&EPA
United States
Environmental Protection
Agency
EPA/600/R-11/118 | October 2011 | wvwv.epa.gov/ord
t
-i -

Utilization Patterns of Estuarine
Intertidal Habitats by Birds
in Yaquina Estury, Oregon
Office of
Research and Development
National Health and
Environmental Effects
Research Laboratory,
Western Ecology Division

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UTILIZATION PATTERNS OF
INTERTIDAL HABITATS BY
BIRDS IN YAQUINA ESTUARY, OREGON
October 2011
Janet O. Lamberson, Melanie R. Frazier, Walter G. Nelson, Patrick J. Clinton
U.S. Environmental Protection Agency
Office of Research and Development
National Health and Environmental Effects Research Laboratory
Western Ecology Division
Newport OR 97365
EPA/600/R-11/118
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Acknowledgements
The authors acknowledge the assistance of Dr. Rich McKinney, Dr. Wayne Hoffman, and
Dr. Robert Ozretich for providing technical reviews of the manuscript and for discussions
in the formative stages of this project. Ms. Karen Ebert and Ms. Marinane Colvin
provided assistance with manuscript production. Support for M.F. was provided by U.S.
EPA postdoctoral fellowships (AMI/GEOSS EP08D00051 and NHEERL).
Disclaimer
The information in this document has been funded wholly or in part by the U.S.
Environmental Protection Agency. 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.
Report Citation
Lamberson,J.O., M.R. Frazier, W.G. Nelson, P.J. Clinton. 2011. Utilization Patterns of
Intertidal Habitats by Birds in Yaquina Estuary, Oregon. U.S. Environmental Protection
Agency, Office of Research and Development, National Health and Environmental
Effects Research Laboratory, Western Ecology Division, Newport OR; EPA/600/R-
11/118.
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SUMMARY
An assessment of bird utilization patterns of the intertidal soft sediment and low
marsh habitats of the Yaquina estuary, Oregon was conducted from December 2007-
November 2008. Daylight censuses of all birds utilizing selected estuarine intertidal
habitats in the Yaquina estuary were conducted by a single observer from shoreline
observation sites in each of five intertidal habitats [Zostera marina (eelgrass), Upogebia
(mud shrimp)/mudflat, Neotrypaea (ghost shrimp)/sandflat, Zostera japonica (Japanese
eelgrass), low marsh], and during five tide levels (<0.3, 0.6-0.9, 1.2-1.5, 1.8-2.4 and >2.4
m above MLLW). Censuses were designed to determine the spatial and seasonal
utilization patterns of estuarine habitat by birds, and how these patterns changed during
the tidal cycle. The estuary was divided into four sectors for surveying, Idaho Flat, Sally's
Bend, Raccoon Flat and Upriver.
Field census data were collected for a one year period, during six, two-month
count cycles. A total of 49,015 birds consisting of 79 distinct species and 10 composite
taxa were recorded from the surveys. Gulls and terns comprised 42% of the total birds
and, together with ducks, shorebirds, corvids and geese, accounted for about 92% of the
total abundance. The addition of herons/egrets, rails (i.e. coots), and
pelicans/cormorants comprised just over 98% of all birds observed. The remaining birds
consisted of songbirds, loons/grebes, raptors and alcids.
Z. marina beds, the habitat lowest in the intertidal, were an important foraging area
for gulls, crows, dabbling ducks, geese and coot when exposed, and for diving ducks,
other diving birds, as well as herons and egrets when flooded. The eelgrass was
consumed by some species of dabbling ducks, coot, Brant and Canada geese. The
l/pogeb/a/mudflat, typically located above the Z. marina beds in the intertidal, supported
large numbers of foraging gulls, crows and shorebirds when exposed, and diving clucks
when flooded. Neotrypaealsandftat was utilized by ducks and gulls for roosting when
lower habitats were flooded at high tide, and by large flocks of shorebirds for foraging
during spring migration. The nonindigenous dwarf eelgrass, Z. japonica was little used in
winter when above-ground biomass was reduced, but was more important during other
seasons and was used by foraging shorebirds, gulls, crows, ducks and Canada geese.
Emergent marsh was used as shelter and for foraging by ducks and coots in winter, as a
roost area for herons, geese and shorebirds at high tide, and for foraging by land birds
including swallows, European starlings and Song Sparrows. Emergent marsh tidal
channels supported foraging shorebirds when exposed and fishing herons and egrets
when flooded. Habitats/sectors with the highest bird densities were Z. marina, low
marsh, Neo/sand, and Upo/mud habitats in Idaho Flat, and low marsh in the Sally's Bend
sector.
To examine the relationship between habitat and bird use, we analyzed three
indices of bird use: bird density, Shannon diversity index, and species richness
standardized for habitat area. We also analyzed the relationship between bird density
and habitat for three taxonomic subgroups: all birds excluding gulls, waterfowl (ducks and
geese), and shorebirds. Analyses statistically controlled for variation in habitat area,
location within the estuary (sector), and time of year (cycle). All metrics of bird use were
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influenced by habitat type. However, regardless of habitat, birds appear to prefer certain
sectors of Yaquina estuary. The embayments in the lower Yaquina estuary supported
greater numbers and densities of birds than upriver areas, but species diversity was
greater upriver. The sector referred to as Raccoon Flat had the lowest abundances and
diversity.
Based on these analyses, Z marina is an important bird habitat based on nearly
all metrics of bird use. Overall bird density was relatively high in Z marina habitats; and
Z marina supported statistically greater densities of waterfowl than other habitats, with
the possible exception of low marsh. Z marina also had statistically greater species
richness than all other habitats, and higher Shannon diversity than all other habitats
except low marsh. According to model estimates that statistically controlled for a
habitat's area and location within the estuary, an average of about two times more
species are predicted to be observed during a tidal cycle in Z marina than the other
habitats. An exception to this pattern was the low density of shorebirds in Z marina.
One issue of recent potential concern is whether the introduction of Z japonica will
negatively affect bird use of intertidal habitat in estuaries, particularly for shorebirds.
Although this study was not designed to address this question, a preliminary evaluation
indicates there is no evidence that birds will be negatively impacted by the presence of
this invasive species in Yaquina estuary. In Yaquina estuary, Z japonica is most likely to
supplant the Neotrypealsand habitat. There were no significant differences between Z
japonica and Neotrypea /sand habitat for any metric of bird use, and many birds were
observed using Z japonica.
There were seasonal patterns in all bird use metrics. The highest total bird
densities were observed in December/January. After this peak, both total density and
diversity declines, reaching an annual low around June/July. During these months,
abundance was only 22% of peak abundance. Shorebirds had a different seasonal
pattern, with density appearing to peak around April/May during spring migration;
however, the overall model affect of sample month was marginally non-significant.
Shannon diversity and species richness metrics appeared to peak around October to
January and again in April/ May.
Tide level was an important factor affecting bird distribution across intertidal
habitats. Birds tended to move upslope across the intertidal flat with the incoming tide,
and then move down slope to forage in newly exposed areas as the tide receded.
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TABLE OF CONTENTS
Acknowledgements		2
Disclaimer		2
Summary		3
List of Tables		6
List of Figures		7
List of Appendices		8
Introduction		9
Methods	11
Habitat Descriptions	14
Yaquina Estuary Sector Descriptions	17
Count Methods	18
Sampling Issues	19
Regional Observations	 20
Statistical Analysis	20
Results	23
Abundance and Raw Species Richness Data	23
Density Patterns	31
Standardized Diversity Patterns	 38
Seasonal Patterns of Density and Diversity	41
Tide Level Patterns	42
Replicate Counts	48
Regional Observations	50
Other Observations	50
Discussion	51
Habitat and Spatial Patterns	51
Seasonal Patterns	53
Tidal Patterns	54
Sampling Issues	 55
Use for Assessing Ecosystem Services	56
References	57
Appendices	61
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LIST OF TABLES
Table 1. Typical flooding or exposure of habitats at various tidal heights in the
Yaquina estuary	 12
Table 2. Areas (ha) of intertidal habitats within each sector of the Yaquina estuary
	 12
Table 3. Summary of weather conditions encountered during count cycles	 18
Table 4. Abundance by species group and count cycle of birds utilizing five
intertidal habitats	 24
Table 5. Abundance by sector and count cycle of birds utilizing five intertidal
habitats	28
Table 6. Abundance by count cycle for birds utilizing five intertidal habitats	 29
Table 7.	Species richness by count cycle for birds utilizing five intertidal habitats. 29
Table 8. Species richness by sector for birds utilizing five intertidal habitats	 29
Table 9.	Bird density (ha"1) by count cycle and sector in five intertidal habitats ... 33
Table 10. Pairwise comparison of modeled density and diversity values among
habitats with p-values after Tukey's correction	 38
Table 11. Pairwise comparison of modeled density and diversity values between
count cycles with p-values after Tukey's correction	 42
Table 12. Abundance by tide level and count cycle of birds utilizing five intertidal
habitats	44
Table 13. Bird density (ha"1) by tidal level and count cycle in five intertidal habitats
	 45
Table 14. Comparison of bird abundance by habitat and sector for replicate
counts of one or more sectors conducted in count cycles 2-6 at low tide
(<0.3 m)	49
Table 15. Average coefficients of variation within treatment groups	 49
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LIST OF FIGURES
Figure 1. Location of the Yaquina estuary on the central Oregon coast	11
Figure 2. Sectors of Yaquina estuary, locations of observation sites, and
bathymetry of the estuary	 13
Figure 3. Selected intertidal habitats of the Yaquina estuary	 15
Figure 4. Percentages of observed bird groups	 23
Figure 5. Abundance of birds by habitat and sector in the Yaquina estuary	27
Figure 6. Species richness of birds by habitat and sector in the Yaquina estuary
	30
Figure 7. Bird densities (ha"1) by habitat and sector in the Yaquina estuary		32
Figure 8. Statistical model estimates for all birds	 34
Figure 9. Statistical model estimates for all birds minus gulls		35
Figure 10. Statistical model estimates for waterfowl (ducks and geese)		36
Figure 11. Statistical model estimates for shorebirds		37
Figure 12. Statistical model estimates for Shannon diversity		39
Figure 13. Statistical model estimates for species richness		40
Figure 14. Comparison of relative bird abundance versus tide level for five intertidal
habitats	 43
Figure 15. Abundances of selected groups of birds on intertidal habitats in Yaquina
estuary at different tide levels	46
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LIST OF APPENDICES
Appendix A. Locations of observation sites in the Yaquina estuary, Oregon	61
Appendix B. Abundance of all birds observed for each count cycle in the Yaquina
estuary during December 2007-December 2008	 62
Appendix C. Abundance of birds observed in five intertidal habitats in the Yaquina
estuary during December 2007-December 2008	 65
Appendix D. Abundance of birds observed in four sectors of the Yaquina estuary
during December 2007- December 2008	 68
Appendix E. Data used in habitat/sector/cycle analyses	 72
Appendix F. Total density of birds (ha"1) observed utilizing five intertidal habitats
by species group and count cycle	75
Appendix G. Regional observations of bird occurrence and activities in estuarine
intertidal habitats in Oregon	77
Appendix H. Observations on feeding in birds	 80
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INTRODUCTION
Increasingly there is an appreciation that many environmental decisions can be
better informed through the use of a framework which takes a comprehensive view of the
ecosystem services provided to humans by natural systems (MEA 2005a). Ecosystem
services are the goods and processes through which natural systems sustain and fulfill
human life (Daily 1997). It has been suggested that the reason many ecosystems are in
decline is that they are not valued as much as the other activities and products that
degrade them due to lack of public awareness of their ecologic, economic, societal, and
cultural value (Daily et al. 1997; Cork et al. 2002). Ecosystem services vary among
habitats (MEA 2005a, b). Some habitats are important for maintaining the structure,
function, and sustainability of ecosystems. Other habitats are critically important for their
high biodiversity, productivity, nursery value, importance to threatened or endangered
species, or for other ecologic, economic, societal or cultural reasons. If the distributions
of habitats change, so will the sum of the ecosystem services provided by the aggregate
of habitats that make up the landscape or seascape.
The primary goal of this research was to describe bird use among five tidal
wetland habitats commonly found in Yaquina estuary, OR, in order to begin assessing
the value of these habitats. This research may help researchers predict how changes in
the distribution of common estuarine habitats, due to current and future stressors, may
affect bird populations. This project is a component of a larger research effort, the
Estuarine Ecosystem Services Research Project (EESRP), of the U.S. EPA's Pacific
Coastal Ecology Branch, Western Ecology Division. The goals of EESRP are to begin
assessing the relative value of common tidal wetland habitats within a representative
Pacific Northwest estuary, as well as to develop tools and approaches for estimating the
effects of habitat alteration on important ecosystem services associated with estuarine
tidal wetlands of the Pacific Northwest. EESRP research is focused on ecosystem
services that are embodied in water quality designated uses (healthy fish, shellfish, and
wildlife populations), or ecosystem services such as nutrient cycling that are critical to
protection of water quality. The project will ultimately develop alternative futures
scenarios that estimate changes in ecosystem services associated with estuarine habitat
alterations resulting from such factors as global climate change.
The inclusion of birds in the EESRP is important due both to ecological and
valuation reasons. A wide variety of bird species are highly dependent on the tidal
wetland habitats found in estuaries in the Pacific Northwest of the U.S. (Buchanan 1988,
Buchanan and Evenson, 1997, Colwell 1992, 1994, Baldwin and Lovvorn 1994a,b,
Wilson and Atkinson 1995, Wetzel 1996, Page et al. 1999). In this region, daily tides of 2-
3 meter amplitude cause large areas of estuaries to be intertidal. These intertidal
habitats are utilized by many bird species for foraging and roosting. The Yaquina estuary
has been designated as a Continentally Important Bird Area by the American Bird
Conservancy (ref. http://yaquina.info/ybn/bird/iba.htm) because it provides critical habitat
for a variety of birds including several gull species, Caspian terns, Brant, and a variety of
shorebird species. Intertidal wetlands in the Yaquina and other Pacific Northwest
estuaries are also important components of the Pacific Coast fly-way for migrating and
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overwintering shorebirds and waterfowl (ducks, geese, and swans). Both groups of birds
forage in various habitats within the intertidal wetlands complex of the estuary.
Bird watching and waterfowl hunting are significant human recreational activities
both in the U.S. and worldwide, and thus are amenable to economic valuation (US F&W
2007, Southwick Associates 2008). In Oregon, estimated expenditures on wildlife
viewing exceed that from fishing, hunting and shellfishing combined (Dean Runyon
Associates 2009). The economic impact of bird watching is now recognized by local
businesses, which are willing to provide financial support to activities promoting bird
watching. For example, with financial support from local businesses, chambers of
commerce, and conservation organizations, the Oregon Coast Birding Trail has been
established to encourage visits to the Oregon Coast from birders in the region
(http://www.oreqoncoastbirdinq.com/). The US Fish and Wildlife (US F&W 2009)
estimates that in 2006 about 27% of Oregon state residents participated in the
recreational activity of bird watching. In that year, 1,046,000 residents and non-residents
in Oregon were either backyard bird watchers or more serious "birders", with 74% of
these individuals being residents of the state (US F&W 2009). Expenditures by birders
contribute to local, regional and national economies. In 2006, the US F&W estimated
that nationally, trip and equipment expenditures of $36 billion associated with bird
watching generated $82 billion in total direct and indirect economic outputs (US F&W
2009). This broad pattern of economic benefits associated with birding is also observed
in economic analyses that focus more narrowly on wetlands. In a meta-analysis of the
economic values associated with wetlands, Woodward and Wui (2001) found that bird
watching was one of the highest valued services of wetlands.
In this study, patterns of bird use among estuarine intertidal habitats were
assessed over tidal and annual cycles in the Yaquina estuary, Oregon. The principal
products are summaries of relative bird habitat utilization expressed by various ecological
metrics. There was no attempt to derive economic or non economic valuation information
as part of the study, but the ecological data forms the basis for such translations as part
of potential future studies.
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METHODS
The Yaquina is a tidally-dominated, drowned river mouth estuary (Lee et al. 2006)
located on the central Oregon coast (44.62° N, 124.06° W; Fig. 1). There are large
intertidal embayments in the lower estuary which include a variety of habitat types, and
narrow fringing marshes are found along much of the undeveloped shoreline. The mean
tidal range at Newport near the mouth of the estuary is 2 m, while maximum tidal range
exceeds 4 m. Principal freshwater input is from the Yaquina River, while several small
streams enter the estuary through side channels locally termed sloughs. The estuary has
a watershed of approximately 650 km2, an estuarine area of 18.8 km and an estuarine
intertidal area of 9.05 km2. While the estuary has a commercial shipping terminal and the
navigation channel is dredged, it is primarily used for recreational boating, recreational
and commercial fishing, crabbing, clamming, wildlife watching and tourism.
124°30'0"W	123o0'0"W
Location
Yaquina Bay
124°30'0"W	I23°0'0"W
Figure 1. Location of the Yaquina estuary on the central Oregon coast.
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Daylight censuses of all birds utilizing selected estuarine intertidal habitats in the
Yaquina estuary were conducted during six, two-month cycles (December 2007-
November 2008). Counts were made by a single observer (J. Lamberson) from shoreline
observation sites (Fig. 2, Appendix A) in each of five intertidal habitats [Zostera marina
(eelgrass), Upogebia (mud shrimp)/mudflat, Neotrypaea (ghost shrimp)/sandflat, Zostera
japonica (Japanese eelgrass), low marsh], and during five tide levels (<0.3, 0.6-0.9, 1.2-
1.5, 1.8-2.4 and >2.4 m above MLLW). Censuses were designed to determine the
spatial and seasonal utilization patterns of estuarine habitat by birds, and how these
patterns changed during the tidal cycle as the habitats became flooded or exposed with
the rising or falling tide (Table 1). The estuary was divided into four sectors (Idaho Flat,
Sally's Bend, Raccoon Flat and Upriver; Fig. 2), which covered the large intertidal
embayments in the lower estuary, with an upriver termination of the census area at 18 km
from the estuary mouth (milepost 11.1, Yaquina Bay Road). Total intertidal areas within
each sector and habitat are presented in Table 2.
Table 1. Typical flooding or exposure of habitats at various tidal heights in the Yaquina
estuary.
Intertidal
Zone
(m)
Z. marina
Upogebial
Mudflat
Neotrypaeal
Sandflat
Z japonica
Low
Marsh
< 0.3
Exposed
Exposed
Exposed
Exposed
Exposed
0.6-0.9
Flooded
Exposed
Exposed
Exposed
Exposed
1.2-1.5
Flooded
Flooded
Exposed
Exposed
Exposed
1.8-2.4
Flooded
Flooded
Flooded
Flooded
Exposed
>2.4
Flooded
Flooded
Flooded
Flooded
Flooded
Table 2. Areas (ha) of intertidal habitats within each sector of the Yaquina estuary.
Sector
Z. marina
Upogebia/
Mudflat
Neotrypaea/
Sandflat
Z.
japonica
Low
Marsh
Total
Idaho Flat
14.32
59.84
43.37
0.87
8.92
127.32
Sally's Bend
104.29
50.29
29.50
23.11
1.66
208.85
Raccoon Flat
30.62
35.61
12.07
1.88
1.58
241.04
Upriver
11.10
31.36
95.06
8.62
95.06
81.76
Total
160.33
177.10
180.00
34.48
107.06
658.97
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o Observation Sites
Idaho Flat
I—l Raccoon Flat
Sally's Bend
I—lUpriver
Meters Re ative to MLLW
-1.DD
-0.99- -0.75
-0.74 - -0.50
-0.49 - -0.25
-0.24 - 0.00
0.01 - D.25
0.26-C.50
0.51 75
0.76- 1.3D
1.01 - 1.25
'.26- 1.50
1.51 - 1.75
1.76 - 2.00
2.01-2.25
2.26-2. E0
Figure 2. Sectors of Yaquina estuary, locations of observation sites (Appendix A), and bathymetry of the estuary.
Highlighted regions are the sector areas exposed between -0.6 and +2.4 meter tidal elevations relative to MLLW.
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Habitat Descriptions
The five intertidal habitats within Yaquina estuary selected for the study of bird
utilization are defined and described in the following paragraphs, and their distribution
within the estuary is shown in Fig. 3.
The Zostera marina (eelgrass) habitat (Fig. 3) occurs typically at the lowest
intertidal elevation as patches or meadows of the seagrass on mudflats, and may also
contain two species of burrowing shrimp, Upogebia pugettensis (mud shrimp) and/or
Neotrypaea californiensis (ghost shrimp) (Ferraro and Cole 2007). If Z marina was
present in mixed habitat the area was classified as Z. marina habitat. Benthic
macrofaunal biodiversity and abundance within this habitat are high (Ferraro and Cole
2007), potentially providing a rich food source for birds when the habitat is flooded.
The blades and rhizomes of Z marina are consumed by dabbling ducks, coot, brant
and geese (Bayer 1996a). Grazing of seagrasses and submerged aquatic vegetation
(SAV) by waterfowl has been well documented (e.g. Phillips 1984, Thayer et al. 1984,
Nienhuis and Groenendijk 1986). When the Z marina habitat floods with the incoming
tide, the eelgrass can provide cover for species such as fish and crabs, which move
into the habitat and serve as prey for some bird species.
The unvegetated mudflat habitat (Fig. 3) typically occurs at a higher intertidal
elevation than Z marina and consists of a mixture of mud to muddy-sand sediments
with relatively low to moderate organic content. U. pugettensis often colonizes this
substrate, forming U-shaped relatively permanent burrows lined with mucus, and is a
prey item for long-billed shorebirds such as whimbrel, curlew and godwit. This habitat
supports abundant populations of macrofaunal benthic species of worms, crustaceans
and molluscs (Ferraro and Cole 2007), a food source for some birds.
The unvegetated sandflat habitat (Fig. 3) is characterized by well sorted
medium quartz sand with a low organic content. N. californiensis colonizes extensive
areas of this habitat within the Yaquina estuary, constructing complex burrows up to
about 1-m deep with numerous openings. N. californiensis is a major bioturbator
(DeWitt et al. 2004), mixing oxygenated sediment to the depth of its burrows.
Biodiversity of macrofaunal benthic species that serve as potential prey items for small
shorebirds is low relative to other intertidal habitats in Yaquina estuary (Ferraro and
Cole 2007). N. californiensis is itself a prey species for long-billed shorebirds such as
whimbrels and marbled godwit.
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*

