (12%) as a measure of the total stream length in the West where
aquatic vertebrate assemblages have significant problems (i.e., 30%).
On a regional basis, the Plains climatic region clearly has the largest proportion of
streams in most disturbed condition with respect to aquatic vertebrates (50%), but the
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An Ecological Assessment of Western Streams ind Bfi
smallest proportion where threatened and endangered species issues precluded
sampling (0%). The Xeric region has 35% of stream length in most-disturbed condition,
and an additional 13% where sampling permits were denied, for a total of 48% with
aquatic vertebrate problems. The Mountain region has the lowest proportion in most-
disturbed condition of any climatic region (9%), and was very similar to the Xeric in its
amount of threatened and endangered species issues (14% of stream length in the
Mountains). The very large total length of streams in the Mountains creates a situation
where west-wide results largely reflect the condition of Mountain streams.
Macroinvertebrate Biotic Integrity
West-wide, 27% of stream length is considered to be in most-disturbed condition with
respect to macroinvertebrate biotic integrity. At most of the scales used in this
assessment, there is a slightly larger proportion of stream length in most-disturbed
condition for macroinvertebrates than for aquatic vertebrates. This generalization may
be influenced by the amount of stream length that is unassessed for vertebrates—if
streams with threatened and endangered fish species (and therefore unassessed) are
included in the proportion of stream length with aquatic vertebrate assemblages in most
disturbed condition, then lack of vertebrate biotic integrity would appear as the more
common problem.
The Xeric climatic region has the largest proportion of streams in most-disturbed
condition for macroinvertebrates (46%), followed by the Plains (42%) and Mountains
(20%). The regions in Figure 5 are ordered from 'worst' to 'best' according to the aquatic
vertebrate results. If the order had been determined by the macroinvertebrate results,
the ranking of the regions would have been Xeric>Plains>Mountains.
Macroinvertebrate O/E
Roughly 17% of stream length west-wide has 50% or fewer of the reference taxa we
expect to see in the macroinvertebrate assemblages. As was the case for the
macroinvertebrate IBI, the climatic region with the largest proportion of high-taxa-loss
streams was the Xeric (33%), followed by the Plains (23%) and the Mountains (13%). At
all of the scales used in this Assessment (west-wide, the three climatic regions, and the
ten ecoregions (see Appendix C)), the O/E results follow closely the macroinvertebrate
IBI, suggesting that taxa loss, as measured by our O/E index, is a good indicator of
biotic integrity15.
Stressor Condition
The summary results for indicators of chemical, physical and biological habitat are
shown in Figures 6 through 8. These figures are formatted identically to Figure 5, so
that west-wide and regional results can be compared across all indicators. The order of
the regions is also the same, with the climatic regions listed from worst to best
according to the aquatic vertebrate IBI results in Figure 5.
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An Ecological Assessment of Western Streams and River"
Biotic Integrity of
Aquatic Vertebrates
Biotic Integrity of
M aero in verte b rates
Loss of
Macroinvertebrate Taxa
West-wide
(305,550 km)
0 10 20 30 40 50 60 70 0 10 20 30 40 50 60 70 0 10 20 30 40 50 60 70
Xeric
(48,800 km)
t-r
Mountains
(220,050 km)
; No Permit
^B Most Disturbed
Intermediate
I Least Disturbed
0 10 20 30 40 50 60 70
> 50% Loss
20-50% Loss
< 20% Loss
% of Stream Length in Region
Figure 5. Summary of results for ecological condition indicators for all of the West, and for
three climatic regions. Bars (with 95% confidence intervals) show the percentage of
stream length in each region with index scores in each condition class. Numbers in
parentheses are the total sampled perennial stream length in each region. Regional results
are sorted according to the aquatic vertebrate results, with regions at top having the
highest proportion of stream length in most disturbed condition. For aquatic vertebrates, a
small percentage of stream length in each region could not be assessed due to small
stream size: West-wide=9%; Plains=1%; Xeric=10%; Mountains=10%.
Chemical Stressors
Phosphorus: Approximately 15% of stream length west-wide was in most-disturbed
condition for phosphorus (see Appendix D for regional thresholds for all indicators), and
roughly 48% would be considered to be in least-disturbed condition for this nutrient
(Figure 6). Of the climatic regions, the Plains had the highest proportion of streams
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An Ecological Assessment of Western Streams and River"
Phosphorus
Nitrogen
Mercury in Fish
Salinity
West-wide
0 20 40 60 80 0 20 40 60 80 0 20 40 60 80 0 20 40 60 80 100
] No Data
• > 0.1 (jg/g
] < 0.1 ug/g
•I Most Disturbed
Intermediate
I I Least Disturbed
•I Most Disturbed
I Intermediate
Least Disturbed
• Most Disturbed
Intermediate
Least Disturbed
Mountains
0 20 40 60 80 0 20 40 60 80
0 20 40 60 80
0 20 40 60 80 100
% of Stream Length in Region
Figure 6. Summary of results for chemical indicators of stress for all of West and in
three climatic regions. Details of figure are as in Figure 5. Both acidity and selenium
were found in most disturbed condition in less than 1% of stream length west-wide (not
shown)
exceeding the phosphorus threshold (23%), followed by the Mountains (15%) and Xeric
(10%) regions.
Nitrogen: West-wide, nitrogen thresholds were exceeded in 15% of stream length, and
44% of streams were considered to be in least-disturbed condition with respect to
nitrogen (Figure 6). The regional and ecoregional results do not follow exactly the
pattern for phosphorus (Figure 6, Appendix C); the Plains had the highest proportion of
stream length in poor condition for nitrogen (38%), and the Xeric and Mountain climatic
regions had identical proportions (26%). In general, most regions exhibited higher
proportions of stream length in poor condition for nitrogen than for phosphorus.
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An Ecological Assessment of Western Streams and River"
Riparian
Disturbance
Riparian
Vegetation
Streambed In-Stream Habitat
Stability Complexity
West-wide
0 20 40 60 80 0 20 40 60 80 0 20 40 60 80 0 20 40 60 80
Mountains
Most Disturbed
Intermediate
Least Disturbed
Most Disturbed
Intermediate
Least Disturbed
H
4B Most Disturbed
Intermediate
! Least Disturbed
0 20 40 60 80 0 20 40 60 80 0 20 40 60 80 0 20 40 60 80
% of Stream Length in Region
Figure 7. Summary of results for physical habitat indicators for all of West and in
three climatic regions. Details of figure are as in Figure 5.
Mercury in Fish Tissue: West-wide 25% of stream length (Figure 6) had one or more
classes offish (large piscivores, large non-piscivores or small forage fish) that exceeded
the level determined to be protective of wildlife (0.1 micrograms of mercury per gram of
fish tissue (ug/g)), but another 21% could not be assessed due to the difficulty of
sampling fish in some subregions (sampling permit restrictions). Because mercury
accumulation in fish tissue is strongly affected by trophic level and size, many of the
results that exceed the 0.1 ug/g criterion were for large, piscivorous fish. Mercury
concentrations exceeding the wildlife criterion were most common in the Plains climatic
region (46% of stream length), followed by the Xeric (38%) and Mountain (17%)
regions.
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An Ecological Assessment of Western Streams and River"
Non-native
Vertebrate Species
Non-native Crayfish
Asian Clam
(13% unassessed)
West-wide
0 20 40 60 80 0 20 40 60 80
0 20 40 60 80 100
(0% unassessed)
Plains
(14% unassessed)
Xeric
Mountains
(15% unassessed)
• Common (=>10%)
1 Present (<10%)
3 Absent
i No Data
•• Present
] Absent
H] No Data
• Present
H Absent
0 20 40 60 80
0 20 40 60 80
0 20 40 60 80 100
% of Stream Length in Region
Figure 8. Summary of results for biological stressor indictors for all of West and in three
climatic regions. Details of figure are as in Figure 5.
Salinity: Roughly 6% of stream length west-wide had salinity levels considered to be in
the most disturbed range, while nearly 85% were considered to be in least-disturbed
condition (Figure 6). As was the case for many of the stressors presented in the
Assessment, the Plains climatic region had the highest proportion of stream length in
poor condition with respect to salinity (27%), followed by the Xeric region (16%). In the
Mountains, salinity was in the most disturbed range in less than 1% of stream length.
