Genetic Stock Composition of Subyearling Chinook Salmonin Seasonal Floodplain Wetlands of the

Lower Willamette River, Oregon

DAVID J. TEEL*National Oceanic and Atmospheric Administration Fisheries, Northwest Fisheries Science Center,

Manchester Research Laboratory, Post Office Box 130, Manchester, Washington 98353, USA

CYNDI BAKER

Ducks Unlimited, 17800 Mill Plain Boulevard, Suite 120, Vancouver, Washington 98683, USA, andDepartment of Fisheries and Wildlife, Oregon State University, 104 Nash Hall,

Corvallis, Oregon 97331, USA

DAVID R. KULIGOWSKI

National Oceanic and Atmospheric Administration Fisheries, Northwest Fisheries Science Center,Manchester Research Laboratory, Post Office Box 130, Manchester, Washington 98353, USA

THOMAS A. FRIESEN

Oregon Department of Fish and Wildlife, 3406 Cherry Avenue Northeast, Salem, Oregon 97303, USA

BARBARA SHIELDS

Department of Fisheries and Wildlife, Oregon State University,104 Nash Hall, Corvallis, Oregon 97331, USA

Abstract.—We used genetic identification methods to

examine the stock composition of subyearling Chinook

salmon Oncorhynchus tshawytscha in floodplain wetland

and main-stem habitats of the lower Willamette River,

Oregon. Using a microsatellite DNA baseline of 13 standard-

ized loci and 30 Columbia River basin populations, we

analyzed 280 subyearlings collected in winter and spring

2005–2006 from wetland and main-stem river sites. Genetic

stock identification analysis indicated that spring Chinook

salmon originating from the Willamette River made up a

substantial proportion of the samples and contributed 16–71%

to sample mixtures representing the wetland habitat sites. Fall

Chinook salmon from lower Columbia River sources were

also present and contributed 58% of winter samples. Spring

Chinook salmon from lower Columbia River populations were

present in both wetland (17%) and river (16%) samples in

spring 2005, and subyearlings from summer–fall-run popula-

tions in the middle and upper Columbia River contributed to

spring wetland samples in 2006 (26%). The results suggest

that floodplain restoration projects intended to improve fish

habitats during winter and spring periods in the lower

Willamette River may benefit Chinook salmon populations

from the upper Willamette River, lower Columbia River, and

upper Columbia River summer–fall evolutionarily significant

units.

Recently, recommendations for recovering imperiled

Pacific salmon Oncorhynchus spp. have highlighted

the value of population structure and life history

variability (Riddell 1993; McElhany et al. 2000; Good

et al. 2007). These recommendations explicitly recog-

nize the importance of complex, interconnected

habitats that support the entire salmon life cycle. A

major concern in the Pacific Northwest is declining life

history diversity resulting from simplification of the

freshwater and estuarine waterways that juvenile

salmon use for rearing and migration (Lichatowich

1999; Bottom et al. 2005b). Loss of rearing and

migration habitats in the region have been extensive,

particularly in estuaries where diking, draining, and

filling activities have greatly reduced fish access to

wetlands and floodplains (NRC 1996). The benefits of

off-channel and seasonal floodplain habitats for

juvenile coho salmon O. kisutch are well documented

(Peterson 1982; Brown and Hartman 1988; Henning et

al. 2006). Much less is known about floodplain habitat

use by juvenile Chinook salmon O. tshawytscha.

However, several recent studies have shown that in

some watersheds, subyearling Chinook salmon move

into inundated floodplain areas to rest, feed, and seek

refuge from high-flow events (Swales and Levings

1989; Sommer et al. 2001, 2005; Brown 2002).

Sommer et al. (2001) found that in California’s

Sacramento River, juveniles with a floodplain rearing

* Corresponding author: david.teel@noaa.gov

Received May 6, 2008; accepted September 8, 2008Published online February 5, 2009

211

Transactions of the American Fisheries Society 138:211–217, 2009� Copyright by the American Fisheries Society 2009DOI: 10.1577/T08-084.1

[Note]

life history had enhanced growth and survival relative

to fish in the main river channel. Wetland restoration

projects intended to increase fish access to floodplain

habitats are therefore potentially important for increas-

ing Chinook salmon life history diversity (Schreffler et

al. 1992; Brown 2002; Bottom et al. 2005a) and

improving survival and population stability.

Assessing the potential benefits that wetland resto-

ration activities might provide for Chinook salmon

requires evaluation of not only when and how juveniles

use the restored habitats but also whether the activity

primarily benefits the local population or serves a

broader segment of salmon within a basin or region.