bird
ftabzones
Habitat

Low Marsh

NMi/SjlAd
¦1
Upo! Mud
¦
Zrelera >apor«ea

Zcatfj mar-ra


Figure 3. Selected intertidal habitats of the Yaquina estuary.
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The nonindigenous Japanese dwarf eelgrass Zostera japonica is present year-
round but its growth is seasonal, appearing lush and vigorous during late summer
months, with significant winter die back (Kaldy 2006). Z. japonica was likely an
unintentional introduction into Pacific Northwest estuaries with the establishment of
Japanese oyster culture (Crassostrea gigas) in the early 20th century (Harrison and
Bigley 1982). It has been gradually increasing in abundance in estuaries from California
to British Columbia, although efforts to eradicate this eelgrass have been made in
California (Kaldy 2006). The species was first reported in Yaquina estuary in 1976
(Bayer 1996a), and now forms patchy to extensive beds in upper intertidal portions
throughout the estuary (Young et al. 2008). Because its presence will replace
unvegetated sandflat habitat, a secondary focus of this study was to determine how
various species of birds use this habitat relative to the sandflat. The blades and
rhizomes of dwarf eelgrass are consumed by ducks, coot and geese (Baldwin and
Lovvorn 1994, Bayer 1996a), and the above-ground eelgrass provides cover for an
invertebrate community that may serve as prey for shorebirds, crows and gulls (Ferraro
and Cole 2009).
Fringing, intertidal, low and high emergent marshes are found primarily in the
upriver sector (Figs. 2, 3), in sloughs where creeks flow into the river, and in the major
bends in the estuary. Dominant plants include Deschampsia caespitosa, Distichlis
spicata, Juncus balticus, Salicornia virginica, Argentina egedii and Carex lyngbyei. The
non-native cordgrass (Spartina spp.) is not present in the Yaquina estuary. Tidal
channels were included as marsh habitat in this study.
Other habitats not included in this study but frequently used by birds include
nearshore rocks and rocky beaches, floating clocks, pilings and other man-made
structures. Gulls, herons, cormorants, shorebirds and other species use these areas for
roosting, sometimes in large numbers. At high tide, gulls roost on grassy areas on
shores, ocean beaches, and roofs of buildings. Gulls and ducks may be found floating
at the water's surface over flooded intertidal and subtidal portions of the estuary when
intertidal areas are flooded while crows and other passerines retreat to terrestrial
habitats. Gulls, some ducks, and shorebirds also move to open ocean, ocean beaches,
freshwater ponds and wet pastures.
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Yaguina Estuary Sector Descriptions
Because it was not possible for one person to survey the entire estuary within the
short tide windows, the estuary was censused by sector (Fig. 2). The Idaho Flat sector
is characterized by extensive areas of unvegetated mudflat in the lower intertidal and
sandflat in the upper intertidal. A fringe of Z marina borders the adjacent river channel,
and a few small patches of Z. japonlca occur in the upper intertidal margin (Young et al.
2008). Fringing emergent low marsh occurs along the western to southern shoreline of
this embayment.
The Sally's Bend sector is characterized by extensive beds of Z marina,
occurring in a large area of the central portion of this embayment and bordering the tidal
channels that drain it. Z marina also occurs along the river channel that forms the
southwestern margin of the area (Figs. 2, 3). Upogebla is present within much of this Z
marina habitat. The upper intertidal margin consists primarily of sandflat with
Neotrypaea burrows and is extensively colonized by Z japonlca (Young et al. 2008);
although in winter the aboveground biomass of Z japonlca is greatly reduced (Kaldy
2006, Harrison 1982). Between the Z marina bed and the sandflat are bands of
unvegetated mudflat adjacent to and comingled with the Z marina bed. Small patches
of emergent low marsh are present at the upper edge of the embayment.
The Raccoon Flat sector includes an intertidal flat bordering the river channel up
the estuary from Idaho Flat. It is adjacent to and contiguous with King's Slough, a
sizeable embayment southeast of Idaho Flat. Because of property access issues, most
of King's Slough was not monitored for birds, although the outer portion of this slough
adjacent to Raccoon Flat was included in the survey as a part of Raccoon Flat. The
main channel margin of Raccoon Flat is bordered by Z marina, while mudflats with
Upogebla, small areas of sandflat, Z japonlca and emergent marsh habitats are found
at higher tidal elevations. The adjacent shoreline is wooded and undeveloped.
"Raccoon Flat" is a nickname applied by EPA (Newport) researchers for the raccoons
which are often observed foraging on the mudflat. This area is also referred to as South
Bay in some publications (e.g. Bayer 1996b).
The Uprlver sector has narrow bands of Z marina bordering much of the main
channel. Z. japonlca occurs in bands in some areas (Young et al. 2008), as well as in
patches in mudflat areas and in the tidal channels within marshes. In areas where the
intertidal flat is wide, mudflats or sandflats with burrowing shrimp provide foraging
opportunities for birds. Extensive areas of emergent marsh within sloughs and of
fringing marsh along the main estuary channel comprise the largest habitat area within
this sector of the estuary. In many areas, the channel is bordered by narrow strips of
rocky beach, and although this area is occasionally used by birds for foraging, it was not
surveyed. An oyster farm maintains extensive floats and pilings, which along with other
privately maintained floating docks, serve as roosting areas for large numbers of gulls,
cormorants, some shorebirds and harbor seals.
17

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Count Methods
All counts were made from shore locations (Fig. 2, Appendix A) using 10X42
binoculars and a 65-mm spotting scope (Swarovski) equipped with a 20-60X zoom
eyepiece. Birds were counted while using the habitats both during low tides when the
habitat was exposed (roosting, preening, foraging) and at higher tides when flooded
(fishing, dabbling, or diving to feed). Counts of birds observed in tidal channels that
flowed through the five habitat classes were combined with counts of birds in the
surrounding habitat. For example, tidal channels within emergent marsh were
considered to be part of the marsh habitat. Data were recorded by habitat and activity,
by exposed vs. flooded condition, and by habitat proper vs. tidal channel. Observations
on food items consumed were made at the same times as the count observations.
Activity and feeding data are qualitatively summarized in this report and are available in
a complete database that is available online
(http://www.epa. gov/wed/pages/models/Yaquina. htm).
Counts were made at various times throughout the two month count cycles at
selected tide levels (see below) in a variety of weather conditions (Table 3). No counts
were made on days when wind velocity exceeded 48 kph (30 mph), due to rough water
conditions and difficulty in seeing birds. Weather conditions (wind speed and air
temperature) were recorded from online data posted by the Hatfield Marine Science
Center (HMSC) weather station (http://weather.hmsc.orst.edu/) in South Beach,
Yaquina estuary. Conditions recorded at the HMSC weather stations are generally
similar to those experienced at the sampling sites. Tide levels were predicted from
online data provided by the South Beach tide station
(http://tbone.biol.sc.edu/tide/index.html). and recalculated using real time online surge
tide corrections provided by NOAA's Water Level Observation Network for South Beach
(http://tidesonline.nos.noaa.gov/qeoqraphic.html).
Table 3. Summary of weather conditions encountered during count cycles.
Cycle
Months
Temp Range
°C
Wind Range
m s"1
General Conditions
During Surveys
1
Dec 2007 - Jan
2008
4-10
0-12
Clear skies to rain and
hail squalls
2
Feb - Mar 2008
5-12
1 - 13
Clear skies to rain and
hail squalls
3
Apr - May 2008
9-29
0-13
Clear skies to cloudy
with light rain
4
Jun - Jul 2008
11 - 17
0-13
Clear skies to cloudy
5
Aug - Sep 2008
11 - 18
0-13
Clear skies to cloudy
with rain and thunder
6
Oct - Nov 2008
10 -21
0-10
Clear skies to cloudy
18

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The tide levels during a census mostly determined whether the target habitats
were exposed or flooded (Table 1). For bird counts occurring at tides <+0.3 m MLLW,
all habitats were exposed. Much of the Zostera marina habitat occurred below the +0.3-
m level, and thus was predominately flooded by tides above that level. For +0.6-0.9 m
tide levels, birds were observed using the remaining exposed habitats, as well as
wading or diving in the flooded Z. marina habitat. For +1.2-1.5 m tides,
l/pogeb/a/mudflat was generally flooded. For tides >+1.8 m, the sandflat and Z
japonica habitats were typically flooded. When tide levels exceeded +2.4 m, all habitats
including lower parts of the emergent marsh were flooded (Table 1). During count
cycles 3 and 4 (April-July), tide levels did not exceed +2.4 m during daylight hours, so
counts could not be made for this tide level.
Identification of birds was made to the lowest taxonomic level possible. In a few
cases, birds were assigned to composite taxa, such as genus, family or order because
viewing conditions made detection of details difficult or birds were too far away to assign
to species. In particular, all scaup were combined as "scaup spp.", and Calidrid
shorebirds were recorded as "sandpipers" if species could not be determined. Large
groups of gulls were not identified to species and were combined as "gulls, spp."
because their behavior and use of estuarine habitats were similar. The gull species
include Bonaparte's Gull (Chroicocephalus Philadelphia), California Gull (Larus
californicus), Glaucous-winged Gull (Larus glaucescens), Herring Gull (Larus
argentatus), Mew Gull (Larus canus), Ring-billed Gull (Larus delawarensis), Thayer's
Gull (Larus thayeri), and Western Gull (Larus occidentalis). Many of the large gulls in
Yaquina estuary are apparent hybrids between Western and Glaucous-winged Gulls.
Birds were assigned to "species groups" representing broad taxonomic
similarities (Table 4). The current report describes bird habitat relationships based on
these groupings, although it is recognized that other users may wish to analyze habitat
relationships at species level or by taxonomic grouping. Thus summary data on
individual taxa are presented in the appendices, and the original data can be obtained
from the online database.
Sampling Issues
To determine whether bird counts demonstrated repeatable patterns across
space and time, replicate counts were made during low tide in one or two sectors during
each count cycle, beginning with count cycle 2 (February-March, 2008). A replicate
count was also made in December 2008 to give some idea of variability for count cycle
1. However, given the elapsed time from the original observations in count cycle 1
(December 2007 vs. 2008), these data were not included in the assessment of count
variability. They are, however, provided for completeness in Appendices B, C, D.
Randomization tests were performed to determine whether the coefficient of
variation (CV) within a sample group was significantly lower than the coefficient of
variation among all the groups. CV was calculated by dividing the standard deviation of
the counts by the average abundance of the counts within a sample group. For the
randomization, habitat/sector/or cycle classes were randomly shuffled and a null
19

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coefficient of variation was calculated from the randomized data. This was repeated
1,000 times to determine the percentage of times that the random CV was smaller than
the observed CV.
Birds may have been counted repeatedly within the same sector at different tide
levels as they moved among habitats with the changing tides, or counted on successive
days. Movement patterns are further complicated by individual species, since some
species, such as gulls, scoters, and alcids, may move among estuarine and non-
estuarine habitats on a daily basis. However, given the objective of this study, we felt
these limitations did not bias the determination of relative usage of the habitats.
Regional Observations
Limited, qualitative observations of bird utilization of a subset of habitat types and
tide levels were made in 8 additional Pacific Northwest estuaries (Alsea, Coos Bay,
Nestucca, Netarts, Salmon, Siletz, Tillamook estuaries in Oregon, Willapa Bay in
Washington). These observations provided an opportunity to compare patterns of
intertidal habitat structure and utilization by birds across systems to determine whether
patterns of habitat utilization in Yaquina estuary were similar regionally.
Statistical Analysis
To analyze patterns of bird use among intertidal habitats and for seasonal trends,
we did not include tidal heights >2.4 m because this tide height could not be collected
for all cycles. Of the remaining surveys (N=480), about 32% had zero observed birds
due to the natural tendency of birds to aggregate. To ameliorate this problem, we
combined the birds observed during all 4 tidal levels (0 to +2.4 m) for each
sector/habitat/cycle (referred to as a "sampling period"), for a sample size of 120
observations (Appendix E). In contrast, for analyses of bird use based on tidal cycle we
used the raw survey data (birds observed for each sector/habitat/cycle/tide, N=600).
We analyzed three indices of bird use: bird density, Shannon diversity index, and
species richness standardized for habitat/sector area. Bird density data were double
square root transformed (VV(number of birds ha"1 sampling period"1)). We also analyzed
the relationship between bird density and habitat for three taxonomic subgroups: all
birds except gulls, waterfowl (ducks and geese), and shorebirds. For analyses of bird
diversity, we excluded some composite taxa (Mergus sp., Calidris spp., Anas spp.,
Podiceps sp., Charadriiformes unid., Emberizidae sp., Tachycineta spp.; Appendices B,
C, D) because they did not necessarily represent unique species. The Shannon
diversity (//') index was calculated for each sampling period as:
5
H' = ^(PilnPi)
i=l
where S is the total # of species, and pt is the proportional abundance of species
i (i.e. the number of individuals of species i divided by the total number of individuals).
For standardized species richness (number of bird species), we corrected for unequal
20