Other chemical stressors: While we focus in this assessment on the chemical
indicators described above, many additional chemical variables were measured in
EMAP West, and two potential chemical stressors deserve mention:
&•< Acidity (either from acidic deposition or mining) can be a concern in many parts of
the U.S. None of the EMAP probability sites was acidic (defined as having an Acid
Neutralizing Capacity [ANC] less than 0 microequivalents per liter), and less than 1%
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An Ecological Assessment of Western Streams incf
of stream length in the West would be considered likely to be acidic during high
runoff periods such as spring snowmelt (ANC < 50 microequivalents per liter).
<^< Selenium is a toxic ion that can accumulate in wildlife. Based on the proposed EPA
chronic criterion for selenium in water (5 parts per billion), less than 1% of stream
length (and in each of the climatic regions) exhibits toxic levels of selenium.
Physical Habitat Stressors
Riparian Disturbance: Levels of riparian disturbance exceeded the regional thresholds
in 47% of stream length west-wide (Figure 7). In the climatic regions, the highest
proportion of stream length with high riparian disturbance was the Xeric (77%), followed
by the Plains (62%) and the Mountains (38%). One of the most striking findings of this
Assessment is the widespread distribution of riparian disturbance, especially in the
Xeric region, where more than three-quarters of stream length has significantly more
riparian disturbance than is found in reference sites. The same is true of nearly two-
thirds of the stream length in the Plains.
Riparian Vegetation: West-wide 13% of stream length had severely simplified riparian
vegetation (Figure 7). The Xeric (28%) and Plains (27%) climatic regions had roughly
equal proportions of stream length with riparian vegetation in most-disturbed condition.
Only a small proportion of streams (7%) in the Mountain climatic region had riparian
vegetation in most-disturbed condition. It is worth noting that these estimates are
considerably smaller than those for riparian disturbance, suggesting that land managers
have done a relatively good job of preserving riparian vegetation, even along streams
where disturbance from roads, agriculture, grazing, etc., is widespread.
Streambed Stability: Across the West, roughly 26% of stream length exhibited
problems with sedimentation, with the highest proportion of streams exceeding the
thresholds in the Plains (40%) and Xeric (36%) climatic regions (Figure 7). While
streams with either very low or very high streambed stability can be considered to be in
the most-disturbed category, the vast majority of the stream length with streambed
stability problems exhibit low stability, indicating that their substrates are dominated by
finer sediments than expected.
In-Stream Habitat Complexity: Degraded habitat complexity was found in 17% of
stream length west-wide (Figure 7). In the climatic regions, the highest proportions of
habitat complexity in most-disturbed condition were found in the Plains (38%) and Xeric
(27%) regions. Simplification of in-stream habitat was found in only 12% of stream
length in the Mountains.
Other physical habitat stressors: We focus in this assessment on the physical habitat
indicators that are well understood and can be easily assessed. Additional indicators will
be possible in future EMAP West assessments, but have not been sufficiently
developed at this time. Two obvious examples about which EMAP scientists are often
asked are stream incision (i.e., arroyo formation) and hydrologic alteration (water
withdrawals, altered flow regimes, and agricultural return-flow). In both of these cases,
the greatest difficulty in interpreting possible indicators of stress results from the need to
separate natural variability from anthropogenic effects. As these indicators, and their
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An Ecological Assessment of Western Streams incf
geographic variability, become better understood, we will be better able to include them
in future assessments.
Biological Stressors
Non-native Vertebrate Species: Non-native fish and/or amphibians were common
(i.e., they represented more than 10% of individuals collected at a site) in roughly 34%
of stream and river length west-wide (Figure 8). Differences among the climatic regions
were not large in the case of this indicator, with the Xeric (46%), Plains (37%) and
Mountains (31%) climatic regions all showing widespread presence of non-native
vertebrate species. Much larger differences were found between ecological regions (see
Appendix C).
Non-native Crayfish: One or more species of non-native crayfish were present in 2%
of stream length west-wide. They were completely absent from the Plains climatic
region. All of the areas with significant stream length where non-native crayfish were
found are in the Southwestern states (see detailed results in Appendix C). This probably
reflects the fact that two of the three species are considered native to the northern
portion of the EMAP West region, and the third species primarily invades warm water
habitats.
Asian Clam: the Asian clam was found in just over 2% of the stream length west-wide.
Like non-native crayfish, they are primarily found in the Xeric and southwestern areas of
the EMAP West region.
Other biological stressors: Although they do not lend themselves to the reporting
format of the rest of EMAP West data, crews also collected data on the presence or
absence of 12 invasive plants in the riparian areas adjacent to each stream reach
(Common Burdock, Giant Reed, Cheatgrass, Musk Thistle, Canada Thistle, Teasel,
Russian-olive, Leafy Spurge, English Ivy, Reed Canary Grass, Himalayan Blackberry
and Salt Cedar). The list of target species varied from state to state, as described in the
Statistical Summary6; on average field crews were looking for 8 of these species within
a particular state. This list of 12 species is only a subset of the full set of plants invading
western riparian areas; as a result, the data are of great use in evaluating these
particular species in the region, but cannot be used to asses the status of riparian plant
invasions throughout the region. West-wide, 34% of stream length had one or more
invasive riparian plant species present.
Ranking of Stressors
An important prerequisite to making wise policy and management decisions is an
understanding of the relative magnitude or importance of potential stressors. There are
multiple ways that we might choose to define "relative importance" with stressors. One
aspect to consider is how common each stressor is—i.e., what is the extent, in
kilometers of stream, of each stressor and how does it compare to the other stressors?
We might also want to consider the severity of each stressor—i.e., how much effect
does each stressor have on biotic integrity, and is its effect greater or smaller than the
effect of the other stressors? Because each view provides important input to policy
decisions, we present separate rankings of the relative extent and the relative severity
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An Ecological Assessment of Western Streams mvA
Riparian Disturbance
Non-native Vertebrates
Nitrogen
Stream bed Stability
Mercury in Fish
Habitat Complexity
Phosphorus
Riparian Vegetation
Salinity
Asian Clam
Non-native Crayfish
0% 10% 20% 30% 40% 50% 60% 70% 80% 90%
% of Stream Length
Riparian Disturbance
Non-native Vertebrates
Nitrogen
Streambed Stability
Mercury in Fish
Habitat Complexity
Phosphorus
Riparian Vegetation
Salinity
Asian Clam
Non-native Crayfish !<1%
-162%
i46%
Plains
0% 10%. 20% 30% 40% 50% 60% 70% 80% 90%
Riparian Disturbance j
Non-native Vertebrates
Nitrogen
Streambed Stability
Mercury in Fish
Habitat Complexity
Phosphorus
Riparian Vegetation
Salinity
Asian Clam
Non-native Crayfish |BB~'7%
-i 77%
i46%
128%
Xeric
0% 10% 20% 30% 40% 50% 60% 70% 80% 90%
Riparian Disturbance
Non-native Vertebrates
Nitrogen
Streambed Stability
Mercury in Fish
Habitat Complexity
Phosphorus
Riparian Vegetation
Salinity (<1%
Asian Clam ||H2%
Non-native Crayfish |ii%
38%
Mountains
0% 10% 20% 30% 40% 50% 60% 70% 80% 90%
% of Stream Length
Figure 9. Relative extent of stressors (proportion of stream length with stressor in most
disturbed condition) west-wide, and each climatic region. The order of stressors (from
highest to lowest percent in most-disturbed condition) is set by the west-wide results
and is consistent in each panel.
of stressors to flowing waters in the West. Ideally, we'd like to combine these two
factors (extent and effect) into a single measure of relative importance. We currently
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An Ecological Assessment of Western Streams ind Bfi
have no methodology for combining the two rankings, and so present both with a
discussion of their implications.
Relative Extent
Figure 9 shows the EMAP West stressors ranked according to the proportion of stream
and river length for each that is in most-disturbed condition. Results are presented for
all of the West (top panel) and for each climatic region, with the stressors ordered (in all
panels) according to their relative extent west-wide.
Riparian disturbance is the most pervasive stressor west-wide, and in each of the
climatic regions. Across all of the West, fully 47% of the stream length shows significant
signs of riparian disturbance. In the Xeric region, this proportion climbs to 77%, while in
the Plains, 62% of stream length is considered to be in most disturbed condition with
respect to riparian disturbance. Even in the Mountains, where levels of disturbance are
in general lower than the other climatic regions, riparian disturbance is found in 38% of
the stream length.