One suite of seasonal floodplain sites that allows us to

address these questions is associated with several

ongoing wetland restoration projects in the lower

portion of the Willamette River in Oregon. Located

adjacent to sloughs and channels in the area where the

Willamette River enters the tidal freshwater portion of

the upper Columbia River estuary, the sites are

potentially accessible by fish originating in the Will-

amette River as well as from other Columbia River

basin tributaries. Use of these floodplain habitats by

juvenile Chinook salmon is of particular interest

because both the upper Willamette River and lower

Columbia River evolutionarily significant units (ESUs)

of this species are considered threatened and are listed

for protection under the U.S. Endangered Species Act

(ESA; Good et al. 2005). In this study, we used a

recently developed microsatellite DNA data set (Seeb

et al. 2007) and standard maximum likelihood genetic

stock identification techniques (Milner et al. 1985;

Brodziak 2005) to examine the stock origins of

subyearling Chinook salmon occupying the sites

during the winter–spring floodplain inundation period.

Our objective was to identify the stocks expected to

benefit from recent improvements to the floodplain

habitats. To broaden the context of our study, we also

report the stock compositions of mixed-stock samples

collected at nearby sites in the lower main-stem

Willamette River.

Study Area

The lower Willamette River flows through Portland,

the largest urban area in Oregon, before entering the

upper Columbia River estuary about 20 km down-

stream (Figure 1). The lower Willamette River has

been heavily modified by engineered structures for

shipping (docks, piers, and bulkheads), many of its

banks have been armored (rock revetments and dikes),

and many of its floodplains have been filled for

development. Several ongoing projects near the

confluence of the Willamette and Columbia rivers are

restoring the area’s seasonal floodplain wetlands. The

projects are designed to increase hydrologic connec-

tivity with the river and extend the duration for which

water inundates the wetlands during winter and spring.

These alterations have provided more winter waterfowl

habitat and access for juvenile salmon to floodplain

habitats in the winter and spring for rearing, refuge, and

feeding (Baker 2003, 2008).

Our study included four wetland habitat sampling

sites associated with the restoration projects (Figure 1,

sites 1–4). Two of the sites, Multnomah North (26 ha)

and Enyart Bottoms (3 ha) are located on the west bank

of Multnomah Channel, a large secondary channel of

the Willamette River. Two additional wetland restora-

tion sites, Ramsey (0.5 ha) and Smith–Bybee (400 ha),

are on the Columbia Slough, another secondary

channel of the Willamette River. All of the restoration

sites are wholly freshwater and under tidal influence,

and tidal fluctuations of approximately 1 m occur twice

daily.

Our study also included four sampling sites in river

habitats in the main-stem lower Willamette River and

in the north Columbia Slough adjacent to the Ramsey

and Smith–Bybee wetland restoration projects (Figure

1, sites 5–8). The Willamette River sites are all in

shallow, sandy shoreline habitats and extend from river

kilometer (rkm) 6.4 upstream to rkm 26.9 in downtown

Portland.

Methods

We collected juvenile Chinook salmon in seasonal

floodplain wetlands using passive trap nets and two-

way traps to catch fish entering and leaving the

wetlands. Sampling was conducted in winter 2005 (28

January–16 March), spring 2005 (1 April–13 June),

and spring 2006 (30 March–22 June). Not all sites were

sampled in every season (Table 1). In 2005 (4 February

and 7 April), we sampled subyearling Chinook salmon

in the main-stem Willamette River with a beach seine

(2.4- 3 45.7-m, straight-wall, buntless net constructed

of 4.8-mm, delta-style nylon mesh with a floating line

at the top and weighted line at the bottom) deployed

from a boat in a semicircular fashion and pulled to

shore.

We measured all fish to the nearest millimeter (fork

length [FL]), obtained a tissue sample from the caudal

fin, and released the fish. Tissue samples were

preserved in nondenatured ethanol. To avoid sampling

fish from multiple brood years, we used the FL

frequency distributions from previous studies to

classify juveniles as subyearlings. These studies

included juvenile Chinook salmon captured in the

lower Willamette River (Friesen et al. 2007) and fish

caught during more-extensive sampling that we

conducted in our wetland sites from 2002 to 2006

212 TEEL ET AL.

TABLE 1.—Number of tissue samples (n) and fish-length range (FL; mm) by sampling site and mixture strata for juvenile

Chinook salmon collected in the lower Willamette River, Oregon, 2005–2006. Site numbers correspond to those in Figure 1.