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habitat areas using rarefaction techniques. The number of individual birds predicted to
occur in 5 ha was calculated, and then rarefaction (Hurlbert 1971, Oksanen et al. 2009)
was used to predict the number of species. For example, if 500 birds were observed in
a sampling period within an area of 100 hectares, the number of species was predicted
for 25 birds (i.e. standard of 5 hectares /100 hectare sample area * 500 individuals = 25
individuals). Samples from habitats/sectors with areas less than 5 hectares were
excluded from further analyses of standardized species richness (analyzed sample size:
N= 96). Excluded samples were the low marsh habitat in the Sally's Bend and Raccoon
sectors of the estuary and the Z japonica habitats from Idaho Flat and Raccoon
sectors. The "vegan" package (Oksanen et al. 2009) was used to generate the
rarefaction estimates of species numbers and to calculate Shannon diversity.
Statistical analyses were performed in the R environment (v. 2.8.1; R
Development Core Team 2008). For analyses of bird use among habitats, predictor
variables included: habitat, count cycle, and In area. Area was included as a predictor
because it often had an effect on bird use metrics even though the metrics were
corrected for sample area (density and rarefaction) or are considered relatively
insensitive to sample effort (Shannon Index). Habitat analyses were similar to
randomized block designs, with each of the five habitats represented in the four sectors
of the estuary. To help control for the influence of sector on bird use we analyzed the
data with mixed effects regression models using the nlme package (Pinheiro et al.
2009). For all but two analyses (total bird density and bird density excluding gulls), we
used a varying intercepts model which makes the simplifying assumption that habitat
effects are the same among the sectors. A more complex model allowed both the
intercepts and slopes to vary, which tests for interactions between habitat and sector.
Based on log-likelihood ratio tests, the use of the more complex model was not
supported (P>0.05) in most cases. One clear exception was the analysis of total bird
density (Likelihood ratio test: %2=29.21, df=14, P = 0.01), and there was marginal
support for the more complex model for analyzing bird density excluding gulls
(X2=23.40, df=14, P=0.05).
Based on these analyses, we present model estimates and standard errors that
can be used to predict bird use. Habitat and cycle are analyzed as factors, and as such,
the estimates for these variables represent the average predicted bird use in each
category; area is analyzed as a continuous variable, and thus, model estimates
describe the change in the bird use variable given a one unit change in In area. To
make the results more intuitive, all model estimates are presented for a 30 ha plot (In
area - In 30), rather than using the model default of a zero hectare plot. For cycle, the
first sample period (Dec. 2007 - Jan. 2008) was used as the reference observation
period against which the other cycles were compared.
Bird use among the habitats and yearly cycles was compared using the pairwise
Tukey's correction for multiple comparisons. These values were calculated using
simultaneous inference methods with the "multcomp" package (Hothorn et al. 2008).
21

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To analyze bird use in regard to tidal cycle, a linear regression model was used
to analyze the direct and interactive effects of tide level and habitat on both VVbird
density and abundance.
22

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RESULTS
Abundance and Raw Species Richness Data
A total of 49,015 birds consisting of 79 species and 10 composite taxa were
recorded from the surveys conducted over a one year study period. Gulls and terns
comprised 42% of the total observed birds, and together with ducks, shorebirds, corvids
and geese comprised 92% of observed birds (Fig. 4, Table 4). The addition of
herons/egrets, rails (i.e. coots), and pelicans/cormorants comprised about 98% of all
birds observed. The remaining birds consisted of songbirds, loons/grebes, raptors and
alcids. If we consider the data from the replicate counts, there were an additional 5,606
bird observations, but only 3 additional taxa. Complete lists of abundance for all bird
taxa collected are given in Appendices B, C, D.
Pelicans/Cormorants, 2%
Rails, 2%
Herons/Egrets, 3%
Geese, 3%
Songbirds
Looris/Grebes
Raptors
Alcids
Corvids
Shorebirds
10%
Gulls and Terns
I	42%
Ducks
32%
Figure 4. Percentages of observed bird groups.
23

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Table 4. Abundance by species group and count cycle of birds utilizing five intertidal
habitats.
Cycle
Group
Z
marina
Upogebia
/mud
Neotrypaea
/sand
Z
japonica
Low
Marsh
Total


Geese
60
0
243
2
0
305
1

Ducks
2510
2689
1222
300
491
7212
Dec-

Loons/Grebes
72
12
2
0
1
87
Jan

Pelicans/Cormorants
1
4
2
0
0
7


Herons/Egrets
35
19
10
0
21
85


Raptors
2
9
1
0
0
12


Rails
490
49
10
114
160
823


Shorebirds
0
251
103
205
45
604


Terns/Gulls
527
1411
421
0
0
2359


Alcids
0
0
0
0
0
0


Corvids
277
50
90
10
0
427


Songbirds
3
1
1
0
83
88
Cycle 1 Total
3977
4495
2105
631
801
12009


Geese
114
17
109
0
57
297
2

Ducks
538
588
121
10
109
1366
Feb-

Loons/Grebes
25
4
5
2
0
36
Mar

Pelicans/Cormorants
3
0
3
0
0
6


Herons/Egrets
14
17
7
1
12
51


Raptors
0
0
4
0
4
8


Rails
52
0
0
0
0
52


Shorebirds
0
0
372
2
293
667


Terns/Gulls
316
1473
111
1
0
2567


Alcids
0
0
0
0
0
0


Corvids
143
160
288
1
7
599


Songbirds
0
0
3
0
32
35
Cycle 2 Total
1205
2259
1689
17
514
5684


Geese
0
2
99
0
73
174
3

Ducks
269
98
96
0
28
491
Apr-

Loons/Grebes
8
9
4
0
0
21
May

Pelicans/Cormorants
16
5
2
0
0
23


Herons/Egrets
52
37
23
0
20
132


Raptors
5
2
8
0
0
15


Rails
0
0
0
0
0
0


Shorebirds
285
2175
304
3
67
2834


Terns/Gulls
538
484
302
1
3
1328


Alcids
4
0
0
0
0
4


Corvids
50
78
70
9
18
225


Songbirds
0
4
6
1
92
103
Cycle 3 Total
1227
2894
914
14
301
5350
24

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Table 4. Continued.


Z
Upogebia
Neotrypaea
Z
Low

Cycle
Group
marina
/mud
/sand
japonica
Marsh
Total

Geese
0
14
17
0
26
57
4
Ducks
14
2
0
0
0
16
Jun-
Loons/Grebes
0
0
0
0
0
0
July
Pelicans/Cormorants
13
0
0
0
0
13

Herons/Egrets
195
73
31
2
4
305

Raptors
3
1
2
0
2
8

Rails
0
0
0
0
0
0

Shorebirds
0
72
299
1
69
441

Terns/Gulls
441
975
656
8
0
2080

Alcids
5
0
0
0
0
5

Corvids
69
99
79
38
3
288

Songbirds
1
12
32
10
163
218
Cycle 4 Total
741
1248
1116
59
267
3431

Geese
45
63
113
132
16
369
5
Ducks
141
16
3
3
166
329
Aug-
Loons/Grebes
9
0
2
0
0
11
Sept
Pelicans/Cormorants
192
80
82
0
5
359

Herons/Egrets
349
91
30
9
58
537

Raptors
2
2
0
0
1
5

Rails
0
0
0
0
0
0

Shorebirds
17
217
98
23
39
394

Terns/Gulls
1486
2522
951
5
1
4965

Alcids
0
0
0
0
0
0

Corvids
44
92
28
74
13
251

Songbirds
1
2
0
2
72
77
Cycle 5 Total
2286
3085
1307
248
371
7297

Geese
10
129
0
26
25
190
6
Ducks
1929
3220
155
0
999
6303
Oct-
Loons/Grebes
69
7
4
0
1
81
Nov
Pelicans/Cormorants
176
112
93
0
106
487

Herons/Egrets
119
61
39
24
92
335

Raptors
0
3
0
1
0
4

Rails
0
2
36
0
0
38

Shorebirds
0
36
121
18
13
188

Terns/Gulls
3104
3208
674
57
0
7043

Alcids
0
0
0
0
0
0

Corvids
121
308
18
66
2
515

Songbirds
0
1
2
0
57
60
Cycle 6 Total
5528
7087
1142
192
1295
15244
Total
14964
21068
8273
1161
3549
49015
25

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The distribution of total annual bird abundance across sectors and habitats (Fig.
5, Tables 5, 6) shows marked spatial variation. Qualitatively, most birds were observed
within the broad intertidal flat areas nearer the mouth of the estuary and in habitats
located across the mid and lower intertidal levels of these sectors. Total bird
abundance was lower in the upriver sector. There was also more than a 10 times
greater abundance in l/pogeb/a/mudflat and Z marina habitats as compared to Z
japonica, a comparison complicated by the fact that the area of these habitats was more
than 4 times greater than that of Z japonica (Table 2). There were intermediate total
bird abundances in A/eofrypaea/sandflat and low marsh habitats.
The seasonal distribution of total bird abundance showed marked variation
(Tables 5, 6). During the peak months of bird abundance (Oct - Jan), there were nearly
4 times as many birds observed than during the months of lowest bird abundance (Jun
-Jul).
The spatial distribution of total annual bird species richness across habitats and
sectors (Fig. 6, Tables 7, 8) shows an appreciably different pattern from total
abundance. Qualitatively, while high total bird abundances were observed on the broad
intertidal flat areas relative to the upriver areas, these areas had similar species
richness. In fact, total bird species richness was actually highest in the upriver sector
(Table 8). All the habitats had about the same total number of bird species observed,
with the exception of Z japonica which was about 50% lower. Subsequent analyses
controlling for differences in area (see below) suggest that this is at least partially due to
the relatively small area of this habitat.
The seasonal distribution of total bird species richness also showed a different
pattern than the total abundance data (Table 7). Peak species richness occurred in the
April - May period, and was nearly 50% greater than for other sample periods.
26

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1
Bird Count
¦1<100
100 -500
500 - 1000
1000 - 1500
1500 -2000
2000 - 5000
H>5000
Subtidal
0 0.5 1
Figure 5. Abundance of birds by habitat and sector in the Yaquina estuary
27

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Table 5. Abundance by sector and count cycle of birds utilizing five intertidal
habitats.
Sector
Cycle
Z
marina
Upogebia
/mud
Neotrypaea
/sand
Z
japonica
Low
Marsh
Total

1
2204
3016
1307
80
200
6807
Idaho
2
157
1336
999
0
353
2845
Flat
3
89
868
511
0
67
1535

4
92
270
896
0
96
1354

5
169
1722
1118
0
210
3219

6
1161
4851
747
0
900
7659
Idaho Flat Total
3872
12063
5578
80
1826
23419

1
169
698
0
0
0
867
Raccoon
2
191
441
0
0
0
632
Flat
3
72
127
0
0
1
200

4
114
683
2
0
0
799

5
443
247
0
0
3
693

6
325
1183
11
1
1
1521
Raccoon Flat Total
1314
3379
13
1
5
4712

1
1292
603
615
551
264
3325
Sally's
2
670
413
351
11
2
1447
Bend
3
1008
1836
123
9
49
3025

4
489
238
126
43
14
910

5
1398
896
128
215
34
2671

6
3894
947
85
118
3
5047
Sally's Bend Total
8751
4933
1428
947
366
16425

1
312
178
183
0
337
1010
Upriver
2
187
69
339
6
159
760

3
58
63
280
5
184
590

4
46
57
92
16
157
368

5
276
220
61
33
124
714

6
148
106
299
73
391
1017
Upriver Total
1027
693
1254
133
1352
4459
Grand Total
14964
21068
8273
1161
3549
49015
28

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Table 6. Abundance by count cycle for birds utilizing five intertidal habitats.
Cycle
Z marina
Upogebia
/mud
Neotrypaea
/sand
Z japonica
Low
Marsh
Total
1 (Dec-Jan)
3977
4495
2105
631
801
12009
2 (Feb-Mar)
1205
2259
1689
17
514
5684
3 (Apr-May)
1227
2894
914
14
301
5350
4 (Jun-July)
741
1248
1116
59
267
3431
5 (Aug-Sep)
2286
3085
1307
248
371
7297
6 (Oct-Nov)
5528
7087
1142
192
1295
15244
Total
14964
21068
8273
1161
3549
49015
Table 7. Species richness by count cycle for birds utilizing five intertidal habitats. Gull
species (n=7) are combined.
Cycle
Z. marina
Upogebia/
mud
Neotrypaea
/sand
Z
japonica
Low
Marsh
Total
1 (Dec-Jan)
27
24
25
8
18
38
2 (Feb-Mar)
21
13
23
8
17
36
3 (Apr-May)
21
26
33
5
22
52
4 (Jun-July)
11
11
18
7
20
35
5 (Aug-Sep)
20
19
17
10
25
40
6 (Oct-Nov)
23
33
19
8
20
42
Total
45
53
51
23
49
79
Table 8. Species richness by sector for birds utilizing five intertidal habitats. Gull
species (n=7) are combined.
Sector
Z
marina
Upogebia
/mud
Neotrypaea
/sand
Z japonica
Low
Marsh
Total
Idaho Flat
24
38
38
1
29
57
Raccoon Flat
22
17
2
1
2
24
Sally's Bend
38
26
27
17
16
52
Upriver
28
33
39
13
37
61
Total of All Sectors
45
53
51
23
49
79
29

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1
Bird Species Number
¦I <10
10-20
20 -30
¦ 30 -40
\
k,l ?
jjTI »¦
\
Figure 6. Species richness of birds by habitat and sector in the Yaquina estuary
30

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Density Patterns
Based on the raw data, habitats/sectors with the highest bird density were Z
marina, low marsh and Upogebialmud habitats in Idaho Flat, and low marsh in the
Sally's Bend sector (Fig. 7, Table 9). Comparison based on bird density increased the
importance of low marsh habitats within the lower estuary sectors relative to bird
abundance.
After statistically controlling for potentially confounding factors of area and sector,
there were significant differences among habitats in bird density for all of the bird
subgroups examined (Figs. 8-11A, Table 10). When all birds were considered (Fig. 8A),
Z. marina (P=0.003) and possibly l/pogeb/a/mudflat (P=0.070) habitats had significantly
greater bird densities than Z.japonica; whereas low marsh and /Veofrypaea/sandflat
were intermediate and statistically indistinguishable from all other habitats. This pattern
was the same when gulls were excluded (Fig. 9A), indicating that the general pattern
was not driven by gulls even though this group accounted for a large proportion of
observed birds. For the waterfowl (Fig. 10A), Z marina had significantly greater
densities than l/pogeb/a/mudflat (P=0.020), Neotrypaealsandflat (P<0.001), and Z
japonica (P<0.001); low marsh had intermediate bird densities and was statistically
indistinguishable from all other habitats. Shorebirds displayed a different distributional
pattern (Fig. 11 A). For this group, estimated mean density was lowest in Z marina
habitat, and densities in Z marina were statistically significantly lower than all other
habitats except Z.japonica, and possibly l/pogeb/a/mudflat (P=0.059).
Models that included a random sector (region within estuary) effect were better
supported (i.e. lower AIC values) than models without this variable, indicating that bird
density varied among the sectors of Yaquina Estuary (Figs. 8B - 11B). Idaho Flat had
the highest estimated total bird densities (Figs. 8B, 9B), perhaps due to the ducks that
used this sector during the winter (Fig. 10B). Sally's Bend supported the highest
density of shorebirds (Fig. 11B). The Raccoon Flat sector was the least used region
within the estuary for all metrics of bird use (Figs. 8-11B).
For analyses of total bird density and total density excluding gulls, there were
significant interactions between sector and habitat on overall bird use (Figs. 8B, 9B).
Qualitatively, Z marina and l/pogeb/a/mudflat habitats were about equally used
regardless of location within the estuary, whereas the other habitats varied in quality
depending on sector. The most variable habitat in terms of estimated bird density was
low marsh, for which bird densities were very high in the Sally's Bend and Idaho Flat
sectors and very low in the Raccoon Flat sector.
Habitats with larger areas were associated with higher densities of waterfowl
(P=0.003, Fig. 10A). The relationship between shorebird density and habitat area was
marginally non-significant (P=0.090, Fig. 11A), suggesting that a response to habitat
area may be present for these taxa as well.
31

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Bird Count per Hectare
i. i ' <10
10-20
20 -50
50-100
100 -200
¦|>20°
Subtidal

\
A
\\
U 1
JWJ
S J
k

X

Mm.
II
/
w \
Figure 7. Bird densities (ha"1) by habitat and sector in the Yaquina estuary.
32

-------
Table 9. Bird density (ha"1) by count cycle and sector in five intertidal
habitats. Sector and Habitat grand totals were calculated by dividing
the total bird abundance in a given habitat or sector by the total area
of the habitat/sector within the estuary. Relative use values for the
habitats were calculated by dividing each habitat grand total by the
least used value.