The least common stressors are the two non-native macroinvertebrate groups (non-
native crayfish and Asian clam), where only 2% of stream length west-wide is affected.
Only in the Xeric region does either of these indicators suggest a relatively widespread
problem: 7% of stream length in the Xeric region had non-native crayfish taxa present.
Between these two extremes (riparian disturbance vs. non-native macroinvertebrates),
the different types of stressors (chemical, physical and biological) rank without any
particular pattern. The top three stressors west-wide are representatives of the physical
(riparian disturbance), biological (non-native vertebrates) and chemical (nitrogen)
classes of stressor. We cannot conclude from this analysis that, for example, physical
habitat is more commonly found in most disturbed condition than either chemical or
biological habitat.
Three stressors occur consistently near the top of the rankings in every panel of Figure
9: riparian disturbance, streambed instability and mercury in fish tissue are among the
five most common stressors west-wide and in each climatic region. Elevated mercury
concentrations in fish are thought to be the result of atmospheric deposition; because
elevated rates of mercury deposition are widespread, one might expect mercury
contamination of fish tissue to be elevated in all regions of the West, which it is.
Riparian disturbance and streambed instability, on the other hand, result from local
disturbance. In fact, disturbance of riparian areas is a likely contributor to erosion and
excess fine sediments in streams, resulting in a close association between the two
indicators.
Relative Risk
In order to address the question of severity of stressor effects, we borrow the concept of
"relative risk" from medical epidemiology, because of the familiarity of the language it
uses. We have all heard, for example, that we run a greater risk of developing heart
disease if we have high cholesterol levels. Often such results are presented in terms of
a relative risk ratio—e.g., the risk of developing heart disease is four times higher for a
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An Ecological Assessment of Western Streams incf
person with total cholesterol level of 300 mg than for a person with total cholesterol of
150mg.
In Figure 10 we present relative risk values for the biological and stressor data on
streams in the West. The relative risk values we present can be interpreted in exactly
the same way as the cholesterol example—how much more likely is a stream to have
poor biotic integrity if a stressor is present (or found in high concentrations) than if it is
absent (or found in low concentrations). In technical terms, the relative risk ratio
represents the proportional increase in the likelihood of finding a biological indicator in
the most-disturbed class when the stressor's condition in the same stream is also in the
most-disturbed class (see Appendix E for details of relative risk calculation). Because
different biological assemblages and different aspects of those assemblages (e.g., biotic
integrity vs. taxa loss) are expected to be affected by different stressors, relative risk is
calculated separately for each of the ecological condition indicators presented in this
Assessment. A relative risk value of 1.0 indicates that there is no association between
the stressor and the biological indicator, while values very much greater than one
suggest greater relative risk. We also calculate confidence intervals (shown as brackets
in Figure 10) for each ratio, in order to focus the discussion only on the most significant
relative risks. When the confidence intervals for any given ratio fall below a value of
one, we do not consider the relative risk to be statistically significant.
The significant relative risks in Figure 10 give us an idea both of how severe each
stressor's effect on the biota is, and which stressors we might want to focus on when a
given assemblage is in poor ecological condition. For the entire West, several stressors
stand out as having impacts of concern for the biotic integrity of both aquatic vertebrates
and macroinvertebrates. Excess nitrogen, excess phosphorus and excess salinity all
have relative risks greater than three for both assemblages. In the case of aquatic
vertebrates, mercury also shows an elevated risk ratio. The geographic differences in
relative risk are interesting. In general, Plains regions are dominated by high relative
risks for excess nitrogen and phosphorus. The Xeric and Mountain regions appear to
have a broader range of stressors that present high relative risks to the biota.
In an assessment of relative risk based on cross-sectional survey data (as opposed to
data from a controlled experiment) it is impossible to separate completely the effects of
individual stressors that often occur together. For example, streams with high nitrogen
concentrations often exhibit high phosphorus as well; streams with high riparian
disturbance often have sediments far in excess of expectations. In the case of EMAP
West, the presence of the Asian clam is associated with poor biotic integrity for both
vertebrates and macroinvertebrates, and with high macroinvertebrate taxa loss. While it
might be tempting to conclude that the presence of this non-native mollusk is affecting
the community structure of streams, it is equally likely that the kinds of streams where
Asian clam has become established are places where biotic integrity is typically low due
to the presence of many other stressors. The analysis presented in Figure 10 treats the
stressors as if they occur in isolation, even though we know they do not. We do not
currently have an analytical technique to separate the effects of correlated stressors,
other than to point out in the discussion where co-occurrence of stressors should be
considered in the interpretation of the assessment.
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An Ecological Assessment of Western Streams and Rivers
Relative Extent
Riparian Disturbance
Streambed Stability
Riparian Vegetation
Habitat Complexity
Nitrogen
Phosphorus
Mercury in Fish
Salinity
Non-native Vertebrates
West-Wide Non-native Crayfish
Asian Clam
0% 20% 40% 60% 80%
% in Most Disturbed Condition
Riparian Disturbance -j
Streambed Stability
Riparian Vegetation
Habitat Complexity
Nitrogen
Phosphorus
Mercury in Fish
Salinity
Non-native Vertebrates
Non-native Crayfish
Plains Asian Clam
Riparian Disturbance
Streambed Stability
Riparian Vegetation
Habitat Complexity
Nitrogen
Phosphorus
Mercury in Fish
Salinity
Non-native Vertebrates
Non-native Crayfish
Asian Clam
Aquatic Vertebrate Integrity Macroinvertebrate Integrity Macroinvertebrate Taxa Loss
345
Relative Risk
345
Relative Risk
345
Relative Risk
Xeric
Riparian Disturbance
Streambed Stability
Riparian Vegetation
Habitat Complexity
Nitrogen
Phosphorus
Mercury in Fish
Salinity
Non-native Vertebrates
Mountains Non-native Crayfish
Asian Clam
123456
7
3
1
12 1
3456
Relative Risk
1
345
Relative Risk
0% 20% 40% 60% 80% 123456
% in Most Disturbed Condition Relative Risk
Figure 10. Relative extent and relative risk of stressors west-wide and in three climatic regions. Stressors are grouped into general classes
(physical, chemical and biological habitat). Scales for all relative risk panels are identical, with the exception of the Aquatic Vertebrate IBI in the
Mountains, where one extremely high ratio necessitates a different scale. Relative risk ratios below 1.0 are not shown. 95% lower confidence
bounds are shown to indicate significance of ratios—intervals that encompass 1.0 are not considered significant.
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An Ecological Assessment of Western Streams incf
Combining Extent and Relative Risk
The most comprehensive assessment of the effect of stressors on ecological condition
comes from combining the relative extent and relative risk results (Figure 10)—stressors
that pose the greatest risk to individual biotic indicators will be those that are both
common (i.e., they rank high in terms of extent in Figure 9) and whose effects are
potentially severe (i.e., exhibit high relative risk ratios in Figure 10). The analogies in
human health persist. To make the greatest overall improvement in human health, one
would focus on factors that are high both in terms of their relative risk (e.g., obesity) and
their occurrence (e.g., obesity occurs at the 50% level in every state). In the case of
EMAP West, we have tried to facilitate this combined evaluation of stressor importance
by including side-by-side comparisons of relative extent and relative risk in Figure 10.
A quick examination of the west-wide results suggests some common patterns among
the biological indicators. In the case of aquatic vertebrates, the four highest relative
risks are for chemical stressors (mercury, salinity, nitrogen and phosphorus, in order of
their relative risk ratios). Of these, only nitrogen and mercury occur in more than 20% of
stream length, making them possible targets for management decisions. Riparian
disturbance is the most common stressor, and has a comparatively moderate relative
risk ratio for aquatic vertebrates (2.5); the combination of widespread occurrence and
significant, though moderate, relative risk may also make it a target for restoration
efforts aimed at fish.
For both macroinvertebrate indices, nitrogen and phosphorus exhibit high relative risks,
but nitrogen is nearly twice as common, suggesting that management decisions aimed
at reducing nitrogen runoff to streams could have broad positive impact on
macroinvertebrate biotic integrity, and prevent further taxa loss. High salinity, where it
occurs, is strongly associated with poor biotic integrity (relative risk > 3), but its rarity
(ca. 6% of stream length west-wide) suggests that focusing on reducing salinity might
only make sense in local situations. As in the case for aquatic vertebrates, riparian
disturbance exhibits a moderate relative risk (2.5 to 3) for macroinvertebrates, but is so
widespread that it might be a reasonable target for widespread restoration efforts.