Sites 1–4 are wetland restoration sites; sites 5–8 are river sites.

Site (north to south) Site numberWinter 2005

River–wetland n (FL)

Spring 2005Spring 2006

Wetland n (FL)River n (FL) Wetland n (FL)

Multnomah North 1 1 (60) 4 (79–107)Enyart Bottoms 2 73 (38–108) 29 (37–83)Ramsey 3 48 (50–106)Smith–Bybee 4 3 (38–44) 2 (54–74)North Columbia Slough 5 10 (38–47)Willamette River rkm 6.4 6 2 (37–41) 14 (37–53)Willamette River rkm 15.6 7 2 (38–44) 30 (37–51)Willamette River rkm 26.9 8 34 (35–51) 28 (36–68)Total 52 72 75 81

FIGURE 1.—Map of the lower Willamette River (Oregon) study area, including wetland restoration and river sites sampled for

juvenile Chinook salmon in 2005 and 2006. Designations for sites 6–8 are river kilometers. Inset map shows location of the river

in northwestern Oregon.

NOTE 213

(data not shown). Fish greater than 60 mm FL in winter

and 110 mm FL in spring were considered to be from

the previous brood year and were excluded from the

genetic analysis. In addition, to minimize the possibil-

ity of sampling hatchery fish, only fish with intact

adipose fins were sampled.

Genomic DNA was isolated from fin tissue samples

using Wizard genomic DNA purification kits (Promega

Corp.) following the manufacturer’s protocols. The

isolated genomic DNA was used in polymerase chain

reactions (PCRs) to amplify 13 microsatellite loci that

had been standardized among several West Coast

genetics laboratories (Seeb et al. 2007). The resulting

PCR products were analyzed with an Applied Biosys-

tems 3100 capillary electrophoresis system. GeneScan

and Genotyper software programs (Applied Biosys-

tems) were used to determine the size and number of

alleles observed at each locus.

The proportional stock compositions of mixture

samples were estimated using the likelihood model of

Rannala and Mountain (1997), as implemented by the

genetic stock identification program ONCOR (Kali-

nowski et al. 2007). Allocations to individual baseline

populations were summed to estimate contributions of

regional stock groups (Table 2). Precision of the stock

composition estimates was calculated by bootstrapping

baseline and mixture data (100 times) in ONCOR

(Kalinowski et al. 2007). Population baseline data were

compiled from a multilaboratory, standardized Chi-

nook salmon genetic database (Seeb et al. 2007) and

are given in Table 2. For the Columbia River basin,

Seeb et al. (2007) presented data for 24 populations and

identified nine genetic stock identification reporting

groups. They used bootstrap means of simulated

mixtures to evaluate the ability of the baseline to

correctly allocate to reporting groups. The reporting

groups within the Columbia River basin were highly

identifiable and had mean correct allocation accuracies

above 94%; the exception was the Deschutes River

fall-run group, which had a mean accuracy of 89.5%.

TABLE 2.—Chinook salmon populations that contributed baseline data for genetic stock identification analysis of juveniles

collected in the lower Willamette River, Oregon. Genetic stock group, evolutionarily significant unit (ESU; in parentheses),

source, run time (Sp¼ spring; Su¼ summer; F¼ fall), and sample size are given. The ESUs (Good et al. 2005) are (1) upper

Willamette River, (2) lower Columbia River, (3) Deschutes River, (4) middle Columbia River spring, (5) upper Columbia River

spring, (6) upper Columbia River summer–fall, (7) Snake River fall, and (8) Snake River spring–summer. Populations marked

with an asterisk (*) are outside the geographic boundary of the given ESU but are included in the stock group because of genetic

similarity. Genetic data are from Seeb et al. (2007) except where noted.

Genetic stock group (ESU) Source Run time Sample size

Willamette River spring (1) North Fork Clackamas River*a Sp 80North Santiam Hatchery Sp 143North Santiam Rivera Sp 96McKenzie Hatchery Sp 142McKenzie Rivera Sp 98

West Cascade tributary fall (2) Cowlitz Hatchery F 140Lewis River F 93Sandy River F 124

West Cascade tributary spring (2) Cowlitz Hatchery Sp 140Kalama Hatchery Sp 144Lewis Hatchery Sp 144

Spring Creek tule fall (2) Spring Creek Hatchery F 144Big Creek Hatcherya F 99Elochoman Rivera F 95Willamette River*a F 46