Sector


Z
Upogebia
Neotrypaea
Z
Low
Grand
Sector
Cycle
marina
/mud
/sand
japonica
Marsh
Total

1
153.9
50.4
30.1
92.0
22.4
53.5
Idaho
2
11.0
22.3
23.0
0.0
39.6
22.3
Flat
3
6.2
14.5
11.8
0.0
7.5
12.1

4
6.4
4.5
20.7
0.0
10.8
10.6

5
11.8
28.8
25.8
0.0
23.5
25.3

6
81.1
81.1
17.2
0.0
100.9
60.2
Idaho Subtotals
270.4
201.6
128.6
92.0
204.7
183.9

1
5.5
19.6
0.0
0.0
0.0
10.6
Raccoon
2
6.2
12.4
0.0
0.0
0.0
7.7
Flat
3
2.4
3.6
0.0
0.0
0.6
2.4

4
3.7
19.2
0.2
0.0
0.0
9.8

5
14.5
6.9
0.0
0.0
1.9
8.5

6
10.6
33.2
0.9
0.5
0.6
18.6
Raccoon Subtotals
42.9
94.9
1.1
0.5
3.2
57.6

1
12.4
12.0
20.8
23.8
159.0
15.9
Sally's
2
6.4
8.2
11.9
0.5
1.2
6.9
Bend
3
9.7
36.5
4.2
0.4
29.5
14.5

4
4.7
4.7
4.3
1.9
8.4
4.4

5
13.4
17.8
4.3
9.3
20.5
12.8

6
37.3
18.8
2.9
5.1
1.8
24.2
Sally's Subtotals
83.9
98.1
48.4
41.0
220.5
78.6

1
28.1
5.7
1.9
0.0
3.6
4.2
Upriver
2
16.8
2.2
3.6
0.7
1.7
3.2

3
5.2
2.0
2.9
0.6
1.9
2.4

4
4.1
1.8
1.0
1.9
1.7
1.5

5
24.9
7.0
0.6
3.8
1.3
3.0

6
13.3
3.4
3.1
8.5
4.1
4.2
Upriver Subtotals
92.5
22.1
13.2
15.4
14.2
18.5
Habitat Density
93.3
119.0
46.0
33.7
33.1
74.4
Habitat Relative Use
2.8
3.6
1.4
1.0
1

33

-------
Density: All birds
Z marina -j
Upo/mud
Neo/sand -
Z japonica -
Low marsh -
P=0.434 ln(area)-ln(30>
Feb/Mar *
05 o
o
X CL
CO
CD O
o P
>> o
Apr/May -
Jun/Jul -
Aug/Sep -
Oct/Nov -
-0.48
-0jl9
-0.54
-0.3
-0.15
05
-0.5
—I
0.0
—r~
0.5
1.1€
2.21 a
ab
2.16
1.61 ab
—T"
1.0
1.77 ab
—r~
1.5
—I-
2.0
2.5
Z marina
Idaho
Raccoon
Sallys
Up river
Upo/mud
Idaho
Raccoon
Sallys
Up river
Neo/sand
Idaho
Raccoon
Sallys
Up river
Z japonica
l< ho
Raccoon
Sallys
Up river
Low marsh
Idaho
Raccoon
Sallys
Up river
0.5
—r
1.0
—r
1.5
	1
2.0
V Density (birds per sampling period per hectare)
Figure 8. Statistical model estimates for all birds: A) Model estimates (± standard error)
for transformed bird density (VVbirds- sample period"1 ha"1) as a function of
habitat, area, and cycle. Zero is the baseline prediction for a 30 ha area sampled
in Jan/Dec. Habitats with the same letters were not significantly different. B)
Model predictions for Wbird density based on habitat and sector (standardized
for a 30 hectare plot and averaged across all sample months).
34

-------
Density: All birds minus gulls
z. marina -
Upo/mud —
05 o
Neo/sand —
Z japonica -
Low marsh -
3—0 lnCareaVlnC30V-

1.92 ab

1.54 ab

1.00 b

1.66 ab
-CLJi

\J. OU niyaicay 111 \-j\j
Feb/Mar -
Apr/May -
CD O
Jun/Jul -
>s O
U X
Aug/Sep -
Oct/Nov —
-0.58

-0.51

-0.64

-0.j8

-0.25

i	1	1	1	r
-0.5 0.0 0.5 1.0 1.5 2.0
Z marina
Idaho
Raccoon
Sallys
Up river
Upo/mud
Idaho
Raccoon
Sallys
Upriver
Neo/sand
Idaho
Raccoon
Sallys
Upriver
Z japonica
Idaho
Raccoon
Sallys
Upriver
Low marsh
Idaho
Raccoon
Sallys
Upriver
I	1	1	1	1
0.0	0.5	1.0	1.5	2.0
•V Density (birds per sampling period per hectare)
Figure 9. Statistical model estimates for all birds minus gulls: A) Model estimates (±
standard error) for transformed bird density (VVbirdssample period"1 ha"1) as a
function of habitat, area, and cycle. Zero is the baseline prediction for a 30 ha
area sampled in Jan/Dec. Habitats with the same letters were not significantly
different. B) Model predictions for VVbird density based on habitat and sector
(standardized for a 30 hectare plot and averaged across all sample months).
35

-------
Density: Waterfowl (ducks and geese)
Z marina
Upo/mud
Neo/sand ~
Z japonica -
Low marsh ~
•3 ln(area)-ln(30)-
Feb/Mar
05 o
^ °
X CL
CD O
o P
>> o
Apr/May -
Jun/Jul-
Aug/Sep -
Oct/Nov -
-0.57
-0.67
-1.20
-0.78
10.16
-0.28
r~
-1.5
—r~
-1.0
-0.5
0.0
—I-
0.5
1.90 a
1.43 b
1.21 b
1.18 b
1.55 ab
—T"
1.0
—T"
1.5
—I
2.0
Z marina B
Idaho
Raccoon
Sallys 	
Up river
Upo/mud
Idaho
Raccoon
Sallys
Up river
Neo/sand
Idaho
Raccoon '
Sallys
Up river
Z japonica
Idaho
Raccoon *
Sallys
Up river
Low marsh
Idaho
Raccoon
Sallys
Up river
0.4 0.6 0.8 1.0 1.2 1.4 1.6
"ensity (birds persampling period per hectare)
Figure 10. Statistical model estimates for waterfowl (ducks and geese): A) Model
estimates (±standard error) for transformed bird density (VVbirds sample period"
1 ha"1) as a function of habitat, area, and cycle. Zero is the baseline prediction for
a 30 ha area sampled in Jan/Dec. Habitats with the same letters were not
significantly different. B) Model predictions for VVbird density based on habitat
and sector (standardized for a 30 hectare plot and averaged across all sample
months).
36

-------
Density: Shorebirds
05 O
O
|?
-L- n
Z marina
Upo/mud
Neo/sand -
Z japonica -
Low marsh-
P=0.090ln(area)-ln(30)
Feb/Mar
CD
o P
>. o
Apr/May -
Jun/Jul -
Aug/Sep -
Oct/Nov
Z marina
Idaho
Raccoon
Sallys
Up river
Upo/mud
Idaho
Raccoon
Sallys
Up river
Neo/sand
Idaho
Raccoon
Sallys
Up river
Z japonica
Idaho
Raccoon
Sallys
Up river
Low marsh
Idaho
Raccoon
Sallys
Up river
-0.2
B
-0.04
0.05
b
0.46
ab
0.60
0.40
ab
0.62
0.08
0.42
-oo4
0.17
0L01
0.0
0.2
0.4
—I-
0.6
0.0
—r
0.2
—r
0.4
—r
0.6
4E
ensity (birds persampling period per hectare)
Figure 11. Statistical model estimates for shorebirds: A) Model estimates (± standard
error) for shorebirds for transformed bird density (VVbirds sample period"1 ha"1) as
a function of habitat, area, and cycle. Zero is the baseline prediction for a 30 ha
area sampled in Jan/Dec. Habitats with the same letters were not significantly
different. B) Model predictions for VVbird density based on habitat and sector
(standardized for a 30 hectare plot and averaged across all sample months).
37

-------
Table 10. Pairwise comparison of modeled density and diversity values among
habitats with p-values after Tukey's correction. Gray highlighted values: p <
0.05.

VV Density
Diversity
Habitats
All
No gulls
Waterfowl
Shorebirds
Shannon
#
Species
Low marsh vs.
A/eo/sand
0.920
0.963
0.313
0.999
0.314
0.999
Low marsh vs.
L/po/mud
0.823
0.942
0.963
0.905
0.147
0.716
Low marsh vs.
Z japonica
0.352
0.310
0.139
0.647
0.033
0.839
Low marsh vs.
Z marina
0.669
0.718
0.218
0.006
0.781
0.001
A/eo/sand vs.
L/po/mud
0.473
0.550
0.642
0.893
0.985
0.405
A/eo/sand vs.
Z japonica
0.751
0.471
0.999
0.826
0.972
0.820
A/eo/sand vs.
Z marina
0.226
0.238
<0.001
0.003
0.006
<0.001
L/po/mud vs.
Z japonica
0.070
0.092
0.722
0.998
0.999
0.175
Upo/mud vs.
Z marina
0.999
0.675
0.020
0.059
0.001
0.011
Z. marina vs.
Z japonica
0.003
0.023
<0.001
0.261
0.003
<0.001
Standardized Diversity Patterns
According to statistical analyses, Bird diversity varied among habitats in the
Yaquina estuary (Table 10). Based on the Shannon diversity index (Fig. 12A), Z
marina had significantly greater diversity than all other habitats, except low marsh which
although higher than the other habitats, was only significantly greater than Z japonica.
With respect to the area standardized estimates of species richness, significantly more
bird species were observed within the Z marina habitat than for any other habitat (Fig.
13A, Table 10). According to model estimates that statistically control for habitat area
and sector, about two times more species are predicted to be observed in Z marina
during a sampling period than the other habitats.
Habitats with larger areas had significantly greater bird diversity based on the
Shannon index (P < 0.001, Fig. 12A). There was no significant relationship between
habitat area and standardized species richness (P = 0.24, Fig. 13A).
38

-------
Diversity: Shannon diversity index
Z. marina -
Upo/mud
Neo/sand
Z. japonica
Low marsh
ln(area)-ln(30)-
Feb/Mar
to o
~ o
X Q_
h-
0 CM
O °
>S O
Apr/May
Jun/Jul
Aug/Sep
Oct/Nov-1
-0.20
-0.19
-0.12
-0.0((
1.53 a
1.06 be
1.12 be
1.03 c
1.38 ab
0.25
0.20
0.0
—I-
0.5
—T"
1.0
1.5
Z. marina
Idaho
Raccoon
Sallys
Upriver
Upo/mud
Idaho
Raccoon
Sallys
Upriver
Neo/sand
Idaho
Raccoon
Sallys
Upriver
Z. japonica
ho
Raccoon
Sallys
Upriver
Low marsh
Idaho
Raccoon
Sallys
Upriver
0.6
	T"
1.0
—r
1.2
—r
1.4
—r
1.6
Shannon diversity (per sampling period)
Figure 12. Statistical model estimates for Shannon diversity: A) Model estimates (±
standard error) of the Shannon diversity index as a function of habitat, area, and
cycle. Zero is the baseline prediction for a 30 ha area sampled in Jan/Dec.
Habitats with the same letters were not significantly different. B) Model
predictions for the Shannon index of diversity based on habitat and sector
(standardized for a 30 hectare plot and averaged across all sample months).
39

-------
05 O
^ °
I?
Z marina -
Upo/mud-
Neo/sand ~
Z japonica
Low marsh ~
35 ln(area)-ln(30)-
Feb/Mar ~
Diversity: Species richness
A
CM
CD O
o P
>< o
Apr/May -
Jun/Jul~
Aug/Sep -
Oct/Nov
-1.71
.38
-0.2ft
-2.32
-1.12
-2
(p.41
8.23
6.26 b
5.23 b
4.32 b
5.31 b
Z marina
Idaho
Raccoon
Sallys
Upriver
Upo/mud
Idaho
Raccoon
Sallys
Upriver
Neo/sand
Idaho
Raccoon
Sallys
Upriver
Z japonica
l< ho
Raccoon
Sallys
Upriver
Low marsh
Idaho
Raccoon
Sallys
Upriver
~r
~T"
4	6
Shannon diversity (persampling period)
Figure 13. Statistical model estimates for species richness: A) Model estimates (±
standard error) the estimated number of species after rarefaction as a function of
habitat, area, and cycle. Zero is the baseline prediction for a 30 ha area sampled
in Jan/Dec. Habitats with the same letters were not significantly different. B)
Model predictions for the estimated number of species after rarefaction based on
habitat and sector (standardized for a 30 hectare plot and averaged across all
sample months).
40

-------
Regardless of habitat, the sector of the estuary had an effect on bird diversity
(Figs. 12B - 13B). Qualitatively, the Upriver sector had the highest mean values of the
Shannon diversity index (Fig. 12B), with the Idaho Flat sector second. In contrast, the
Idaho Flat had the highest rarefaction estimate of number of species (Fig. 13B), with the
Upriver sector second. The Raccoon sector had the lowest diversity for both metrics.
Seasonal Patterns of Density and Diversity
There was a statistically significant relationship between count cycle and total
bird density (P=0.003), total density excluding gulls (P<0.001), and waterfowl (P<0.001).
In general, the densities of these groups appear to peak around Dec/Jan (count cycle 1,
Figs. 8-10, Table 11). Densities then decline during Feb/Mar, with abundance at only
about 22% of peak abundance (Table 6, Appendix F). Densities remain low through
Jun/Jul and then increase from Aug/Nov. Peak densities correspond to a period when
waterfowl were present (Table 3), gulls were abundant, and foraging crows and
overwintering flocks of shorebirds were common. The low densities during
February/March (count cycle 2) correspond to decreases in abundance of American
Wigeon, Northern Pintail and American Coot (Tables 4, 11). The increase in density
that occurs during Aug/Nov corresponds to a period when herons, egrets, gulls, ducks,
and geese returned to the estuary (Table 4). Brown Pelicans were present in the lower
Yaquina estuary in September.
Shorebirds had a different seasonal density pattern than the other taxonomic
groups, with their numbers peaking around April/May (Fig. 11) during spring migration.
However, none of the pairwise comparisons among sample cycles were significantly
different (Table 11), and the overall model effect of cycle was marginally non-significant
(P=0.051).
Seasonal patterns of Shannon diversity and species richness are somewhat
more complicated (Figs. 12-13, Table 11). The analyses suggest there may be two
yearly peaks in diversity, one around Oct-Jan and then around Apr/May. For Shannon
diversity, Apr/May had significantly greater diversity than either Feb/Mar or Jun/Jul. For
species richness, Oct/Nov had significantly greater diversity than either Feb/Mar or
Jun/Jul. Interestingly the period of high diversity in Apr/May corresponds to a period of
relatively low bird abundance. Similar to the density data, species diversity metrics
were relatively low in June/July (Figs. 12-13, Table 11).
41

-------
Table 11. Pairwise comparison of modeled density and diversity values between count
cycles with p-values after Tukey's correction. Gray highlighted values: p <0.05.

VVDensity
Diversity
Sample
Months
All
No gulls
Waterfowl
Shorebirds
Shannon
# Species
Dec vs. Feb
0.023
0.003
0.010
0.999
0.631
0.171
Dec vs. Apr
0.020
0.014
0.001

0.133
0.630
0.999
Dec vs. Jun
0.006
<0.001
<0.001

0.999
0.708
0.017
Dec vs. Aug
0.361
0.028
<0.001

0.910
0.947
0.638
Dec vs. Oct
0.934
0.580
0.565
1.000
0.999
0.994
Feb vs. Apr
1.000
0.997
0.993
0.070
0.024
0.339
Feb vs. Jun
0.999
0.999
0.003
1.000
1.000
0.959
Feb vs. Aug
0.863
0.984
0.846
0.795
0.987
0.964
Feb vs. Oct
0.255
0.286
0.516
0.999
0.825
0.041
Apr vs. Jun
0.999
0.957
0.024
0.074
0.034
0.050
Apr vs. Aug
0.842
1.000
0.990
0.699
0.139
0.843
Apr vs. Oct
0.233
0.575
0.199
0.154
0.416
0.943
Jun vs. Aug
0.638
0.893
0.132
0.807
0.995
0.557
Jun vs. Oct
0.107
0.128
<0.001

0.999
0.880
0.002
Aug vs. Oct
0.912
0.716
0.043
0.930
0.993
0.287
Tide Level Patterns
Tide level was also an important factor in bird distribution across the intertidal
habitats. Bird use of habitat changed with the tide as indicated by the significant
interaction between tide and habitat (P< 0.001) regardless of whether bird abundance or
VVdensity was analyzed. Bird use is highest, as the tide approaches or recedes from
the habitat. Bird densities decline dramatically when the habitat is flooded (Fig. 14).
Within the broad general pattern, responses to tidal level varied among both bird
groups and habitats (Fig. 15A-E). Both abundance and density was generally higher for
birds foraging on intertidal Z marina and l/pogeb/a/mudflat habitats at low to mid tide
levels (<0.3 - 0.9 m) than at tidal levels above +1.5 m (Tables 12, 13). At mid tide
levels (+1.2-1.5 m) most gulls moved to intertidal Neotrypaea/sandflats higher in the
intertidal zone to rest and preen as the lower elevation habitats became flooded (Fig.
15C). Over the winter, dabbling ducks drifted on the water's surface at mid tide levels
without utilizing the intertidal habitats, and thus were not counted. In contrast, diving
ducks and herons moved in to forage on invertebrates and fish as the lower habitats
were flooded and prey became available. At higher tide levels (+1.8 to >2.4) gulls
dispersed to higher ground or floated in the main estuary channel, ducks and geese fed
on marsh plants and in some cases on Z.japonica in the upper intertidal region, while
herons and geese roosted in exposed, emergent marsh. Shorebirds followed the tide at
the water's edge, foraging in Z. marina and l/pogeb/a/mudflats when those habitats
42

-------
were exposed, then moving across A/eofrypaea/sandflats and Z japonica habitats as
the tide rose, and roosting on exposed rocks, floats and in emergent marsh at high tide
Corvids had similar foraging patterns in the intertidal habitats to the gulls, but retreated
to trees or other terrestrial habitats at high tide. Other passerines occasionally visited
emergent marsh and other habitats to forage when those habitats were exposed.

_05
2.4
Tide level, m above MLLW
Figure 14. Comparison of relative bird abundance versus tide level for five
intertidal habitats. Relative abundance was calculated using the average
bird counts of observation periods for each habitat and tide cycle. Within
each habitat, the average bird abundance for each tide cycle was divided
by the tide cycle with the highest abundance. Within a habitat, bird use is
highest just before or after habitat flooding.
Neo/sand
Z. japonica
Exposed	Flooded
Low marsh
43

-------
Table 12. Abundance by tide level and count cycle of birds utilizing five intertidal
habitats. Tide levels did not exceed +2.4 m during daylight hours in count cycles
3 and 4 (April-July).


Z
Upogebia
Neotrypaea
Z
Low

Cycle
Tide (m)
marina
/mud
/sand
japonica
Marsh
Total
1
< 0.3
2892
326
146
3
7
3374
Dec-
0.6-0.9
604
2300
201
80
84
3269
Jan
1.2-1.5
148
1365
472
513
171
2669

1.8-2.4
270
360
1170
2
499
2301

>2.4
63
144
116
33
40
396
Cycle 1 Total
3977
4495
2105
631
801
12009
2
< 0.3
874
802
304
1
330
2311
Feb-
0.6-0.9
95
744
207
7
61
1114
Mar
1.2-1.5
88
547
1093
0
28
1756

1.8-2.4
123
133
70
7
79
412

>2.4
25
33
15
2
16
91
Cycle 2 Total
1205
2259
1689
17
514
5684
3
< 0.3
1100
429
272
2
38
1841
Apr-
0.6-0.9
78
2378
120
10
41
2627
May
1.2-1.5
7
14
165
2
96
284

1.8-2.4
42
73
357
0
126
598
Cycle 3 Total
1227
2894
914
14
301
5350
4
< 0.3
602
153
312
9
90
1166
Jun-
0.6-0.9
124
1078
79
15
36
1332
July
1.2-1.5
6
13
371
35
39
464

1.8-2.4
9
4
354
0
102
469
Cycle 4 Total
741
1248
1116
59
267
3431
5
< 0.3
1646
973
110
71
32
2832
Aug-
0.6-0.9
549
1990
127
95
21
2782
Sept
1.2-1.5
25
100
641
82
57
905

1.8-2.4
24
10
419
0
66
519

>2.4
42
12
10
0
195
259
Cycle 5 Total
2286
3085
1307
248
371
7297
6
< 0.3
4533
2706
74
67
5
7385
Oct-
0.6-0.9
571
3520
250
54
84
4479
Nov
1.2-1.5
57
362
462
71
56
1008

1.8-2.4
279
307
329
0
317
1232

>2.4
88
192
27
0
833
1140
Cycle 6 Total
5528
7087
1142
192
1295
15244
Total
14964
21068
8273
1161
3549
49015
44

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Table 13. Bird density (ha"1) by tidal level and count cycle in five intertidal habitats.