At the scale of the EMAP West climatic regions, small sample sizes make it more
difficult to draw clear conclusions. Nitrogen is the stressor that exhibits the highest
relative risk in the Plains for all biological indicators, but it is not statistically significant
for any of them. Salinity shows a significant relative risk value for biotic integrity of
macroinvertebrates in the Plains and Xeric regions, as well as for fish in the Xeric
region—it occurs in more than 25% of stream length in the Plains, suggesting that is the
area most likely to benefit from salinity control efforts. High salinity is less common in
the Xeric (16% of stream length), but because it might pose a risk to both fish and
macroinvertebrates, land managers may choose to focus control efforts in the Xeric
region as well as the Plains.
In the Mountains, many of the stressors exhibit significant relative risks. For fish,
mercury, Asian clam presence, salinity and phosphorus all have ratios over 5. Of these,
mercury is the most common. For macroinvertebrate biotic integrity, phosphorus,
nitrogen, Asian clam and riparian disturbance all exhibit relative risk values near 4 or
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An Ecological Assessment of Western Streams ind Bfl
above. Of these, riparian disturbance is the most obvious target for restoration efforts—
it is the most common stressor in the Mountains, occurring in 38% of stream length.
Conclusions
The Western U.S. is an enormous and diverse landscape. Not surprisingly, the
ecological condition of its streams and rivers varies widely geographically. The vast
majority (i.e., more than 70%) of stream and river length in the West is located in the
mountainous areas, where the condition of the biology is relatively good. The three
measures of biological condition we use in this report range from 17% to 26% (of
stream length) in most-disturbed condition for the mountainous areas of the West. The
poorest overall condition is probably found in the Plains, where aquatic vertebrates
exhibit most-disturbed biotic integrity in ca. 45% of stream length; the macroinvertebrate
indices suggest 24% to 42% of the Plains stream resource is in most-disturbed
condition. The Plains, however, is the region with the fewest streams (in terms of
length—12% of the west-wide total). In the Xeric region, biological conditions are
intermediate between the Mountains and the Plains, with 35-45% of stream length in
most-disturbed condition for the biological indicators. Xeric streams represent about
16% of the total stream length in the West. One surprising conclusion to be drawn from
all of this is that, while the Plains have the highest proportion of their stream length with
poor biotic integrity, there are more kilometers of streams in the Mountains with poor
biotic integrity than anywhere else in the West, because stream the resource is so much
more extensive there.
Of the potential stressors we examine in this report, disturbance of riparian areas is by
far the most wide-spread. Just under half (47%) of stream length west-wide has riparian
disturbance in the most-disturbed category, but this proportion ranges from 38% in the
Mountains to more than three-quarters of stream length (77%) in the Xeric region.
Readers may be surprised to learn that mercury in fish tissue is also a widespread
stressor. Using a mercury criterion intended to protect fish-eating wildlife (e.g., river
otters), we find that 21% of stream length west-wide exceeds the criterion, but that this
proportion is as high as 46% in the Plains and 38% in the Xeric region. Nutrients are
also common stressors in the West, with nitrogen concentrations found in the most-
disturbed category in 27% of stream length west-wide, but in 38% of the Plains stream
length.
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An Ecological Assessment of Western Streams ind Bfl
Appendix A: References
EMAP Stream and River Sampling Methods
1. Peck, D. V., Averill, D. K., Herlihy, A. T., Hughes, R. M., Kaufmann, P. R., Klemm,
D. J., Lazorchak, J. M., McCormick, F. H., Peterson, S. A., Cappaert, M. R., Magee,
T. & Monaco, P. A. (2005). Environmental Monitoring and Assessment Program -
Surface Waters Western Pilot Study: Field Operations Manual for Non-Wadeable
Rivers and Streams. EPA Report EPA600/R-05/xxx, U.S. Environmental Protection
Agency, Washington, DC.
2. Peck, D. V., Herlihy, A. T., Hill, B. H., Hughes, R. M., Kaufmann, P. R., Klemm, D.
J., Lazorchak, J. M., McCormick, F. H., Peterson, S. A., Ringold, P. L, Magee, T. &
Cappaert, M. R. (2005). Environmental Monitoring and Assessment Program -
Surface Waters Western Pilot Study: Field Operations Manual for Wadeable
Streams. EPA Report EPA 600/R-05/xxx, U.S. Environmental Protection Agency,
Office of Research and Development, Washington, DC.
Probability Designs
3. Olsen, A. R., Sedransk, J., Edwards, D., Gotway, C. A., Liggett, W., Rathbun, S.,
Reckhow, K. H. & Young, L. J. (1999). Statistical issues for monitoring ecological
and natural resources in the United States. Environmental Monitoring and
Assessment 54, 1 -45.
4. Stevens Jr., D. L. (1997). Variable density grid-based sampling designs for
continuous spatial populations. Environmetrics 8, 167-195.
5. Stevens Jr., D. L. & Urqhart, N. S. (2000). Response designs and support regions in
sampling continuous domains. Environmetrics 11, 11-41.
EMAP West
6. Stoddard, J. L., Peck, D. V., Olsen, A. R., Larsen, D. P., Van Sickle, J., Hawkins, C.
P., Hughes, R. M., Whittier, T. R., Lomnicky, G., Herlihy, A. T., Kaufmann, P. R.,
Peterson, S. A., Ringold, P. L., Paulsen, S. G. & Blair, R. (2005). Environmental
Monitoring and Assessment Program (EMAP): Western Streams and Rivers
Statistical Summary. EPA Report EPA600/R-05/xxx, U.S. Environmental Protection
Agency, Washington, DC.
Ecological Regions
7. Omernik, J. M. (1987). Ecoregions of the conterminous United States. Annals of the
Association of American Geographers 77, 118-125.
Indices of Biotic Integrity
8. Karr, J. R. & Dudley, D. R. (1981). Ecological perspective on water quality goals.
Environmental Management 5, 55-68.
9. Frey, D. G. (1977). The integrity of water - an historical approach. In The Integrity of
Water. (Ballentine, S. K. & Guarala, L. J., Eds), pp. 127-140. U.S. Environmental
Protection Agency, Washington DC.
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An Ecological Assessment of Western Streams ind Bfl
10. Barbour, M. T., Stribling, J. B. & Karr, J. R. (1995). Multimetric approach for
establishing biocriteria and measuring biological condition. In Biological assessment
and criteria: tools for water resource planning and decision making. (Davis, W. S. &
Simon, T. P., Eds), pp. Chapters, pg. 63-77. Lewis, Boca Raton, FL.
11. Karr, J. R. (1981). Assessment of biotic integrity using fish communities. Fisheries
6,21-27.
Observed/Expected Models
12. Van Sickle, J., Hawkins, C. P., Larsen, D. P. & Herlihy, A. T. (2005). A null model
for the expected macroinvertebrate assembalge in streams. Journal of the North
American Benthological Society 24, 178-191.
13. Wright, J. F. (2000). An introduction to RIVPACS. In Assessing the Biological
Quality of Fresh Waters. (Wright, J. F., Sutcliffe, D. W. & Furse, M. T., Eds), pp. 1-
24. Freshwater Biological Association, Ambleside, UK.
14. Hawkins, C. P., Morris, R. H., Hogue, J. N. & Feminella, J. W. (2000). Development
and evaluation of predictive models for measuring the biological integrity of streams.
Ecological Applications 10, 1456-1477.
15. Hawkins, C. P. (In Press (2005)). Quantifying biological integrity with predictive
models: comparisons with three other assessment methods. Ecological
Applications.
Physical Habitat
16. Kaufmann, P. R., Levine, P., Robison, E. G., Seeliger, C. & Peck, D. (1999).
Quantifying Physical Habitat in Wadeable Streams. EPA Report EPA/600/3-
88/021 a, U.S. EPA, Washington, D.C.
Reference Condition
17. Stoddard, J. L, Larsen, D. P., Hawkins, C. P., Johnson, R. K. & Morris, R. H. (In
Press (2005)). Setting expectations for the ecological condition of running waters:
the concept of reference condition. Ecological Applications.
18. Bailey, R. C., Morris, R. H. & Reynoldson, T. B. (2004). Bioassessment of
Freshwater Ecosystems: Using the Reference Condition Approach. Kluwer
Academic Publishers, New York.
19. Hughes, R. M. (1995). Defining acceptable biological status by comparing with
reference conditions. In Biological Assessment and Criteria: Tools for Water
Resource Planning and Decision Making for Rivers and Streams. (Davis, W. &
Simon, T., Eds), pp. Chapter 4, pg. 31-47. Lewis, Boca Raton, FL.
Other EMAP Assessments
20. Stoddard, J. L., Herlihy, A. T., Hill, B. H., Hughes, R. M., Kaufmann, P. R., Klemm,
D. J., Lazorchak, J. M., McCormick, F. H., Peck, D. V., Paulsen, S. G., Olsen, A. R.,
Larsen, D. P., Van Sickle, J. & Whittier, T. R. (In Press). Mid-Atlantic Integrated
Assessment (MAIA)-State of the Flowing Waters Report. EPA Report EPA 600/R-
05/xxx, U.S. Environmental Protection Agency, Washington, DC.
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An Ecological Assessment of Western Streams incf
21. U.S. Environmental Protection Agency (2000). Mid-Atlantic Highlands Streams
Assessment, p. 64. EPA Report EPA/903/R-00/015, U.S. Environmental Protection
Agency, Region 3, Philadelphia, PA.
Biological Condition Gradient/Quality of Reference Sites
22. Lattin, P. D. (In Preparation). A process for characterizing watershed level
disturbance using orthophotos.
23. Davies, S. P. & Jackson, S. K. (In press). The Biological Condition Gradient: A
conceptual model for interpreting detrimental change in aquatic ecosystems.
Ecological Applications.
Toxic contaminant criteria
24. Lazorchak, J. M., McCormick, F. H., Henry, T. R. & Herlihy, A. T. (2003).
Contamination offish in streams of the Mid-Atlantic Region: an approach to regional
indicator selection and wildlife assessment. Environmental Toxicology and
Chemistry 22, 545-553.
Relative Risk
25. Van Sickle, J., Stoddard, J. L, Paulsen, S. G. & Olsen, A. R. (In Press). Using
relative risk to compare the effects of aquatic stressors at a regional scale.
Environmental Management.
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An Ecological Assessment of Western Streams ind Bfl
Appendix B: Quality Assurance
EMAP West included extensive quality assurance (QA), designed to ensure that the
data were of the highest quality. Interested readers are referred to the EMAP West
Statistical Summary6 for details of EMAP's QA program and its results. Some key
elements of the QA program include:
£*•« Field protocols and training—both wadeable and non-wadeable sites were
sampled according to extensively documented and tested field methods1'2. Over
the course of the study, more than 200 state, federal and contract crew members
were trained in these methods directly by the EMAP scientists that developed
them. Training included annual refresher courses for returning crew members.
<^< Laboratory QA and inter-laboratory comparisons—the laboratories for analyzing
water chemistry, fish tissue contaminants and macroinvertebrate samples
developed and followed extensive internal QA procedures. In addition, all labs
participated in inter-laboratory comparisons (e.g., by analyzing audit samples).
$*< Vouchering and archiving of aquatic vertebrates—wherever possible,
identification of vertebrate species was done in the field, with vouchering of
specimens from each taxon found. Taxonomic identification of preserved fish and
amphibians was conducted by the Smithsonian Institute's National Museum of
Natural History, specimens were also archived by this organization.
£"< Automated entry of field data—EMAP utilized standard field forms for data
collection in the field, with centralized data entry via scanning and automated
generation of electronic data files. This system has extensive internal QA and
consistency checks.
£*< Internal consistency checks for physical habitat, chemistry and biological data—
all data generated as part of this project underwent internal consistency checks
to verify the validity of the data.
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An Ecological Assessment of Western Streams incf
Appendix C: Ecoregional Results
In the main body of this report, we present results for all of the EMAP West region, and
for each of three climatic regions. In this appendix, we present results for the ten
ecological regions shown in Figure 3. These results are presented in exactly the same
formats as previously, with indicators of ecological condition (Figure 11), and chemical,
physical and biological habitat indicators (Figures 13, 14 and 15) shown on sequential
pages to allow the reader to compare indicators for any ecoregion of interest. In the
interest of space, we present only limited interpretation of these ecoregional results, but
encourage the reader to study the figures and draw his or her own conclusions.
Among the conclusions to be drawn from the ecoregional results:
<^< The Cultivated Plains has the highest proportion of length in most-disturbed
condition for aquatic vertebrates (63%), followed by the Southwestern Mountains
(56%) and Eastern Xeric Plateaus (50%). The smallest proportions of streams in
most-disturbed condition (with respect to aquatic vertebrates) were found in the
Pacific Northwest (7%) and Northern Rockies (9%) (Figure 11).
&< The Xeric Northern Basins had the highest proportion of stream length where fish
could not be sampled due to permit restrictions (31%); most of these restrictions
were due to the presence of endangered bull trout. If combined with the proportion in
most-disturbed condition for biotic integrity, the Xeric Northern Basins would have
47% of stream length with aquatic vertebrate problems.
<^< As was the case for climatic regions, macroinvertebrate IB I results do not mirror the
vertebrate results at the finer ecoregional level (Figure 11). The Xeric California
Lowlands (53%) and Xeric Southern Basin and Range (53%) have the highest
proportions in most-disturbed condition for macroinvertebrates. The Xeric California
Lowlands, in particular, shows a stark contrast between vertebrate and
macroinvertebrate results, perhaps reflecting the presence of different stressors to
which these two assemblages react. At the less disturbed end of the scale, the
mountainous ecoregions (e.g., Northern Rockies [17%] and Pacific Northwest [22%])
have the smallest proportions of stream length in poor condition, but the highest total
lengths of streams and rivers (100,900 km and 84,200 km, respectively).
fr* The rank order of ecoregions (highest to lowest percentage in most-disturbed
condition) for the macroinvertebrate 0/E index is very similar to that of the
macroinvertebrate IBI (Figure 11). The highest proportion of stream length with more
than 50% taxa loss is found in the Xeric California Lowlands (53%), followed by the
Xeric Southern Basin and Range (43%). The lowest percentages are in the Southern
Rockies (11%) and Northern Rockies (12%).
<^< The Cultivated Plains has 54% of its stream length in most-disturbed condition with
respect to phosphorus (Figure 12), followed by the Southwestern Mountains (45%)
and Southern Rockies (24%). The smallest proportions of streams with high
phosphorus concentrations were found in the Xeric Eastern Plateau (6%) and Pacific
Northwest (11%).
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An Ecological Assessment of Western Streams and River"
Biotic Integrity of
Aquatic Vertebrates
Biotic Integrity of
Macroinvertebrates
Loss of
Macroinvertebrate Taxa
Cult. Plains (8,000 km)
So. West Mtns (2,850 km)
Xe. E. Plateaus (21,000 km)
Range Plains (27,150 km)
Xe. So. Basins (9,400 km)
Xe. No. Basins (11,500 km)
Xe. California (6,850 km)
So. Rockies (31,750 km)
No. Rockies (100, 900km)
Pacific Nwest (84,200 km)
I I No Permil
H Most Disturbed
I I Intermediate
I I Least Disturbed
M Most Disturbed
I I Intermediate
I I Least Disturbed
•I > 50% Loss
I I 20-50% Loss
I < 20% LOSS
0 10 20 30 40 50 60 70 80 90 0 10 20 30 40 50 60 70 80 900 10 20 30 40 50 60 70 80 90
% of Stream Length in Region
Figure 11. Summary of results for ecological condition indicators for 10 ecological
regions. Bars (with 95% confidence intervals) show the percentage of stream length in
each region with index scores in each condition class. Numbers in parentheses are the
total sampled perennial stream length in each region. Regional results are sorted
according to the aquatic vertebrate results, with regions at top having the highest
proportion of stream length in most disturbed condition. In each region a small percentage
of stream length could not be assessed for aquatic vertebrate due to insufficient sampling
or small stream size. These percentages ranged from 0% in the Cultivated Plains to nearly
20% in the Southern Rockies.