Tidal


Z
Upogebia
Neotrypaea
Z
Low
Level or
Cycle
Tide (m)
marina
/mud
/sand
japonica
Marsh
Cycle
1
< 0.3
18.0
1.8
0.8
0.1
0.1
5.1
Dec-
0.6-0.9
3.8
13.0
1.1
2.3
0.8
5.0
Jan
1.2-1.5
0.9
7.7
2.6
14.9
1.6
4.1

1.8-2.4
1.7
2.0
6.5
0.1
4.7
3.5

>2.4
0.4
0.8
0.6
1.0
0.4
0.6
Cycle 1 Total
24.8
25.4
11.7
18.3
7.5
18.2
2
< 0.3
5.5
4.5
1.7
0.0
3.1
3.5
Feb-
0.6-0.9
0.6
4.2
1.2
0.2
0.6
1.7
Mar
1.2-1.5
0.5
3.1
6.1
0.0
0.3
2.7

1.8-2.4
0.8
0.8
0.4
0.2
0.7
0.6

>2.4
0.2
0.2
0.1
0.1
0.1
0.1
Cycle 2 Total
7.5
12.8
9.4
0.5
4.8
8.6
3
< 0.3
6.9
2.4
1.5
0.1
0.4
2.8
Apr-
0.6-0.9
0.5
13.4
0.7
0.3
0.4
4.0
May
1.2-1.5
0.0
0.1
0.9
0.1
0.9
0.4

1.8-2.4
0.3
0.4
2.0
0.0
1.2
0.9
Cycle 3 Total
7.7
16.3
5.1
0.4
2.8
8.1
4
< 0.3
3.8
0.9
1.7
0.3
0.8
1.8
Jun-
0.6-0.9
0.8
6.1
0.4
0.4
0.3
2.0
July
1.2-1.5
0.0
0.1
2.1
1.0
0.4
0.7

1.8-2.4
0.1
0.0
2.0
0.0
1.0
0.7
Cycle 4 Total
4.6
7.0
6.2
1.7
2.5
5.2
5
< 0.3
10.3
5.5
0.6
2.1
0.3
4.3
Aug-
0.6-0.9
3.4
11.2
0.7
2.8
0.2
4.2
Sept
1.2-1.5
0.2
0.6
3.6
2.4
0.5
1.4

1.8-2.4
0.1
0.1
2.3
0.0
0.6
0.8

>2.4
0.3
0.1
0.1
0.0
1.8
0.4
Cycle 5 Total
14.3
17.4
7.3
7.2
3.5
11.1
6
< 0.3
28.3
15.3
0.4
1.9
0.0
11.2
Oct-
0.6-0.9
3.6
19.9
1.4
1.6
0.8
6.8
Nov
1.2-1.5
0.4
2.0
2.6
2.1
0.5
1.5

1.8-2.4
1.7
1.7
1.8
0.0
3.0
1.9

>2.4
0.5
1.1
0.2
0.0
7.8
1.7
Cycle 6 Total
34.5
40.0
6.3
5.6
12.1
23.1
45

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7000
6000
5000
01
u
c
(C
¦c 4000
c
3
-D
< 3000
"D
Zoster a marina
CO
2000
1000
¦ l.ll
1
cn
LD
¦3-
¦3-

cn
¦
LD
¦3-
pM.
¦3-

cn
LD



cn
LD
JL.
¦3-

cn
LD
¦3-
¦3-
m
cn
LD
¦3-

m
cn
LD

o
rH
(N
(N
o
o
rH
(N
(N
o
o
rH
-------
2500
Neotrypaea/sand
2000
01
U
TO 1500
-a
c
3
-D
<
"C 1000
CO
500
1
ll
lu
¦
cn
LD
"tf
"tf
m
cn
¦
LD


m
cn
LD

¦3-
m
cn
LD
¦3-
¦3-
m
cn
LD


m
cn
in
¦3-
¦3-
m
cn
LD
¦3-
o
rH
(N
(N
o
o
rH

(N
00
O
rH
rH


O
rH
rH


O
rH
rH


O
rH
rH


o
rH
rH


O
rH
rH


O
rH
rH
Geese


Ducks

Herons/Egrets

Rails

Shorebirds
Terns/Gulls

Corvids
350
01
u
c
(C
-a
c
3
.a
<
"O
5
300
250
200
150
100
50
Zostera japonica
cn
LD


m
cn
LD
JL.

m
cn
LD
¦3-
¦3-
m
cn
in
¦3-

m
cn
LD
¦3-
¦3-
m
cn
in
¦3-
¦3-
m
cn
in
¦3-
o
rH
Csl
(N
o
o
rH
-------
900
800
700
2	600
c
(G
"O 500
3
< 400
¦a
5 300
200
100
0
Low Marsh
1
mJ
cn
Ln


CO
cn
Ln


CO
cn
Ln


CO
cn
Ln
¦st;

rn
cn
in


rn
cn
in


rn
cn
in

o
rH
(N
-------
Table 14. Comparison of bird abundance by habitat and sector for replicate counts of
one or more sectors conducted in count cycles 2-6 at low tide (<0.3 m). CV -
Coefficient of Variation.
Cycle
Sector
Habitat
Original
Count
Repeat
Count
Average
SD
O
<
2
Idaho
Z marina
130
271
200.5
99.70
0.50


L/po/mud
545
336
440.5
147.79
0.34


A/eo/sand
59
27
43.0
22.63
0.53


Z japonica
0
0
0.0
0.00
0.00


Low Marsh
297
2
149.5
208.60
1.40
3
Sally's
Z marina
928
556
742.0
263.04
0.35

Bend
L/po/mud
19
43
31.0
16.97
0.55


A/eo/sand
1
3
2.0
1.41
0.71


Z japonica
1
0
0.5
0.71
1.41


Low Marsh
3
1
2.0
1.41
0.71
4
Upriver
Z marina
20
16
18.0
2.83
0.16


L/po/mud
53
154
103.5
71.42
0.69


A/eo/sand
0
0
0.0
0.00
0.00


Z japonica
0
0
0.0
0.00
0.00


Low Marsh
0
0
0.0
0.00
0.00

Raccoo
Z marina
36
32
34.0
2.83
0.08

n
L/po/mud
24
93
58.5
48.79
0.83


A/eo/sand
65
18
41.5
33.23
0.80


Z japonica
0
7
3.5
4.95
1.41


Low Marsh
28
29
28.5
0.71
0.02
5
Idaho
Z marina
83
310
196.5
160.51
0.82


L/po/mud
854
1268
1061.0
292.74
0.28


A/eo/sand
20
56
38.0
25.46
0.67


Z japonica
0
0
0.0
0.00
0.00


Low Marsh
9
0
4.5
6.36
1.41
6
Sally's
Z marina
3506
1036
2271.0
1746.55
0.77

Bend
L/po/mud
126
190
158.0
45.25
0.29


A/eo/sand
10
12
11.0
1.41
0.13


Z japonica
10
243
126.5
164.76
1.30


Low Marsh
0
0
0.0
0.00
0.00

Total Average CV =
(SD all counts/avg. all counts)
2.669
Average CV within
Cycle/Sector/Habitat =
0.538
When both counts were 0, CV was c
assified as 0.
Table 15. Average coefficients of variation within treatment groups. Relative CV values
are calculated by dividing the within group CVs by the total CV of all the counts.
P-values indicate whether the CV within a group is significantly smaller than
expected by chance. * Calculations in Table 14.


Variation within group

All
Counts*
Cycle/Sector/
Habitat*
Sector/
Habitat
Avg CV
2.67
0.54
0.67
Relative CV
1.00
0.20
0.25
P-value
—
<0.001
<0.001
49
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Regional Observations
Observations on birds occupying estuarine intertidal habitats in estuaries other
than Yaquina were made opportunistically in conjunction with other studies (Appendix
G). These observations, though not as rigorous as those in this study, showed that bird
use of intertidal habitats in Pacific Northwest estuaries from Coos Bay, Oregon to
Willapa Bay, Washington were generally consistent with bird use in Yaquina. However,
some birds observed in the Low Marsh habitats of these estuaries were not commonly
encountered in Yaquina salt marshes, such as Savannah Sparrow, Marsh Wren and
Virginia Rail, which primarily use more freshwater marsh habitats.
Other Observations
People and other mammals
Observations of habitat use by people and other mammals were recorded as bird
counts were conducted. Harbor seals used l/pogeb/a/mudflat and Z. marina habitats
adjacent to channels in Sally's Bend for haul-outs. Raccoons were frequently seen
foraging on l/pogeb/a/mudflat on Raccoon Flat and Idaho Flat, and deer or their tracks
were occasionally observed on /Veofrypaea/sandflat or rocky beaches. People were
observed walking, collecting burrowing shrimp, digging clams or conducting research,
primarily on l/pogeb/a/mudflats and Neotrypaea/sandflats, as well as boating, kayaking
and kite boarding over flooded sandflats, mudflats and eelgrass beds. Flocks of gulls,
ducks and shorebirds were occasionally disturbed during counts by helicopters, boats,
kite boarders and people with children or dogs chasing birds, though the primary source
of disturbance was raptors such as Peregrine Falcons or Bald Eagles.
Use of Other Habitats
Bird use of other habitats was noted but not counted or included in the analyses
for this report because these habitats were outside of the survey design. This included
birds that sometimes foraged on rocky beaches, as well as the flocks of gulls and
cormorants, as well as smaller numbers of herons and shorebirds that roosted on rocks,
floats and pilings during high tide. Green Herons were seen fishing from floats, bald
eagles often perched on pilings above mudflats and sandflats, and Black-crowned Night
Herons were seen roosting in trees above emergent marsh.
50
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DISCUSSION
The primary goal of this study was to assess the relative usage of five different
tidal wetland habitats within the Yaquina estuary in regard to bird use. Previous studies
of tidal wetland habitat use in west coast estuaries have tended to focus on either single
species (Warnock and Takedawa 1995, Wilson and Atkinson 1995), or on a limited
group of species (Baldwin and Lovvorn 1994a), particularly shorebirds (Colwell 1993,
Conners 2008, Warnock et al. 2002). Our assessment of the relative use of tidal
habitats by the complete bird assemblage was complicated by the fact that bird use
within the estuary is affected by location within the estuary (sector), type of bird, season,
and by the tidal level. However, given the large amount of data collected in this study,
patterns of differences in habitat utilization among sectors, tide levels, time of year, and
habitats were apparent. One limitation of the study is that results for the Z japonica
habitat should be interpreted cautiously due to the small area of this habitat relative to
others.
Habitat and Spatial Patterns
Z. marina is a valuable bird habitat in Yaquina estuary based on almost all
metrics of bird use. Z marina, along with low marsh, supported statistically greater
densities of waterfowl than the other habitats. Z marina also had higher species
diversity (Shannon index, standardized richness) than all other habitats, except low
marsh for the Shannon index. An exception was that Z marina had significantly lower
densities of shorebirds than any other habitat except Z. japonica and l/pogeb/a/mudflat.
Z marina habitat provides a foraging area for Brant, large numbers of clucks, gulls,
crows, herons, and shorebirds when exposed at low tides. The habitat also serves as a
roosting area for herons and cormorants. The Z marina bed was the preferred habitat,
when exposed at low tide, by dabbling ducks (wigeon spp., Northern Pintail, Mallard,
Green-winged Teal), American Coot, and Brant. Based on feeding observations (online
database, Appendix H), when inundated at tide levels >0.3 m, flooded eelgrass flats
were used by birds dabbling for Z marina (wigeon, Brant, and American Coot), diving
for fish and intertidal mollusks and crustaceans (Bufflehead, Common Goldeneye,
scaup spp., Ruddy Duck and scoters), foraging or diving for fish (herons, egrets, loons,
grebes, mergansers, cormorants, Osprey and Belted Kingfisher). Flooded channels
were used by ducks (wigeon spp., Bufflehead, scaup spp., Ruddy Duck, scoters)
foraging for invertebrates, and by herons, egrets, mergansers and cormorants for
fishing. Eelgrass plants in these channels were consumed by coots and wigeon, and
the channels were used for roosting by cormorants.
These results are consistent with other studies that have shown close spatial
association of some birds to estuarine food resources. Brant usage of estuarine
habitats in Willapa Bay, Washington was positively associated with presence of Z
marina habitat and negatively associated with oyster bed habitat (Wilson and Atkinson
1995) as a result of the direct use of eelgrass as food by the birds. Balwin and Lovvorn
(1994a) examined three intertidal elevations zones in Boundary Bay, British Columbia,
Canada, and found that the biomass and numbers of most food items for dabbling
51
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ducks and Brant were greatest in the zones with Z japonica and Z marina, which is
where the birds were observed to primarily feed.
The l/pogeb/a/mudflat habitat appears to support relatively high total bird
densities regardless of the sector in the estuary (Fig. 8B). Furthermore, this habitat was
extensively used at low to mid-tide (<0.3 to 0.6-0.9 m) by foraging gulls (many of which
were also foraging in Z marina). At mid-tide levels (0.6-0.9 m), when Z marina was
flooded and inaccessible, exposed l/pogeb/a/mudflat was used by foraging ducks and
gulls, feeding and roosting Canada Geese, foraging and roosting herons, shorebirds
(foraging Dunlin and "peep" sandpipers, Whimbrel foraging and feeding on burrowing
shrimp), foraging crows, and occasionally by roosting Caspian Terns and raptors such
as Bald Eagle. The flooded mudflat (tide levels >1.2 m) was utilized by diving ducks
(Bufflehead, Common Goldeneye, scaup, scoter and merganser), herons, loons,
grebes, cormorants, kingfisher, and terns for preying on fish and invertebrates such as
cockles; and by dabbling ducks (wigeon spp., Northern Pintail) and American Coot
feeding on drift plant material. Flooded channels were used by foraging ducks (wigeon,
feeding on drift Z marina) and by herons, egrets and cormorants.
The Neotrypaealsandftat habitat was utilized primarily when flooded at mid to
high tide levels by foraging ducks and shorebirds, and, when it was exposed, by
roosting gulls when the preferred feeding grounds (Z marina and l/pogeb/a/mudflat)
were flooded. The exposed sandflat was used by geese (Brant and Canada Geese) for
roosting or foraging on green macroalgae (Appendix H), and by roosting herons and a
few raptors (osprey and eagle). The exposed sandflat was also used at mid to high tide
levels (>1.5 m), by some foraging gulls, crows, and a few dabbling ducks (Mallard,
wigeon and Northern Pintail) feeding on drift plant material. A variety of shorebirds
foraged in the habitat, especially Whimbrel, which were observed to capture and
consume Neotrypaea shrimp. The flooded sandflat (>1.8 m tide levels) was used by
dabbling ducks foraging on drift plant material at the water's edge, and by diving ducks
preying on intertidal invertebrates. Herons fished at water's edge as the tide came in,
and grebes, cormorants, osprey and kingfisher foraged when the sandflat flooded.
Channels within the flooded habitat were also used by herons and diving ducks for
foraging and fishing, and when the habitat was exposed, the channels provided foraging
habitat for a variety of shorebirds.
The Z. japonica beds were used primarily by ducks (mostly mallards) and rails
(coot) foraging on Z japonica blades either at mid-tide levels (0.6-1.5 m) when Z
marina beds were flooded, or at high tide (>1.8 m) when the Z japonica was flooded but
shallow. In late winter, the aboveground biomass of this eelgrass species died and was
largely reduced to stubble, and shorebirds foraged both within this habitat and in the
adjacent Neotrypaealsandflat without apparent regard to the presence of the stubble.
The Z japonica habitat was used as a foraging area by a few crows, and occasionally
as a roosting area by gulls, herons, terns and geese. Based on feeding observations
(online database, Appendix H), Z japonica was consumed by American Coot, wigeon,
Northern Pintail and Canada Geese. Mallard consumed Z japonica, but no Brant were
observed feeding or roosting in Z japonica beds in Yaquina estuary during this study.
52
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One issue of recent potential concern is whether the introduction of Z japonica
will negatively affect bird use of intertidal habitat in estuaries, particularly for shorebirds.
Although this study was not primarily designed to address this question, it provided a
preliminary evaluation of the issue. In Yaquina estuary, Z japonica is most likely to
supplant the Neotrypealsand habitat. There were no significant differences between Z
japonica and Neotrypea /sand habitat for any metric of bird use. Currently, there is no
evidence that birds will be negatively impacted by the presence of this invasive species
in Yaquina estuary. Baldwin and Lovvorn (1994a) have shown that Z japonica is
readily fed on and is an important food source for brant and a variety of dabbling ducks
including American Wigeon, Northern Pintail, and Mallard. In the Yaquina, Canada
Geese and American Coots were also observed to feed on Z japonica (Appendix H).
Low marsh habitat is a potentially valuable habitat, particularly for waterfowl (Fig.
10) and shorebirds (Fig. 11), and may have high Shannon diversity (Fig. 12). The low
marsh habitat was exposed at low to mid-tide levels (<1.8-2.4 m), and served as
roosting and foraging grounds for herons, Mallard and Canada geese, and as hunting
and foraging area for a variety of shorebirds as well as swallows, blackbirds, starlings
and other passerines (Appendix C). When tidal channels were flooded (>1.8 m) and the
lower portions of the marsh were inundated (>2.4 m), the habitat served as foraging and
fishing ground for American Wigeon, Northern Pintail, American Coot, a variety of diving
ducks, herons and kingfishers.
The division of the estuary into four sectors was driven by the logistical demands
of sampling. However, spatial location within the estuary as represented by the sectors
influenced all metrics of bird use. The Idaho Flat sector generally supported the largest
total bird densities, waterfowl densities, and species richness. The Sally's Bend sector
supported the largest density of shorebirds. The Upriver sector had high Shannon
diversity. The Raccoon Flat sector had the lowest bird use based on all metrics. The
specific factors driving the observed bird use patterns among sectors are unknown.
However, it is clear that bird use varies depending on location within the estuary, even
when the dominant habitat is the same. It is likely that unmeasured variables
associated with different regions of the estuary - such as human development
(McKinney et al. 2006), distance from estuary mouth, etc. - influence bird use. Wetzel
(1996) noted that human activities on the water and on the shore adjacent to eelgrass
beds in Yaquina estuary were a major influence on the use of these habitats by Brant.
Studies comparing the relative value of habitats in regard to bird use should consider
these potentially confounding variables.
Seasonal Patterns
Bird use of the estuary varied dramatically over the course of a year. In general,
total bird densities appeared to peak around Dec/Jan (Figs. 8-10); then declined around
Feb/Mar and remained relatively low until after Jun/Jul; after which, they began to
increase. In Dec/Jan ducks were the most abundant group of birds observed, while
gulls predominated in Feb/Mar. Gull abundance on intertidal habitats decreased in
Apr/May during breeding season and increased during Jun/Jul with the dispersal of
young Western and Glaucous-winged Gulls and hybrid gulls from local nesting grounds.
53
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There was also an influx of California Gulls from their inland breeding grounds, joined
by Caspian Terns and their young dispersing from Columbia River nesting grounds.
Shorebirds have a different seasonal pattern, and their densities appeared greatest
during spring migration in Apr/May (Fig. 11).
Seasonal patterns of Shannon diversity and species richness are somewhat
more complicated. Similar to total density, species diversity metrics appeared relatively
low in Jun/Jul (Figs. 12-13). The analyses suggest there may be two yearly peaks in
diversity, one around Oct-Jan and then around Apr/May.
The seasonal trends observed are consistent with those observed by Merrifield
(1998, 2001) during extensive bird surveys conducted in the Yaquina estuary during
1993-94 and 1997-99. Counts of individual species differed between the two studies
because the present study focused on birds directly utilizing intertidal estuarine habitats,
whereas Merrifield recorded all birds present on the estuary. Additionally, Merrifield's
counts were primarily at low tide, while in the present study counts were made at five
tide levels.
Tidal Patterns
In the Yaquina estuary, and presumably in other Pacific Northwest estuaries with
similar tidal patterns, the tides drive bird feeding patterns and habitat utilization across
the intertidal zone (Fig. 14, Tables 12 and 13). Overall, bird abundance is highest as
the tide approaches or recedes from the habitat. Bird densities are lower when the
habitat is flooded (Fig. 14).
Based on observations during this study, different bird groups respond differently
to tidal stage (Fig. 15). The observational data yields the following general patterns of
tidal response. At low tide when all intertidal habitats were exposed, gulls, dabbling
ducks, geese, crows and shorebirds forage for invertebrates and feed on plant material
in the lower intertidal habitats: Zostera marina and unvegetated mudflat. These habitats
are rich in invertebrate prey (Ferraro and Cole, 2007). As the tide rises and the
seagrass habitat is covered, gulls and shorebirds move upslope and continue to forage
on exposed plant material and invertebrates on the exposed mudflat. Herons, egrets
and diving species such as cormorants, loons, grebes and pelicans were observed
eating fish and crabs that moved in with the tide (Appendix H; online data). Shorebirds
follow the water's edge, and diving ducks move over the flooded intertidal habitats to
dive for mollusks and other invertebrates. As the rising tide covers the lower intertidal
seagrass and mudflat habitats, birds move upslope, and gulls roost and preen in the
upper intertidal sandflat, while shorebirds and crows continue to forage in this habitat.
Herons and diving birds forage in the flooded seagrass and mudflat, while crows,
shorebirds, dabbling ducks and geese forage in upper intertidal Z.japonica patches. As
the unvegetated habitats and Zostera patches are flooded, herons, geese and dabbling
ducks rest or forage in non-flooded portions of exposed marsh, shorebirds roost on
rocks, floating docks or in the marsh or head for ocean beaches, gulls drift offshore or
54
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roost on land, crows take refuge in trees, and diving ducks continue to feed in flooded
habitats.
In addition to the broader group responses described above, a range of studies
have demonstrated that the responses of birds to the tidal cycle in estuaries may vary
depending on species. Similar to the pattern observed in the Yaquina, abundance of
Sanderlings in Bodega Bay decrease sharply on intertidal flats at higher tide levels
(Conners et al. 1981). In this case, the birds are moving off of the estuarine flats to the
outer coast sand beaches at mid-level and high tides on a regular basis. This
movement is consistent with observations on the location of maximum density of prey
items for Sanderlings, which is higher at lower elevations on the tide flats. In Elkhorn
Slough, California, small sandpipers are more abundant at high tide within wetlands with
muted tidal action, moving from the open tide flats to these areas where the substrate
stays exposed longer (Conners 2008). In contrast, the larger stilts and avocets which
can forage in shallow water generally show no difference between the two habitat types
over the tidal cycle.
For waterfowl such as Brant, tidal depth is also important in terms of habitat
utilization. Wetzel (1996) found that Brant dispersed across the Yaquina at high tide,
and concentrated at the shore to feed on eelgrass at lower tidal stages. Moore and
Black (2006) found strong tidal stage effects on Brant foraging in Humboldt Bay. Birds
tended to feed in the deepest possible areas permitted by tidal stage, which tended to
be where eelgrass plants had highest levels of protein, calcium and biomass.
Sampling Issues
The aggregated nature of birds requires very large sample sizes in order to
resolve patterns of bird use among habitats. Within a given habitat/sector/tide/season
the variation in observed birds on a single observation can be very large due to
stochastic sources of variation, such as weather, local human disturbance, or presence
of a predator. A complex issue is the relation of bird abundance to area of the habitat
being sampled. Even after converting abundance to density for comparison in the
present study, the effect of area was often still statistically present. Benoit and Askins
(2002) examined the relationship of habitat area and abundance and distribution of
specialized tidal marsh birds in Connecticut. Rather than a complete areal census,
constant areas were sampled. Responses were species specific. Salt Marsh Sparrow
and Willet were found in higher abundance in larger marshes, especially those
exhibiting lower levels of fragmentation, while other species such as Virginia Rail, Marsh
Wren and Swamp Sparrow showed no response to marsh area. We have not
attempted to determine habitat responses at the species level in the present study.
All results of the present study are based on day time visual surveys. Shepherd
et al. ( 2003) used radio telemetry to examine diurnal differences in Dunlin habitat
usage in the Fraser River estuary, British Columbia, and found that the birds spent
equal times foraging in both day and night. The Dunlin used terrestrial habitats adjacent
to the intertidal areas more frequently at night. Sole use of day time surveys thus may
underestimate the importance of near estuary terrestrial habitats to some shorebird
55
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species, with important consequences to conservation planning. In the Yaquina
estuary, the lowest tides during the winter period occur at night, presenting considerable
foraging opportunity. The extent of nocturnal usage and its relative distribution among
estuarine habitats is presently unknown for this system.
Use for Assessing Ecosystem Services
The present bird habitat assessment study is part of an EPA research program to
develop approaches to quantify the benefits, or ecosystem services (Millennium
Ecosystem Assessment 2005), that estuaries provide for people. One aim of the
research program is to determine whether it is feasible to use major estuarine habitats
as a framework to assess ecosystem services. This approach may be ideal because
habitats can be mapped using a variety of remote sensing and ground based
approaches. If services can be associated to habitats then it may be possible to predict
how changes in habitat from various causes will alter the services we derive from
ecosystems.
The results from this study suggest that alterations of the most common habitats
in the Yaquina estuary will affect bird use. Various habitats have different ecological
roles, and the loss of a given habitat will affect various species differently. For example,
if Z marina populations decline, overall bird usage may be negatively affected given the
overall diversity and abundance of birds associated with this habitat, but shorebird
populations will likely be less affected than waterfowl.
Predictions using the present study data should be made cautiously. There are
many complicating factors that may confound the results. We could not control for
several variables that will covary with habitat. For example, some habitats are more
likely to be located near the margins of the estuary, which may be perceived by birds as
less safe. The best way to control for these confounding variables is to conduct similar
studies in other estuaries to determine which habitat patterns persist
The present study has determined that assessing bird use among habitat type
within estuaries can establish relative usage patterns. The results do indicate that
usage within a habitat type is not constant across the spatial extent of the estuary, and
thus location must be considered in ecosystem services assessments. There was no
attempt during the present study to collect data that would allow quantification of final
ecosystem services, either monetized or non-monetized, which would require collection
of socioeconomic data in addition to biological data. However, we conclude that a
habitat based assessment approach is generally feasible for use in developing
estimates of ecosystem services related to the presence of birds within estuarine
systems.
56
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Appendix A. Locations of observation sites in the Yaquina estuary, Oregon.
Sector
No.
Stop ID
Latitude
Longitude
Mileage
Description
Idaho Flat
11
Pumphouse
44.6240
-124.0427
0
HMSC pump house dock