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An Ecological Assessment of Western Streams and River"
Phosphorus Nitrogen Mercury in Fish Salinity
Cultivated Plains
Southwestern Mtns.
Xeric E. Plateaus
Rangeland Plains
Xeric So. Basins
Xeric No. Basins
Xeric Calif. Lowlands
rr-jr—
Southern Rockies
Northern Rockies
Pacific Northwest
• Most Disturbed
I I Intermediate
I I Least Disturbed
±H
I 1 No Data
H »0lpg.'g
CD
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An Ecological Assessment of Western Streams and River"
Riparian Riparian
Disturbance Vegetation
Streambed
Stability
In-Stream Habita
Complexity
Cultivated Plains
Southwestern Mtns.
Xeric E. Plateaus
Rangeland Plains
Xeric So. Basins
i
Xeric No. Basins
Xeric Calif. Lowlands
Southern Rockies
Northern Rockies
^H Most Disturbed
I I Intermediate
I I Least Disturbed
Pacific Northwest
0 20 40 60 80 0 20 40 60 80 0 20 40 60 80 0 20 40 60 80
% of Stream Length in Region
Figure 13. Summary of results for physical habitat indicators for 10 ecological regions.
Symbols and details of figure are as in Figure 11.
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An Ecological Assessment of Western Streams and River"
Non-native
Vertebrate Species Non-native Crayfish
Asian Clam
Cultivated Plains
Southwestern Mtns.
Xeric E. Plateaus
Rangeland Plains
Xeric So. Basins
Xeric No. Basins
O;—r
Xeric Calif. Lowlands
Southern Rockies
Northern Rockies
Pacific Northwest
I I No Data
|H Present
I Absent
I I No Data
HI Present
I I Absent
^H Common (>10%)
I I Present (<10%) ,
I I Absent
0 20 40 60 80 0 20 40 60 80 0 20 40 60 80 100
% of Stream Length in Region
Figure 14. Summary of results for biological indicators of stress for 10 ecological regions.
Symbols and details of figure are as in Figure 11.
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An Ecological Assessment of Western Streams ind Bfi
<^< The Cultivated Plains (81%) and Southwestern Mountains (50%) ecoregions also
had high proportions in most-disturbed condition for nitrogen (Figure 12), while the
regions with the smallest percentages were the Northern Rockies (18%) and Xeric
Eastern Plateaus (18%).
fa The Rangeland Plains (33%), Xeric Eastern Plateaus (25%) and Xeric Southern
Basin and Range (19%) had the highest proportions of stream length with high
salinity (Figure 12). In the Northern and Southern Rockies and the Pacific Northwest,
salinity problems were virtually non-existent, with <1% of stream length exceeding
the regional criteria.
fa Riparian disturbance was most common in the Northern and Southern Xeric Basin
and Range ecoregions (81% and 82% in most disturbed condition, respectively,
Figure 13), followed by the Xeric Eastern Plateaus (77%) and Cultivated Plains
(70%). The lowest proportions of stream length with high amounts of riparian
disturbance were in the Southwestern Mountains (28%) and Southern Rockies
(31%).
fa The ecoregion with the highest proportion of stream length with Riparian Vegetation
in most-disturbed condition (Figure 13) was the Xeric Eastern Plateaus (36%),
followed by the Xeric Northern Basin and Range (30%), the Cultivated Plains (27%)
and Rangeland Plains (26%). The lowest percentages of streams with low structural
complexity in riparian areas occurred in the Xeric California Lowlands (1%) and
Pacific Northwest (3%).
<^< Three ecoregions had more than 50% of stream length in most disturbed condition
for streambed stability (Figure 13): the Xeric Southern Basin and Range (53%),
Xeric Northern Basin and Range (51%), and the Cultivated Plains (51%). Problems
with sediments were least common in the Xeric California Lowlands (4%) and
Southern Rockies (12%).
fa The Rangeland Plains was the ecoregion with the highest proportion of in-stream
habitat complexity in most-disturbed condition (40%), followed by the Eastern Xeric
Plateaus (36%) and Cultivated Plains (34%) ecoregions (Figure 13). The fewest
streams with severely simplified habitat were found in the Pacific Northwest (6% in
most-disturbed condition) and Southwestern Mountains (6%).
fa Non-native fish and/or amphibians were common (more than 10% of individuals
collected) in 80% of the stream length in the Southern Rockies ecoregion (Figure
14). The Xeric Southern Basin and Range (73%), Xeric Eastern Plateaus (59%) and
Southwestern Mountains (55%) all had abundant non-native vertebrates in more
than half their stream length. The Pacific Northwest had the smallest proportion of
stream length with high non-native abundance (13%). The Xeric Northern Basin and
Range appears to have a relatively low proportion of streams with non-natives
making up more than 10% of the assemblage (16%), but the high proportion of
unassessed streams in this ecoregion (37%) make this number unreliable.
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An Ecological Assessment of Western Streams ind Rill
fa All of the areas with significant stream length where non-native crayfish were found
(Figure 14) are in the Southwestern states: the Xeric California Lowlands (17%),
Xeric Southern Basins (16%) and Southwestern Mountains (16%).
fa Asian clams, like non-native crayfish, were primarily found in the Xeric and
Southwestern areas of the EMAP West region (Figure 14). 28% of the stream length
in the Xeric California Lowlands was populated with Asian clam, along with 21% of
the Southwestern Mountains and 7% of the Xeric Southern Basin ecoregion.
fa Among the invasive riparian plants included in EMAP West surveys (but not shown
in Figures 13-15), Cheatgrass and English Ivy were on the list of target species in all
states. West-wide, Cheatgrass was found on 11% of the stream length; its presence
varied from less than 0.1% in the Pacific Northwest ecoregion to 42% in the Xeric
Northern Basin ecoregion. West-wide English Ivy was found on less than 0.5% of
the stream length, but its presence ranged from 0% of stream length in at least six of
the ten ecoregions, to 7.7% of stream length in the Xeric California Lowlands.
The relative extent of stressors in the 10 ecological regions is illustrated shown in Figure
15, with the order of stressors set by the west-wide results shown in Figure 9, and listed
consistently in each panel of Figure 15. Among the most striking results:
fa Riparian disturbance was the most commonly occurring stressor in seven of the ten
ecological regions.
fa The Northern and Southern Xeric Basin and Range regions were typified by high
rates of habitat disturbance (riparian disturbance, streambed stability and habitat
complexity).
fa Non-native vertebrates were the first or second most common stressor in six of ten
ecoregions, three of which are mountain ecoregions.
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An Ecological Assessment of Western Streams incf
Riparian Disturbance
Non-native Vertebrates
Nitrogen
Strean*ed Stability
Mercury in Fish
Habitat Complexity
Phosphorus
Riparian Vegetation
Salinity
Asian Clam
Non-native Crayfish
Riparian Disturbance
Non-native Vertebrates
Nitrogen
Streambed Stability
Mercury in Fish
Habitat Complexity
Phosphorus
Riparian Vegetation
Salinity
Asian Clam
Non-native Crayfish
Riparian Disturbance
Non-native Vertebrates
Nitrogen
Streambed Stability
Mercury in Fish
Habitat Complexity
Phosphorus
Riparian Vegetation
Salinity
Asian Clam
Non-native Crayfish
Riparian Disturbance
Non-native Vertebrates
Nitrogen
Streambed Stability
Mercury in Fish
Habitat Complexity
Phosphorus
Riparian Vegetation
Salinity
Asian Clam
Non-native Crayfish
Riparian Disturbance
Non-native Vertebrates
Nitrogen
Streambed Stability
Mercury in Fish
Habitat Complexity
Phosphorus
Riparian Vegetation
Salinity
Asian Clam
Non-native Crayfish
Cultivated Plains
Southwestern
Mountains
Eastern Xeric
Plateaus
Southern Xeric
Basin & Range
Riparian Disturbance
Non-native Vertebrates
Nitrogen
Streambed Stability
Mercury in Fish
Habitat Complexity
Phosphorus
Riparian Vegetation
Salinity |i
Asian Clam }
Non-native Crayfish JO
Riparian Disturbance
Non-native Vertebrates
Nitrogen
Streambed Stability |H
Mercury in Fish
Habitat Complexity
Phosphorus
Riparian Vegetation
Salinity
Asian Clam
Non-native Crayfish
Riparian Disturbance
Non-native Vertebrates
Nitrogen
Streambed Stability
Mercury in Fish
Habitat Complexity
Phosphorus
Riparian Vegetation
Salinity
Asian Clam
Non-native Crayfish
Riparian Disturbance
Non-native Vertebrates
Nitrogen
Streambed Stability
Mercury in Fish
Habitat Complexity
Phosphorus
Riparian Vegetation
Salinity 1
Asian Clam
Non-native Crayfish
Riparian Disturbance
Non-native Vertebrates
Nitrogen
Streambed Stability
Mercury in Fish
Habitat Complexity
Phosphorus
Riparian Vegetation Sr<
Salinity
Asian Clam 1H-1
Non-native Crayfish |H
Northern Xeric
Basin & Range
Xeric California
Lowlands
Southern Rockies
Northern Rockies
Pacific Northwest
0% 10% 20% 30% 40% 50% 60% 70% 80% 90%
% of Stream Length
0% 10% 20% 30% 40% 50% 60% 70% 80% 90
% of Stream Length
Figure 15. Relative extent of stressors in each ecoregion of the West. Order of stressors is
the same as in Figure 9 (set by the west-wide results, with the most common stressors
west-wide at the top of each panel).