12
EPA Beach
44.6219
-124.0417
0.2
HMSC nature trail east of EPA building

13
Low Bench
44.6212
-124.0415
0.26
Bench near nature trail opposite EPA building

14
Shelter
44.6205
-124.0420
0.3
HMSC nature trail wooden shelter

15
Trail
44.6201
-124.0429
0.35
HMSC nature trail

16
High Bench
44.6196
-124.0446
0.4
HMSC nature trail elevated observation point with bench

17
Bridge
44.6192
-124.0452
0.5
HMSC natural trail bridge

18
Log Pond
44.6184
-124.0465
0.9
South end of HMSC trail at HMSC drive

19
35th St Marsh
44.6125
-124.0426
1.1
Salt marsh along road at south section of Idaho Flat

110
Leeks High Road
44.6114
-124.0352
1.6
SE 35th and SE Leeks High Road

111
Idaho Point
44.6144
-124.0260
2.0
End of peninsula between Idaho Flat and Kings Slough
Sally's Bend
S1
LNG
44.6247
-124.0247
0
End of road adjacent to gate into LNG property

S2
Base
44.6285
-124.0249
1.3
North end of road leading to LNG facility

S3
Benson
44.6293
-124.0215
1.5
Roadside pullout along Yaquina Bay Road near Benson Road

S4
George
44.6275
-124.0133
1.9
Roadside pullout near SE George St.

S5
Little Cut
44.6263
-124.0094
2.1
Roadside pullout halfway between SE George St. and SE John Nye Road

S6
Nye
44.6251
-124.0065
2.3
Roadside pullout near SE John Nye Road

S7
Cut Bank
44.6231
-124.0048
2.4
Roadside pullout near vertical road cut along Yaquina Bay Road

S8
Grassy
44.6197
-124.0041
2.7
Roadside grassy area along Yaquina Bay Road

S9
Brown Sign
44.6168
-124.0038
2.9
Roadside pullout nearly opposite two driveways

S10
Tele Pole
44.6137
-124.0063
3.2
Yaquina Bay Road overview

S11
Coquille
44.6114
-124.0104
3.4
Coquille Point, overview of Sally's Bend
Raccoon Flat
R1
Raccoon Flat
44.6105
-124.0108
3.5
Coquille Point, looking across the river
Upriver
U1
Sawyers
44.6026
-124.0108
4.0
Sawyer's Landing Marina

U2
Storage
44.5932
-124.0123
4.4
Storage building parking area

U3
Parker Slough
44.5897
-124.0159
4.7
Parker's Slough bridge

U4
Oneatta Pt
44.5837
-124.0161
5.4
Oneonta Point pullout

U5
Winant
44.5836
-124.0063
6.1
Winant Slough pullout, just upstream of milepost 6

U6
OR Oyster
44.5809
-123.9950
6.6
Bridge overlooking slough and Oregon Oyster facility floats

U7
Johnson Slough
44.5780
-123.9893
7.0
Johnson Slough bridge

U8
Old Barge
44.5757
-123.9846
7.3
Pullout next to an old beached barge

U9
Martin Houses
44.5750
-123.9775
7.6
Pullout near pilings with purple Martin houses

U10
Boone Family
44.5759
-123.9692
8.2
Pullout with historical sign, walk back downstream to marsh channel under road

U11
Boone Trestle
44.5817
-123.9660
8.6
Pullout near old railroad trestle adjacent to Boone Slough marshland

U12
Boone High Trestle
44.5851
-123.9628
8.9
Pullout near old railroad trestle overlooking tidegate into Boone Slough

U13
Nute Slough
44.5871
-123.9592
9.1
Pullout near old railroad trestle adjacent to entrance into Nute Slough (yellow sign)

U14
Port of Toledo Park
44.5913
-123.9422
10.1
Fishing pier at Port of Toledo park and boat launch

U15
Critesers Landing
44.5933
-123.9417
10.2
Criteser's Landing Marina

U16
Mp 11 Pullout
44.6074
-123.9488
11.1
Roadside pullout just upstream from milepost 11
61
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Appendix B. Abundance of all birds observed for each count cycle in the Yaquina estuary during December 2007-
December 2008. Counts are provided for both the Base assessment and for the comparative counts (QA). Values
are sums of all birds seen on all four sectors, all five habitats, and at all tide levels (QA* - data listed in the QA
column for Count Cycle 1 were collected in December 2008).

Count Cycle
1

2

3
4
5
6

Total
Group
Common Name, Species
Base
QA*
Base
QA
Base QA
Base QA
Base QA
Base
QA

Geese
Brant, Branta bernicla
Cackling Goose, Branta hutchinsii
303
94
230
2
94
52
1


129

902
3

Canada Goose, Branta canadensis
2
10
65

121
57 41
369
61

726
Ducks
American Wigeon, Anas americana
3768

154

2

134
3727

7785

Bufflehead, Bucephala albeola
1010
69
442
49
135


981
30
2716

Canvasback, Aythya valisineria
5








5

Common Goldeneye, Bucephala clangula
27
4
20




5

56

Common Merganser, Mergus merganser
3





10
2

15

Eurasian Wigeon, Anas penelope
5

1




11

17

Gadwall, Anas strepera


2






2

Green-winged Teal, Anas crecca


3

33


4

40

Hooded Merganser, Lophodytes cucullatus
2
3





4

9

Mallard, Anas platyrhynchos
186
118
85

69 6
2
151
370

987

merganser sp., Mergus sp.
1








1

Northern Pintail, Anas acuta
707
2
6



31
904

1650

Northern Shoveler, Anas clypeata




6




6

Red-breasted Merganser, Mergus serrator
20
12
21

24 3


23

103

Ruddy Duck, Oxyura jamaicensis
22

8
2



0

32

scaup sp., Aythya spp.
224

463
55
191
14

173
30
1150

Surf Scoter, Melanitta perspicillata
243

161
15
29

3
98

549

White-winged Scoter, Melanitta fusca
19



2




21

wigeon and pintail, Anas spp.
970








970

Wood Duck, Aix sponsa







1

1
Loons/Grebes
Common Loon, Gavia immer
grebe sp., Podiceps sp.
14
6
6

9 1

2
3
11

49
3

Horned Grebe, Podiceps auritus
34

18
3
1

2
51

109
62
-------

Pacific Loon, Gavia pacifica


5
1



1

2

9

Pied-billed Grebe, Podilymbus podiceps









2

2

Red-necked Grebe, Podiceps grisegena
2






2

5

9

Red-throated Loon, Gavia stellata
7

5






2

14

Western Grebe, Aechmophorus occidentaiis
30

2
10



1

8
5
56
Pelicans
Brandt's Cormorant, Phaiacrocorax penicillatus



1
74
5

2



82
/Cormorants
Brown Pelican, Pelecanus occidentaiis




1


80
3
215

299

Double-crested Cormorant, Phaiacrocorax













auritus
7

5
20

8

277
1
272

590

Pelagic Cormorant, Phaiacrocorax pelagicus


1
2







3
Herons/Egrets
Great Blue Heron, Ardea herodias
85
28
51
5 103
66
299
23
345
41
202
7
1255

Great Egret, Ardea alba

2
0
29
3
6

192
3
133
4
372

Green Heron, Butorides virescens

1









1
Vultures/Raptors
Bald Eagle, Haliaeetus leucocephalus
12
1
4
1

3

2

3

26

Northern Harrier, Circus cyaneus


2


1
1




4

Osprey, Pandion haliaetus



4

3

3



10

Peregrine Falcon, Falco peregrinus









1

1

Red-tailed Hawk, Buteo jamaicensis


1








1

Turkey Vulture, Cathartes aura



10

1





11

White-tailed Kite, Elanus leucurus


1








1
Rails
American Coot, Fulica americana
823
75
52
9





38

997
Shorebirds
Black Turnstone, Arenaria melanocephala








2


2

Black-bellied Plover, Pluvialis squatarola



1

1



11

13

dowitcher sp., Limnodromus spp.



35
1


7

1

44

Dunlin, Calidris alpina
49


169



5

11

234

Greater Yellowlegs, Tringa melanoleuca
13
2
10
1
2
9

11

10

58

Killdeer, Charadrius vociferus
33
2
3
1
1
7
1
11

20
9
88

Least Sandpiper, Calidris minutilla
26


9

60
5
38

74
3
215

Long-billed Curlew, Numenius americanus



1







1

Marbled Godwit, Limosa fedoa



1





22

23

peeps, Calidris spp.
250

40




60

15

365

Red Knot, Calidris canutus



3







3

Red-necked Phalarope, Phalaropus lobatus



25







25
63
-------
149
59
5
15
I42
>77
70
>27
5
5
>32
2
5
14
11
38
3
2
1
;42
3
22
25
1
2
61
1
22
15
42
2
:21
Sanderling, Calidris alba
Semipalmated Plover, Charadrius semipalmatus
shorebirds unid., Charadriiformes unid.
Spotted Sandpiper, Actitis macularius
Western Sandpiper, Calidris mauri
Whimbrel, Numenius phaeopus	
149
4
80
90
610
65
53
4
4
2367
160
1
207
153
1
3
198
60
Caspian Tern, Hydroprogne caspia
gulls spp., Larus spp.	
2359
280
2567 380
11	47	12
1317 422 2033 215 4953 1575
Common Murre, Uria aalge
Pigeon Guillemot, Cepphus columba
American Crow, Corvus brachyrhynchos
Common Raven, Corvus corax	
427
37
599 24 225 21
286
2
34 251
American Goldfinch, Carduelistristis
American Robin, Turdus migratorius
Barn Swallow, Hirundo rustica
Belted Kingfisher, Megaceryle alcyon
Brewer's Blackbird, Euphagus cyanocephalus
Bushtit, Psaltriparus minimus
Cliff Swallow, Petrochelidon pyrrhonota
European Starling, Sturnus vulgaris
Fox Sparrow, Passerella iliaca
Purple Martin, Progne subis
Red-winged Blackbird, Agelaius phoeniceus
Rufous Hummingbird, Selasphorus rufus
Savannah Sparrow, Passerculus sandwichensis
Song Sparrow, Melospiza melodia
sparrow sp., Emberizidae sp.
swallows spp., Tachycineta spp.
Tree Swallow, Tachycineta bicolor
Violet-green Swallow, Tachycineta thalassina
White-crowned Sparrow, Zonotrichia leucophrys
7
29
1
70
3
33
10
2
5
61
12
1
63
9
25
1
1
16
8
2
2
30
9
38
2
11
6
4
10
12009
903 5684 636 5350 603 3431 349 7297 1634
64
-------
Appendix C. Abundance of birds observed in five intertidal habitats in the Yaquina estuary during December 2007-
December 2008. Counts are provided for both the Base assessment and for the comparative counts (QA).

Habitat
Z. marina
Upogebia/muti
Neotrypaea/santi
Z. japonica
Low Marsh
Total
Group
Common Name, Species
Base
QA
Base
QA
Base
QA
Base QA
Base
QA

Geese
Brant, Branta bernicla
174
188
142

398




902

Cackling Goose, Branta hutchinsii




1


2

3

Canada Goose, Branta canadensis
55
10
83
41
182

160
195

726
Ducks
American Wigeon, Anas americana
2357

3347

854

303
924

7785

Bufflehead, Bucephala albeola
1614
141
682
2
181
5
7
84

2716

Canvasback, Aythya valisineria
2

3






5

Common Goldeneye, Bucephala clangula
29
4
13

10




56

Common Merganser, Mergus merganser
3

9

3




15

Eurasian Wigeon, Anas penelope
4

6

2


5

17

Gadwall, Anas strepera
2








2

Green-winged Teal, Anas crecca
20

15

2


3

40

Hooded Merganser, Lophodytes cucullatus
1

4

1
3



9

Mallard, Anas platyrhynchos
224
24
202

112
45
3
322
55
987

merganser sp., Mergus sp.
1








1

Northern Pintail, Anas acuta
233

748

232


435
2
1650

Northern Shoveler, Anas clypeata


6






6

Red-breasted Merganser, Mergus serrator
48
10
22

18
5



103

Ruddy Duck, Oxyura jamaicensis
29
2


1




32

scaup sp., Aythya spp.
500
85
425

120


20

1150

Surf Scoter, Melanitta perspicillata
326
15
148

60




549

White-winged Scoter, Melanitta fusca
8

12

1




21

wigeon and pintail, Anas spp.


970






970

Wood Duck, Aix sponsa


1






1
Loons/Grebes
Common Loon, Gavia immer
28
7
7

6

1


49

grebe sp., Podiceps sp.
3








3

Horned Grebe, Podiceps auritus
90
3
8

7

1


109

Pacific Loon, Gavia pacifica
7

1




1

9

Pied-billed Grebe, Podilymbus podiceps
2








2
65
-------

Red-necked Grebe, Podiceps grisegena
4

3

2




9

Red-throated Loon, Gavia stellata
10

3




1

14

Western Grebe, Aechmophorus occidentalis
39
5
10

2




56
Pelicans
Brandt's Cormorant, Phalacrocorax penicillatus
7
74


1




82
/Cormorants
Brown Pelican, Pelecanus occidentalis
73
4
164

48


10

299

Double-crested Cormorant, Phalacrocorax auritus
321
1
35

132


101

590

Pelagic Cormorant, Phalacrocorax peiagicus


2

1




3
Herons/Egrets
Great Blue Heron, Ardea herodias
618
151
221
7
116
9
21
109
3
1255

Great Egret, Ardea alba
146
12
77

24

15
98

372

Green Heron, Butorides virescens





1



1
Vultures
Bald Eagle, Haliaeetus leucocephalus
4

13
1
6

1
1

26
/Raptors
Northern Harrier, Circus cyaneus







3
1
4

Osprey, Pandion haliaetus
4

2

4




10

Peregrine Falcon, Falco peregrinus


1






1

Red-tailed Hawk, Buteo jamaicensis







1

1

Turkey Vulture, Cathartes aura
4

1

5


1

11

White-tailed Kite, Elanus leucurus







1

1
Rails
American Coot, Fulica americana
542
9
51
75
46

114
160

997
Shorebirds
Black Turnstone, Arenaria melanocephala

2







2

Black-bellied Plover, Pluvialis squatarola


8

2


3

13

dowitcher sp., Limnodromus spp.

1
12

23


8

44

Dunlin, Calidris alpina
3

150

28

47
6

234

Greater Yellowlegs, Tringa melanoleuca

2
2

33
2
3
16

58

Killdeer, Charadrius vociferus




34
11
15
26
2
88

Least Sandpiper, Calidris minutilla
16

16

89
3
14
72
5
215

Long-billed Curlew, Numenius americanus


1






1

Marbled Godwit, Limosa fedoa


7

11


5

23

peeps, Calidris spp.


285

75


5

365

Red Knot, Calidris canutus




3




3

Red-necked Phalarope, Phalaropus lobatus
2

23






25

Sanderling, Calidris alba



90
320

149
290

849

Semipalmated Plover, Charadrius semipalmatus


3
2
54




59
66
-------

shorebirds unid., Charadriiformes unid.




1



4
5

Spotted Sandpiper, Actitis macularius


3

5



7
15

Western Sandpiper, Calidris mauri
274

2067
66
465

12

58
2942

Whimbrel, Numenius phaeopus
7

174
3
154
1
12

26
377
Terns/Gulls
Caspian Tern, Hydroprogne caspia
2

26

42




70

gulls spp., Larus spp.
6410
1468
10047
2221
3739
123
72
243
4
24327
Alcids
Common Murre, Una aalge
Pigeon Guillemot, Cepphus columba
5
4
1







5
5
Corvids
American Crow, Corvus brachyrhynchos
Common Raven, Corvus corax
704
281
785
2
34
573
12
198

43
2 2632
2
Songbirds
American Goldfinch, Carduelis tristis








3
2 5
(including
American Robin, Turdus migratorius






2

11
1 14
hummingbirds
Barn Swallow, Hirundo rustica


4

11
1
7

84
4 111
and











kingfishers)
Belted Kingfisher, Megaceryle alcyon
Brewer's Blackbird, Euphagus cyanocephalus
Bushtit, Psaltriparus minimus
Cliff Swallow, Petrochelidon pyrrhonota
5

7
1
7
1
2
1
17
2
1
38
3
2
1

European Starling, Sturnus vulgaris


9

16

2
6
209
242

Fox Sparrow, Passerella iliaca








3
3

Purple Martin, Progne subis




10



12
22

Red-winged Blackbird, Agelaius phoeniceus








25
25

Rufous Hummingbird, Selasphorus rufus









1 1

Savannah Sparrow, Passerculus sandwichensis








2
2

Song Sparrow, Melospiza melodia








59
2 61

sparrow sp., Emberizidae sp.








1
1

swallows spp., Tachycineta spp.








11 11 22

Tree Swallow, Tachycineta bicolor








15
15

Violet-green Swallow, Tachycineta thaiassina








42
42

White-crowned Sparrow, Zonotrichia ieucophrys








2
2
Grand Total

14964
2500
21068
2543
8273
222
1161
250
3549 91 54621
67
-------
Appendix D. Abundance of birds observed in four sectors of the Yaquina estuary during December 2007- December 2008.
Counts are provided for both the Base assessment and for the comparative counts (QA).

Sector
Idaho Flat
Raccoon Flat
Sally's Bend
Upriver
Total
Group
Common Name, Species
Base
QA
Base QA
Base
QA
Base
QA

Geese
Brant, Branta bernicla
Cackling Goose, Branta hutchinsii
540
94
108 94
66

3

902
3

Canada Goose, Branta canadensis
240


212

223
51
726
Ducks
American Wigeon, Anas americana
5613

278
1628

266

7785

Bufflehead, Bucephala albeola
974
49
286 40
1097
30
211
29
2716

Canvasback, Aythya valisineria



5



5

Common Goldeneye, Bucephala clangula
3

8
34

7
4
56

Common Merganser, Mergus merganser
11




4

15

Eurasian Wigeon, Anas penelope
12


5



17

Gadwall, Anas strepera





2

2

Green-winged Teal, Anas crecca
17


20

3

40

Hooded Merganser, Lophodytes cucullatus
1


5


3
9

Mallard, Anas platyrhynchos
29

256 9
91
6
487
109
987

merganser sp., Mergus sp.
1






1

Northern Pintail, Anas acuta
1267

1
350

30
2
1650

Northern Shoveler, Anas clypeata
6






6

Red-breasted Merganser, Mergus serrator
7

16 2
36
3
29
10
103

Ruddy Duck, Oxyura jamaicensis
15
2

14

1

32

scaup sp., Aythya spp.
644
55
25
357
30
39

1150

Surf Scoter, Melanitta perspicillata
199
15
45
285

5

549

White-winged Scoter, Melanitta fusca
6


2

13

21

wigeon and pintail, Anas spp.
970






970

Wood Duck, Aix sponsa





1

1
Loons/Grebes
Common Loon, Gavia immer
grebe sp., Podiceps sp.
3

1
15
3
1
23
6
49
3
68
-------

Horned Grebe, Podiceps auritus
16
3
8

58

24

109

Pacific Loon, Gavia pacifica
2



5

2

9

Pied-billed Grebe, Podilymbus podiceps




2



2

Red-necked Grebe, Podiceps grisegena




8

1

9

Red-throated Loon, Gavia stellata




5

9

14

Western Grebe, Aechmophorus occidentaiis
26

4

5
5
16

56
Pelicans
Brandt's Cormorant, Phaiacrocorax penicillatus


1

6
74
1

82
/Cormorants
Brown Pelican, Pelecanus occidentaiis
87
3
126

29
1
53

299

Double-crested Cormorant, Phaiacrocorax auritus
160
1
32

158

239

590

Pelagic Cormorant, Phaiacrocorax peiagicus






3

3
Herons/Egrets
Great Blue Heron, Ardea herodias
265
46
250
18
344
73
226
33
1255

Great Egret, Ardea alba
88
3
20
2
90
7
162

372

Green Heron, Butorides virescens







1
1
Vultures/Raptors
Bald Eagle, Haliaeetus leucocephalus
15


1
6

4

26

Northern Harrier, Circus cyaneus






3
1
4

Osprey, Pandion haliaetus
6



2

2

10

Peregrine Falcon, Falco peregrinus
1







1

Red-tailed Hawk, Buteo jamaicensis






1

1

Turkey Vulture, Cathartes aura






11

11

White-tailed Kite, Elanus leucurus
1







1
Rails
American Coot, Fulica americana
290
9
82

314

227
75
997
Shorebirds
Black Turnstone, Arenaria melanocephala

2






2

Black-bellied Plover, Pluvialis squatarola
12





1

13

dowitcher sp., Limnodromus spp.
30



8
1
5

44

Dunlin, Calidris alpina
66



146

22

234

Greater Yellowlegs, Tringa melanoleuca
6




2
48
2
58

Killdeer, Charadrius vociferus
2



41
10
32
3
88

Least Sandpiper, Calidris minutilla




36
3
171
5
215

Long-billed Curlew, Numenius americanus


1





1

Marbled Godwit, Limosa fedoa
22



1



23

peeps, Calidris spp.
55

250



60

365
69
-------

Red Knot, Calidris canutus
3







3

Red-necked Phalarope, Phalaropus lobatus
23

2





25

Sanderling, Calidris alba
560



199


90
849

Semipalmated Plover, Charadrius semipalmatus
23
2


29

5

59

shorebirds unid., Charadriiformes unid.






5

5

Spotted Sandpiper, Actitis macularius




3

12

15

Western Sandpiper, Calidris mauri
566



1928

382
66
2942

Whimbrel, Numenius phaeopus
120
3
105

146
1
2

377
Terns/Gulls
Caspian Tern, Hydroprogne caspia
61



8

1

70

gulls spp., Larus spp.
9344
1955
2708
395
7894
1605
326
100
24327
Alcids
Common Murre, Uria aalge
Pigeon Guillemot, Cepphus columba

1


5

4

5
5
Corvids
American Crow, Corvus brachyrhynchos
Common Raven, Corvus corax
814
27
97
6
658
231
734
2
65
2632
2
Songbirds
American Goldfinch, Carduelis tristis
2





1
2
5
(including
American Robin, Turdus migratorius
1



3

9
1
14
hummingbirds
Barn Swallow, Hirundo rustica
38



7

61
5
111
and kingfishers)
Belted Kingfisher, Megaceryle aicyon
Brewer's Blackbird, Euphagus cyanocephalus
Bushtit, Psaltriparus minimus
Cliff Swallow, Petrochelidon pyrrhonota
1
2
1

2

4

29
2
2
1
38
3
2
1

European Starling, Sturnus vulgaris
102



42

92
6
242

Fox Sparrow, Passerella iliaca




3



3

Purple Martin, Progne subis
3



2

17

22

Red-winged Blackbird, Agelaius phoeniceus
25







25

Rufous Hummingbird, Selasphorus rufus







1
1

Savannah Sparrow, Passerculus sandwichensis






2

2

Song Sparrow, Melospiza melodia
4



5

50
2
61

sparrow sp., Emberizidae sp.






1

1

swallows spp., Tachycineta spp.
2




1
9
10
22

Tree Swallow, Tachycineta bicolor
13





2

15
70
-------

Violet-green Swallow, Tachycineta thalassina
3
39
42

White-crowned Sparrow, Zonotrichia leucophrys

2
2
Grand Total

23419 2270 4712
567 16425 2084 4459 685
54621
71
-------
Appendix E. Data used in habitat/sector/cycle analyses. Bird observations from tides 0
to 2.4 m are combined. Observations from tides >2.4 and composite species are
not included. For analyses, "Total birds ha"1" was double square root transformed.
/cle
Sector
Habitat
Area
(ha)
Total
birds
Number
species
Shannon
diversity
Total
birds ha"1
Predicted
number specie
in 5 ha area