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An Ecological Assessment of Western Streams ind Bfi
Appendix D: Reference Condition and Condition Classes
In an assessment of this type there are multiple options for establishing reference
condition and deciding where to place the thresholds between condition classes. To
some extent, this discussion detracts from the real value of probability data like those
collected for EMAP West. The statistical design of EMAP West allows us to extrapolate
results for any indicator from a relatively small number of sites to the target population
of concern. In many ways, the most quantitative description of the results is the resulting
distribution (see Figure 16), or cumulative distribution function (CDF). Once this
distribution is established, thresholds can be drawn at any point in the distribution, by
any number of methods (e.g., based on best professional judgment, set by societal
values, or the distribution approach we describe below). Although presenting EMAP
West results in terms of condition classes (most-disturbed, intermediate and least-
disturbed) requires us to estimate thresholds, there is additional information present in
the CDF beyond the simple estimates of the percentages of stream length in each
class. The thresholds we use in this report, which are described in some detail in the
following pages, are based on a scientifically justifiable approach, and are repeatable.
They have been made by EMAP West scientists, in conjunction with the personnel in
EPA Regions 8, 9 and 10. But they are still just the best professional judgment of a
small group of people, with the aim of turning a continuous distribution like the one in
Figure 16 into a three discrete condition classes. Other methods are possible, and if
applied might be equally valid. The main value of a dataset like the one collected in
EMAP West is that, in the future, any such alternative thresholds can be applied to the
data to produce an Assessment based on a different set of decisions and judgments.
Cumulative Distribution Function
for Macroinvertebrate IBI
West-wide
h 300000
- 250000
ro
CD
o
- 200000 -E
- 150000
- 100000
- 50000
CO
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An Ecological Assessment of Western Streams incf
For the purposes of this assessment, we have uses a reference site approach18'19 to set
expectations:
<^< A collection of Least Disturbed sites in each region is identified using regional
reference site screening criteria. These may be either probability sites or hand-
picked sites (because they are not used in making population estimates, only to
set the reference baseline).
<^< The Least Disturbed sites are sampled using methods identical to those used at
the sites we are trying to assess.
£*< The range of conditions found in these "reference sites" describe a distribution of
values, and extremes of this distribution are used as thresholds to distinguish
sites in relatively good condition from those that are clearly not.
Of course, we can't ignore the possibility that using the Least Disturbed sites in each
region as references creates a sliding scale—it is very likely that historical development
patterns, and types of landuse that predominate in different regions, have created a
mosaic of disturbance patterns. Some ecological regions may still be dominated by
relatively undisturbed streams, while in others no sites could truly be described as
undisturbed. In the case of the West, the Mountain climatic region has a large
proportion of its stream length in relatively pristine condition. In the Plains region, on
the other hand, it is extremely difficult to find streams that have not been altered by
grazing, farming, removal or modification of riparian forests, or roads. "Least Disturbed
Conditions" are not equivalent in these two regions.
In order to calibrate these regional differences, we have tried to quantify the relative
quality of Least Disturbed reference sites in each of the climatic regions of the West.
Two of the indicators we have used to assess reference site quality are illustrated in
Figure 17 (watershed disturbance) and Figure 18 (non-tolerant macroinvertebrates).
The index of watershed disturbance in Figure 17 is developed by examining aerial
photos for each stream's watershed, and tallying the presence or absence of various
types of visible human disturbance (e.g., mining, gravel pits, roads, trails, off-road
vehicle use, row-crop agriculture, logging, grazing, etc.)22. The resulting scores range
from 0 (no disturbance visible) to 10 (heavily disturbed). Figure 17 shows the range of
disturbance scores in the Least Disturbed sites in each of the 10 ecological regions we
examine in the West. Note that the two ecoregions of the Plains have some Least
Disturbed sites with scores as high as 9, but no sites with scores of 0 or 1 (in fact the
Cultivated Plains had no sites with values below 5). In the mountainous ecoregions, on
the other hand, zero scores were common. The range of scores in the xeric ecoregions
were generally intermediate between the Plains and Mountains. Remember that these
scores are not for all of the stream and river sites in these ecoregions, but only for the
very "best of what's left."
Figure 18 shows a similar plot for one of the key characteristics of the
macroinvertebrate assemblages in Least Disturbed sites. We calculate the percentage
of individuals found at each site that would be classified as non-tolerant (i.e., they are
classified as either sensitive or moderately sensitive to pollution). As the biological
condition at stream and river sites degrades (either through time, or across a gradient of
low to high disturbance), the dominance of the macroinvertebrate assemblage by non-
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An Ecological Assessment of Western Streams and Staff
tolerant taxa is expected to decrease23. In the case of the Least Disturbed sites in
EMAP West, the same pattern observed for disturbance at the watershed level (Figure
17) is evident in the biota—ecoregions in the Plains exhibit a pattern of more
disturbance, while ecoregions in the Mountains show relatively little. Least Disturbed
sites in the Xeric ecoregions are intermediate between the Plains and the Mountains.
Our approach for deciding what constitutes relatively good vs. relatively poor condition
in each of the three major climatic regions needs to incorporate this diminution in
reference site quality. In general, our approach has been to use the percentiles
described above (the 5th and 25th percentiles of the reference distribution) to establish
thresholds for the Mountains and Xeric climatic regions, but to relax these criteria in the
Plains. In the Plains most of our indicators are scored using the 25th and 50th
percentiles. Actual threshold values for each indicator and the percentages of the
reference distribution they represent are shown in Table B-1.
o
b
Magnitude of Local Human Disturbance at Least Disturbed Sites
10
8 -
0
8
CO 6
o>
o
c
TO
4 -
2 -
Plains
IT
T
Xeric
T *
1
Mountains
I
•V
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An Ecological Assessment of Western Streams and Wfffi
tn
CD
o c
b o
CO Z
Dominance at Least Disturbed Sites by Non-Tolerant Taxa
100
80 -
60 -
40 -
r
a! 20 H
Plains
•
Xeric
i
T
Mountains
Figure 18. The dominance of Least Disturbed sites in each ecological region by
macroinvertebrates considered to be non-tolerant. Low values suggest sites and
regions where tolerant taxa are common. High values indicate sites and regions
where many taxa are sensitive to human disturbance. Boxes, bars and symbols are
as in Figure 17.
One further detail in establishing each threshold is important to explain. For each
indicator where the reference distribution was used to estimate thresholds, the
reference site selection was carried out without referring to the results for the specific
indicator being assessed. For example, thresholds for the biological indicators were
developed from a set of Least Disturbed sites determined using the chemical and
physical habitat variables only. To avoid circularity, none of the biological data
themselves were used. The process for setting thresholds for physical habitat indicators
followed a similar philosophy-reference site criteria were redefined using a mixture of
chemical and physical variables, but avoiding the variables used in the physical habitat
index in question. A similar process was used to estimate thresholds for the chemical
stress indicators. The only exceptions to this process (using a reference site approach,
and the resulting reference distribution to estimate thresholds) were the following:
<^< For macroinvertebrate taxa loss (the 0/E Index) we used common sense
thresholds as criteria. The most-disturbed condition was defined as having lost
more than 50% of the expected taxa—most people would recognize a 50% loss
of species as significant. The intermediate class was defined as having lost
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An Ecological Assessment of Western Streams ind Bfl
between 20% and 50% of taxa, and the least-disturbed condition class included
only sites with less than 20% loss of macroinvertebrate taxa.
For mercury in fish tissue we used a published wildlife criterion (0.1 ug/g) derived
from research on mercury effects on American river otter (Lontra canadensis)24—
any site where any fish species exceeded this concentration was considered to
be in most-disturbed condition with respect to mercury.
For non-native vertebrates, the reference site approach has limited applicability.
Because non-native fish and amphibians are so widespread in the West, even
sites with the best possible chemical and physical habitat condition are likely to
have some non-native species present. For this reason, we again applied a
common sense approach to set thresholds for this indicator. We placed any site
where more than 10% of the individuals sampled were non-natives in the most-
disturbed condition class for this indicator. The intermediate class consisted of
sites with non-natives present, but where they represented less than 10% of the
individuals sampled. The least-disturbed class had sites where no non-natives
were found.
For non-native crayfish and Asian clams, where only presence or absence could
be established, the most-disturbed class consisted of all sites where one of these
non-native taxa was found. Non-natives were absent from sites in the least-
disturbed class.
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An Ecological Assessment of Western Streams ind Bfi
Table D-1. Thresholds used in this Assessment to separate condition classes, and the
approximate percentage of the reference site distribution they represent. Thresholds
were estimated separately for each climatic region; Habitat Complexity and Streambed
Stability thresholds were estimated separately at the ecoregion level in the Mountain
climatic region. Names in parentheses are variable names from the EMAP West
database.
MOUNTAINS
Aquatic Vertebrate IBI
(MMI_VERT)
Macroinvertebrate IBI
(MMI_BUG)
0/E Index
(OE_BEST)
Phosphorus
(PTL)
Nitrogen
(NTL)
Salinity
(COND)
Mercury
Riparian Disturbance
(W1JHALL)
Habitat Complexity
(XFC_NAT)
Streambed Stability
(LRBS_BW5)
Riparian Vegetation
(XCMGW)
Non-native Vertebrates
Non-native Crayfish
Asian clam
MOST-DISTURBED
Threshold
<37
<57
<0.5
>40 ug/L
>200 ug/L
>1000 uS/cm
>0.1 ug/g
>0.95
<0.18(NRock)
<0.14(PNW)
<0.31 (SRock)
<0.10(SWest)
<-1.8or>0.1 (NRock)
<-1.3or>0.6(PNW)
<-1.6or>0.3(SRock)
<-1.3or>0.6(SWest)
<0.23
>10% of Individuals
Present
Present
%
5tn
5tn
a
5tn
5tn
5tn
b
95tn
5tn
5th
5th
5th
5tn
5th
5th
5th
5tn
c
c
c
LEAST-DISTURBED
Threshold
>62
>71
>0.8
<10ug/L
<125 |jg/L
<500 |jS/cm
^0.1 |jg/g
<0.35
>0.34 (NRock)
>0.33 (PNW)
>0.56 (SRock)
>0.37 (SWest)
>-1.1 & <-0.4 (NRock)
>-0.7&<0.1 (PNW)
>-0.9 & <-0.2 (SRock)
>-0.6&<0.1 (SWest)
>0.67
Absent
Absent
Absent
%
25th
25th
a
25th
25th
25th
b
75th
25th
25th
25th
25th
25th
25th
25th
25th
25th
c
c
c
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An Ecological Assessment of Western Streams incf
Table D-1, Continued
XERIC
Aquatic Vertebrate IBI
(MMI_VERT)
Macroinvertebrate IBI
(MMI_BUG)
0/E Index
(OE_BEST)
Phosphorus
(PTL)
Nitrogen
(NIL)
Salinity
(COND)
Mercury
Riparian Disturbance
(W1JHALL)
Habitat Complexity
(XFC_NAT)
Streambed Stability
(LRBS BW5)
Riparian Vegetation
(XCMGW)
Non-native Vertebrates
Non-native Crayfish
Asian clam
MOST-DISTURBED
Threshold
<29
<47
<0.5
>175ug/L
>600 ug/L
>1000 uS/cm
>0.1 ug/g
>0.9
<0.132
<-1.7 or>0.3
<0.32
>10% of Individuals
Present
Present
%
5tn
5tn
a
5tn
5tn
5tn
b
90m
10tn
10th
5tn
c
c
c
LEAST-DISTURBED
Threshold
>40
>56
>0.8
<40 |jg/L
<200 |jg/L
<500 |jS/cm
^0.1 ug/g
<0.7
>0.270
>-0.9&<-0.1
>0.60
Absent
Absent
Absent
%
25tn
25tn
a
25tn
25tn
25tn
b
75tn
35tn
25tn
25tn
c
c
c
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An Ecological Assessment of Western Streams incf
Table D-1, Continued
PLAINS
Aquatic Vertebrate IBI
(MMI_VERT)
Macroinvertebrate IBI
(MMI_BUG)
0/E Index
(OE_BEST)
Phosphorus
(PTL)
Nitrogen
(NIL)
Salinity
(COND)
Mercury
Riparian Disturbance
(W1JHALL)
Habitat Complexity
(XFC_NAT)
Streambed Stability
(LRBS_BW5)
Riparian Vegetation
(XCMGW)
Non-native Vertebrates
Non-native Crayfish
Asian clam
MOST-DISTURBED
Threshold
<35
<41
<0.5
>300 ug/L
>1100|jg/L
>2000 |jS/cm
>o.i |jg/g
>1.3
<0.125
<-2.5or>0.3
<0.15
>10% of Individuals
Present
Present
%
25tn
25tn
a
25tn
25tn
25tn
b
75tn
25tn
10th
10th
c
c
c
LEAST-DISTURBED
Threshold
>45
>51
>0.8
<40 |jg/L
<300 |jg/L
<1 000 uS/cm
^0.1 |jg/g
<1.0
>0.359
>-1.7&<-0.5
>0.35
Absent
Absent
Absent
%
50tn
50tn
a
50tn
50tn
50tn
b
50tn
50tn
25tn
35tn
c
c
c
Thresholds for 0/E Index were not based on the reference site distribution (see text)
b Thresholds for mercury were based on a published wildlife criterion
c Thresholds for Non-native Taxa were not based on the reference site distribution (see
text)
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An Ecological Assessment of Western Streams ind Bfl
Appendix E: Estimating Relative Risk
Relative risk measures the likelihood that the most-disturbed condition of a biological
indicator will occur in streams that are also most-disturbed for a stressor20'25. We define
relative risk (RR) as the ratio of two probabilities, or 'risks':
RR
Pr(most - disturbed biological condition most - disturbed stressor condition )
Pr(most - disturbed biological condition | least - disturbed stressor condition)
where the numerator and denominator are conditional probabilities of most-disturbed
biological condition, given that sites are in either most-disturbed (numerator) or least-
disturbed (denominator) stressor condition.
Relative risk is calculated from the estimated lengths of stream that have various
combinations of biological and stressor conditions. These estimates can be arranged in
a contingency table, as illustrated below for Aquatic Vertebrate Integrity versus the
Riparian Habitat stressor.
Estimated stream length, west-wide (km)
Aquatic vertebrate
disturbance class
Least
Most
Riparian Habitat disturbance class
Least Most
51432
11112
44521
31188
From this table, the risk of finding a most-disturbed condition for aquatic vertebrates, in
streams having most-disturbed riparian habitat, is estimated to be:
311887(31188+ 44521) = 0.42
Similarly, the risk of finding a most-disturbed condition for aquatic vertebrates, in
streams having least-disturbed riparian habitat, is estimated to be:
11112/(11112 + 51432) = 0.18
Comparison of these two risks shows that a most-disturbed condition for aquatic
vertebrates has a greater risk of occurring when riparian habitat conditions are also
most disturbed (risk = 0.42) than when they are least-disturbed (risk = 0.18). Relative
risk expresses this comparison as a ratio, that is:
RR = 0.42/0.18 = 2.33
In other words, we are 2.33 times more likely to find a most-disturbed aquatic vertebrate
condition in streams with most-disturbed riparian habitat than in streams with least-
disturbed riparian habitat.
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