Idaho
Low Marsh
8.92
200
6
1.127
22.4
5.1

Idaho
Neo/sand
43.37
1257
12
1.617
29
7.5

Idaho
Upo/mud
59.84
2960
6
1.058
49.5
5.2

Idaho
Z japonica
0.87
80
1
0.000
92
--

Idaho
Z marina
14.32
2201
15
1.428
153.7
13.7

Raccoon
Low Marsh
1.58
0
0
0.000
0
--

Raccoon
Neo/sand
12.07
0
0
0.000
0
0

Raccoon
Upo/mud
35.61
689
9
1.056
19.3
7

Raccoon
Z japonica
1.88
0
0
0.000
0
--

Raccoon
Z marina
30.62
165
9
1.507
5.4
5.9

Sallys
Low Marsh
1.66
263
8
1.237
158.4
--

Sallys
Neo/sand
29.5
563
8
0.668
19.1
5.6

Sallys
Upo/mud
50.29
584
10
1.004
11.6
4.6

Sallys
Z japonica
23.11
518
8
1.084
22.4
5.8

Sallys
Z marina
104.29
1237
19
1.764
11.9
9.1

Upriver
Low Marsh
94.9
298
13
1.995
3.1
6.6

Upriver
Neo/sand
95.06
169
15
2.094
1.8
5.3

Upriver
Upo/mud
31.36
118
14
1.858
3.8
6.8

Upriver
Z japonica
8.62
0
0
0.000
0
0

Upriver
Z marina
11.1
311
15
1.906
28
12.5
2
Idaho
Low Marsh
8.92
338
6
0.566
37.9
5.5
2
Idaho
Neo/sand
43.37
998
10
1.392
23
6.8
2
Idaho
Upo/mud
59.84
1325
11
1.262
22.1
6.3
2
Idaho
Z japonica
0.87
0
0
0.000
0
--
2
Idaho
Z marina
14.32
145
8
1.332
10.1
6.3
2
Raccoon
Low Marsh
1.58
0
0
0.000
0
--
2
Raccoon
Neo/sand
12.07
0
0
0.000
0
0
2
Raccoon
Upo/mud
35.61
441
3
0.168
12.4
2.3
2
Raccoon
Z japonica
1.88
0
0
0.000
0
--
2
Raccoon
Z marina
30.62
191
8
1.355
6.2
5.6
2
Sallys
Low Marsh
1.66
1
1
0.000
0.6
--
2
Sallys
Neo/sand
29.5
337
4
0.684
11.4
3.2
2
Sallys
Upo/mud
50.29
391
7
0.803
7.8
4
2
Sallys
Z japonica
23.11
9
3
0.684
0.4
1.4
2
Sallys
Z marina
104.29
657
18
1.784
6.3
7.6
2
Upriver
Low Marsh
94.9
159
13
1.728
1.7
4.1
2
Upriver
Neo/sand
95.06
339
19
1.664
3.6
6.1
72
-------
2
Upriver
Upo/mud
31.36
69
6
1.550
2.2
4.4
2
Upriver
Z japonica
8.62
6
3
1.011
0.7
2.3
2
Upriver
Z marina
11.1
187
9
1.375
16.8
7.4
3
Idaho
Low Marsh
8.92
67
8
1.577
7.5
7
3
Idaho
Neo/sand
43.37
511
23
1.784
11.8
11.7
3
Idaho
Upo/mud
59.84
868
16
1.684
14.5
10.2
3
Idaho
Z japonica
0.87
0
0
0.000
0
--
3
Idaho
Z marina
14.32
89
11
1.806
6.2
7.2
3
Raccoon
Low Marsh
1.58
1
1
0.000
0.6
--
3
Raccoon
Neo/sand
12.07
0
0
0.000
0
0
3
Raccoon
Upo/mud
35.61
127
5
1.094
3.6
3.8
3
Raccoon
Z japonica
1.88
0
0
0.000
0
--
3
Raccoon
Z marina
30.62
72
11
1.726
2.4
5.2
3
Sallys
Low Marsh
1.66
49
9
1.697
29.5
--
3
Sallys
Neo/sand
29.5
123
11
2.097
4.2
8
3
Sallys
Upo/mud
50.29
1836
13
0.645
36.5
7.3
3
Sallys
Z japonica
23.11
9
3
0.849
0.4
1.6
3
Sallys
Z marina
104.29
1008
14
1.566
9.7
7.6
3
Upriver
Low Marsh
94.9
184
17
2.316
1.9
6.2
3
Upriver
Neo/sand
95.06
280
18
1.819
2.9
6
3
Upriver
Upo/mud
31.36
63
13
2.166
2
6.1
3
Upriver
Z japonica
8.62
5
3
0.950
0.6
2.2
3
Upriver
Z marina
11.1
58
7
1.669
5.2
6.5
4
Idaho
Low Marsh
8.92
96
11
1.777
10.8
9.4
4
Idaho
Neo/sand
43.37
896
11
1.075
20.7
6.1
4
Idaho
Upo/mud
59.84
270
7
0.956
4.5
4.2
4
Idaho
Z japonica
0.87
0
0
0.000
0
--
4
Idaho
Z marina
14.32
92
5
1.042
6.4
4.1
4
Raccoon
Low Marsh
1.58
0
0
0.000
0
--
4
Raccoon
Neo/sand
12.07
2
1
0.000
0.2
1
4
Raccoon
Upo/mud
35.61
683
3
0.479
19.2
3
4
Raccoon
Z japonica
1.88
0
0
0.000
0
--
4
Raccoon
Z marina
30.62
114
4
0.433
3.7
2.3
4
Sallys
Low Marsh
1.66
14
2
0.410
8.4
--
4
Sallys
Neo/sand
29.5
126
7
1.517
4.3
5.1
4
Sallys
Upo/mud
50.29
238
4
0.812
4.7
3
4
Sallys
Z japonica
23.11
43
5
1.085
1.9
3.2
4
Sallys
Z marina
104.29
489
9
0.875
4.7
3.7
4
Upriver
Low Marsh
94.9
157
14
1.773
1.7
4.2
4
Upriver
Neo/sand
95.06
92
11
1.997
1
3.6
4
Upriver
Upo/mud
31.36
57
7
1.377
1.8
3.7
4
Upriver
Z japonica
8.62
16
5
1.037
1.9
3.5
4
Upriver
Z marina
11.1
46
4
1.025
4.1
3.4
73
-------
5
Idaho
Low Marsh
8.92
48
7
1.641
5.4
6.3
5
Idaho
Neo/sand
43.37
1115
9
0.703
25.7
5.6
5
Idaho
Upo/mud
59.84
1722
12
0.649
28.8
7.5
5
Idaho
Z japonica
0.87
0
0
0.000
0
--
5
Idaho
Z marina
14.32
155
8
1.406
10.8
7.5
5
Raccoon
Low Marsh
1.58
3
1
0.000
1.9
--
5
Raccoon
Neo/sand
12.07
0
0
0.000
0
0
5
Raccoon
Upo/mud
35.61
247
4
0.424
6.9
3
5
Raccoon
Z japonica
1.88
0
0
0.000
0
--
5
Raccoon
Z marina
30.62
440
8
1.242
14.4
5.5
5
Sallys
Low Marsh
1.66
34
3
0.444
20.5
--
5
Sallys
Neo/sand
29.5
127
6
1.334
4.3
4.5
5
Sallys
Upo/mud
50.29
893
7
0.500
17.8
5.1
5
Sallys
Z japonica
23.11
215
7
1.073
9.3
5
5
Sallys
Z marina
104.29
1375
12
0.639
13.2
5.4
5
Upriver
Low Marsh
94.9
91
17
2.511
1
4.2
5
Upriver
Neo/sand
95.06
55
8
1.651
0.6
2.4
5
Upriver
Upo/mud
31.36
211
11
1.411
6.7
6.4
5
Upriver
Z japonica
8.62
33
6
1.543
3.8
5.6
5
Upriver
Z marina
11.1
274
11
1.892
24.7
8.8
6
Idaho
Low Marsh
8.92
294
4
0.102
33
3
6
Idaho
Neo/sand
43.37
747
8
0.551
17.2
5.3
6
Idaho
Upo/mud
59.84
4844
21
1.324
80.9
11.3
6
Idaho
Z japonica
0.87
0
0
0.000
0
--
6
Idaho
Z marina
14.32
1136
11
1.553
79.3
9.1
6
Raccoon
Low Marsh
1.58
0
0
0.000
0
--
6
Raccoon
Neo/sand
12.07
11
2
0.305
0.9
1.5
6
Raccoon
Upo/mud
35.61
1077
10
1.026
30.2
7.1
6
Raccoon
Z japonica
1.88
1
1
0.000
0.5
--
6
Raccoon
Z marina
30.62
321
9
1.633
10.5
7.2
6
Sallys
Low Marsh
1.66
3
1
0.000
1.8
--
6
Sallys
Neo/sand
29.5
58
5
1.176
2
3.6
6
Sallys
Upo/mud
50.29
868
9
1.129
17.3
5.2
6
Sallys
Z japonica
23.11
118
7
1.478
5.1
5.7
6
Sallys
Z marina
104.29
3835
19
1.149
36.8
11.1
6
Upriver
Low Marsh
94.9
165
11
1.868
1.7
4.9
6
Upriver
Neo/sand
95.06
299
16
2.286
3.1
7.9
6
Upriver
Upo/mud
31.36
106
12
1.749
3.4
6
6
Upriver
Z japonica
8.62
73
5
0.795
8.5
4.5
6
Upriver
Z marina
11.1
148
15
2.426
13.3
13.8
74
-------
Appendix F. Total density of birds (ha"1) observed utilizing five intertidal habitats by
species group and count cycle. Counts are sums of all birds seen in each habitat
within species groups, calculated by estimated area of each habitat within each
sector of the estuary.
Count


Upogebia
Neotrypaea

Low

Cycle
Group
Z marina
/mud
/sand
Z japonica
Marsh
Total

Geese
0.4
0.0
1.4
0.1
0.0
0.5
1
Group
15.7
15.2
6.8
8.7
4.6
10.9
Dec-
Loons/Grebes
0.4
0.1
0.0
0.0
0.0
0.1
Jan
Pelicans/Cormorants
0.0
0.0
0.0
0.0
0.0
0.0

Herons/Egrets
0.2
0.1
0.1
0.0
0.2
0.1

Raptors
0.0
0.1
0.0
0.0
0.0
0.0

Rails
3.1
0.3
0.1
3.3
1.5
1.2

Shorebirds
0.0
1.4
0.6
5.9
0.4
0.9

Terns/Gulls
3.3
8.0
2.3
0.0
0.0
3.6

Alcids
0.0
0.0
0.0
0.0
0.0
0.0

Corvids
1.7
0.3
0.5
0.3
0.0
0.6

Songbirds
0.0
0.0
0.0
0.0
0.8
0.1
Cycle 1 Total All Species
24.8
25.4
11.7
18.3
7.5
18.2

Geese
0.7
0.1
0.6
0.0
0.5
0.5
2
Ducks
3.4
3.3
0.7
0.3
1.0
2.1
Feb-
Loons/Grebes
0.2
0.0
0.0
0.1
0.0
0.1
Mar
Pelicans/Cormorants
0.0
0.0
0.0
0.0
0.0
0.0

Herons/Egrets
0.1
0.1
0.0
0.0
0.1
0.1

Raptors
0.0
0.0
0.0
0.0
0.0
0.0

Rails
0.3
0.0
0.0
0.0
0.0
0.1

Shorebirds
0.0
0.0
2.1
0.1
2.7
1.0

Terns/Gulls
2.0
8.3
4.3
0.0
0.0
3.9

Alcids
0.0
0.0
0.0
0.0
0.0
0.0

Corvids
0.9
0.9
1.6
0.0
0.1
0.9

Songbirds
0.0
0.0
0.0
0.0
0.3
0.1
Cycle 2 Total All Species
7.5
12.8
9.4
0.5
4.8
8.6

Geese
0.0
0.0
0.6
0.0
0.7
0.3
3
Ducks
1.7
0.6
0.5
0.0
0.3
0.7
Apr-
Loons/Grebes
0.0
0.1
0.0
0.0
0.0
0.0
May
Pelicans/Cormorants
0.1
0.0
0.0
0.0
0.0
0.0

Herons/Egrets
0.3
0.2
0.1
0.0
0.2
0.2

Raptors
0.0
0.0
0.0
0.0
0.0
0.0

Rails
0.0
0.0
0.0
0.0
0.0
0.0

Shorebirds
1.8
12.3
1.7
0.1
0.6
4.3

Terns/Gulls
3.4
2.7
1.7
0.0
0.0
2.0

Alcids
0.0
0.0
0.0
0.0
0.0
0.0

Corvids
0.3
0.4
0.4
0.3
0.2
0.3

Songbirds
0.0
0.0
0.0
0.0
0.9
0.2
Cycle 3 Total All Species
7.7
16.3
5.1
0.4
2.8
8.1
75
-------

Geese
0.0
0.1
0.1
0.0
0.2
0.1
4
Ducks
0.1
0.0
0.0
0.0
0.0
0.0
Jun-
Loons/Grebes
0.0
0.0
0.0
0.0
0.0
0.0
July
Pelicans/Cormorants
0.1
0.0
0.0
0.0
0.0
0.0

Herons/Egrets
1.2
0.4
0.2
0.1
0.0
0.5

Raptors
0.0
0.0
0.0
0.0
0.0
0.0

Rails
0.0
0.0
0.0
0.0
0.0
0.0

Shorebirds
0.0
0.4
1.7
0.0
0.6
0.7

Terns/Gulls
2.8
5.5
3.6
0.2
0.0
3.2

Alcids
0.0
0.0
0.0
0.0
0.0
0.0

Corvids
0.4
0.6
0.4
1.1
0.0
0.4

Songbirds
0.0
0.1
0.2
0.3
1.5
0.3
Cycle 4 Total All Species
4.6
7.0
6.2
1.7
2.5
5.2

Geese
0.3
0.4
0.6
3.8
0.1
0.6
5
Ducks
0.9
0.1
0.0
0.1
1.6
0.5
Aug-
Loons/Grebes
0.1
0.0
0.0
0.0
0.0
0.0
Sept
Pelicans/Cormorants
1.2
0.5
0.5
0.0
0.0
0.5

Herons/Egrets
2.2
0.5
0.2
0.3
0.5
0.8

Raptors
0.0
0.0
0.0
0.0
0.0
0.0

Rails
0.0
0.0
0.0
0.0
0.0
0.0

Shorebirds
0.1
1.2
0.5
0.7
0.4
0.6

Terns/Gulls
9.3
14.2
5.3
0.1
0.0
7.5

Alcids
0.0
0.0
0.0
0.0
0.0
0.0

Corvids
0.3
0.5
0.2
2.1
0.1
0.4

Songbirds
0.0
0.0
0.0
0.1
0.7
0.1
Cycle 5 Total All Species
14.3
17.4
7.3
7.2
3.5
11.1

Geese
0.1
0.7
0.0
0.8
0.2
0.3
6
Ducks
12.0
18.2
0.9
0.0
9.3
9.6
Oct-
Loons/Grebes
0.4
0.0
0.0
0.0
0.0
0.1
Nov
Pelicans/Cormorants
1.1
0.6
0.5
0.0
1.0
0.7

Herons/Egrets
0.7
0.3
0.2
0.7
0.9
0.5

Raptors
0.0
0.0
0.0
0.0
0.0
0.0

Rails
0.0
0.0
0.2
0.0
0.0
0.1

Shorebirds
0.0
0.2
0.7
0.5
0.1
0.3

Terns/Gulls
19.4
18.1
3.7
1.7
0.0
10.7

Alcids
0.0
0.0
0.0
0.0
0.0
0.0

Corvids
0.8
1.7
0.1
1.9
0.0
0.8

Songbirds
0.0
0.0
0.0
0.0
0.5
0.1
Cycle 6 Total All Species
34.5
40.0
6.3
5.6
12.1
23.1
Total All Cycles
93.3
119.0
46.0
33.7
33.1
74.4
76
-------
Appendix G. Regional observations of bird occurrence and activities in estuarine intertidal habitats in Oregon.
Habitat
Exposure
Estuary
Species
Calling Foraging Hunting Resting
Low Marsh
Exposed
Alsea
American Crow, Corvus brachyrhynchos
Barn Swallow, Hirundo rustica
Great Blue Heron, Ardea herodias
Greater Yellowlegs, Tringa melanoleuca
Red-tailed Hawk, Buteo jamaicensis
Red-winged Blackbird, Agelaius phoeniceus
Savannah Sparrow, Passerculus sandwichensis
Song Sparrow, Melospiza melodia
Tree Swallow, Tachycineta bicolor
Turkey Vulture, Cathartes aura
4
30
1
2
1
4 6
3
3
4
13
Nestucca
American Robin, Turdus migratorius
Barn Swallow, Hirundo rustica
Savannah Sparrow, Passerculus sandwichensis
Song Sparrow, Melospiza melodia
1
3
8
4
Netarts
Barn Swallow, Hirundo rustica
Canada Goose, Branta canadensis
Great Blue Heron, Ardea herodias
Savannah Sparrow, Passerculus sandwichensis
Turkey Vulture, Cathartes aura
3
4
40
5
1
Salmon
American Crow, Corvus brachyrhynchos
Barn Swallow, Hirundo rustica
Great Blue Heron, Ardea herodias
Greater Yellowlegs, Tringa melanoleuca
Marsh Wren, Cistothorus palustris
Savannah Sparrow, Passerculus sandwichensis
Song Sparrow, Melospiza melodia
Virginia Rail, Rallus limicola?
12
8
3
12
2
10
4
1
Siletz
Barn Swallow, Hirundo rustica
Canada Goose, Branta canadensis
Savannah Sparrow, Passerculus sandwichensis
Song Sparrow, Melospiza melodia
9
25
2
2
Tillamook
American Crow, Corvus brachyrhynchos
American Robin, Turdus migratorius
1
2
77
-------



Barn Swallow, Hirundo rustica
Canada Goose, Branta canadensis
Common Yellowthroat, Geothlypis trichas
Red-winged Blackbird, Agelaius phoeniceus
Savannah Sparrow, Passerculus sandwichensis
Song Sparrow, Melospiza melodia
1
2
1
1
4
4
Flooded
Siletz
Belted Kingfisher, Megaceryle alcyon
1
Tillamook
Great Blue Heron, Ardea herodias
3
Neotrypaea/santi
Exposed
Alsea
Great Blue Heron, Ardea herodias
1
Nestucca
American Crow, Corvus brachyrhynchos
Canada Goose, Branta canadensis
Great Blue Heron, Ardea herodias
Mallard, Anas piatyrhynchos
2
22
1
15
Netarts
American Crow, Corvus brachyrhynchos
Bald Eagle, Haiiaeetus ieucocephaius
Bonaparte's Gull, Chroicocephaius Philadelphia
gulls, spp.
16
2
2
1 38
Salmon
American Crow, Corvus brachyrhynchos
Canada Goose, Branta canadensis
gulls, spp.
Mallard, Anas piatyrhynchos
2
6
16
2
Siletz
Common Goldeneye, Bucephala clangula
3
Tillamook
American Crow, Corvus brachyrhynchos
Brant, Branta bernicla
Canada Goose, Branta canadensis
Caspian Tern, Hydroprogne caspia
Great Blue Heron, Ardea herodias
gulls, spp.
Semipalmated Plover, Charadrius semipalmatus
Whimbrel, Numenius phaeopus
2
22
15
15
7
86
9
39
Flooded
Netarts
Great Blue Heron, Ardea herodias
2 6
Upogebia/muti
Exposed
Siletz
American Crow, Corvus brachyrhynchos
Barn Swallow, Hirundo rustica
Canada Goose, Branta canadensis
gulls, spp.
Mallard, Anas piatyrhynchos
21
10
6
19
2
78
-------



Whimbrel, Numenius phaeopus
6

Flooded
Salmon
Great Blue Heron, Ardea herodias
Great Egret, Ardea alba
2
1


Siletz
Great Blue Heron, Ardea herodias
3
Z japonica
Exposed
Netarts
American Crow, Corvus brachyrhynchos
Canada Goose, Branta canadensis
1
4
Z marina
Flooded
Netarts
gulls, spp.
1
79
-------
Appendix H. Observations on feeding in birds. Food items were observed through binoculars or spotting scope.

Feeding
habit
Z
marina
z
japonica
Macroalgae
Marsh
Vegetation
Fish
Fish
Species
Inverts
Invert
Species
Other
Notes
Brant
dabble
X

X





grass
1 seen eating grass on
Yaquina south jetty
Canada Goose
dabble
X
X
X
X






Gadwall
dabble
X









American Wigeon
dabble
X
X
X
X






Mallard
dabble

X

X






Pintail
dabble

X
X
X






Scaup
dive
X
X








Surf Scoter
dive






X
Bivalve


White-winged Scoter
dive






X
Cockle


Common Goldeneye
dive



X






Common Merganser
dive



X
X





Red-breasted
Merganser
dive




X





Hooded Merganser
dive






X
Crabs


Common Loon
dive




X

X
Clam


Western Grebe
dive




X
gunnel




Horned Grebe
dive




X





Brown Pelican
dive




X





Brandt's Cormorant
dive




X





Double-crested
Cormorant
dive
X



X
sculpin




Great Blue Heron
wade




X
sculpin




Great Egret
wade




X
smolts



salmon smolts in "Log
Pond"
Osprey





X





Coot
dabble
X
X
X
X





diving for Z japonica
Whimbrel
probe






X
Upogebia,
Neotrypaea


Marbled Godwit
probe






X
Neotrypaea


Western Gull
forage






X
Dungeness
crab


80
-------
Glaucous-winged
and Western Gull
forage




X
Discarded
fish head
X
Cockles

cockles from
Upogebialmu61\at
dropped on parking lots
and roofs
Belted Kingfisher
dive




X





American Crow
forage
X









81
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Agency
Office of Research and Development (8101R)
Washington, DC 20460
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Penalty for Private Use
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-------