Deschutes River fall (3) Lower Deschutes River F 144Middle and upper Columbia

River spring (4, 5)Carson Hatchery* Sp 144

John Day River Sp 143Upper Yakima River Sp 199Warm Springs Hatchery Sp 143Wenatchee River Sp 62

Upper Columbia River summer–fall (6) Hanford Reach F 284Methow River Su 143Wells Hatchery Su 144

Snake River fall (7) Lyons Ferry Hatchery F 186Snake River spring–summer (8) Imnaha River Su 144

Minam River Sp 144Rapid River Hatchery Sp 144Secech River Su 144Tucannon Hatchery Sp 42

a National Oceanic and Atmospheric Administration Fisheries, Northwest Fisheries Science Center,

unpublished data.

214 TEEL ET AL.

Genotypic data for six additional populations in the

Willamette River spring-run group and the Columbia

River ‘‘tule’’ (early) fall-run group were also included

in our baseline data set (Table 2) and are available upon

request (D.J.T., unpublished data).

Results

Genotypes for 13 microsatellite DNA loci were

scored for 281 Chinook salmon tissue samples

collected in the lower Willamette River in 2005 and

2006 (Table 1). Two samples collected at the Enyart

Bottoms site in spring 2005 had identical multilocus

genotypes, indicating that a fish had been captured and

sampled twice. The duplicate genotype was excluded

from the genetic stock identification analysis. Samples

were grouped into four strata based on season and

habitat type (Table 1). Because few fish were caught in

wetland sites (n¼ 14 fish) and river sites (n¼ 38 fish)

during winter 2005, those samples were analyzed as a

single mixture. Chinook salmon collected in winter

ranged from 35 to 60 mm FL, and those captured in

spring ranged from 36 to 108 mm FL; all were

considered subyearling fish.

Stock proportions of spring 2005 samples were

similar between river and wetland habitats (Table 3).

The largest contributions to both mixtures were

Willamette River spring-run fish (63% and 71%) and

spring Chinook salmon of the west Cascade tributary

group (16% and 17%). Members of the Willamette

River spring run were also estimated to make up a

smaller, though substantial, proportion of the 2005

combined winter samples (40%).

A seasonal shift in proportions was apparent for

spring Chinook salmon from the west Cascade

tributary stock group, which contributed an estimated

2% of the winter samples and 6–16% of the spring

samples. In contrast to these patterns for the spring-run

stocks, fall-run fish from the Spring Creek group

contributed a greater proportion to the winter 2005

samples (49%) than to the spring 2005 samples from

either wetland (6%) or river (11%) habitat (Table 3).

The wetland sample collected in spring 2006 was the

only mixture with substantial proportions estimated for

the west Cascade tributary fall-run group (23%) or for

the upper Columbia River summer–fall group (26%).

Differences between the compositions of the wetland

samples in 2005 and 2006 reflect interannual variation

and also the inclusion of samples in the second year

from an additional site in the Columbia Slough

(Ramsey). Overall, we estimated that our samples

contained very few fall-run Chinook salmon from the

Deschutes River (0–3%); fish from the Snake River fall

run, middle and upper Columbia River spring run, and

Snake River spring run were estimated to have no

contribution to any of the mixtures.

Discussion

Subyearling juveniles from a diverse group of

Columbia River basin Chinook salmon stocks occupy

seasonal floodplain wetlands in the lower Willamette

River. We estimated that all of the major lower

Columbia River basin stock groups identified in two

recent large-scale genetic studies of Chinook salmon

(Waples et al. 2004; Seeb et al. 2007) were present in

substantial proportions in our wetland samples. We

analyzed relatively few samples from a limited set of

collections; therefore, we do not suggest that these data

provide a quantitative assessment of the spatial or

temporal variability in juvenile stock compositions in

lower Willamette River wetland areas. Nonetheless,

our results provide an initial snapshot of the origins of

subyearlings accessing off-channel habitats in the

lower Willamette River.

Our genetic data showing winter and spring use of

lower river habitats by spring Chinook salmon

subyearlings from the Willamette River are consistent

TABLE 3.—Estimated proportional stock composition and 95% confidence intervals (CI) for subyearling Chinook salmon

sampled in the lower Willamette River, Oregon, during 2005 and 2006. Confidence intervals are from 100 bootstrap resamplings

of baseline and mixture genotypes. Sample sizes are given in Table 1.

Stock group

Winter 2005River–wetland

Spring 2005Spring 2006

WetlandRiver Wetland

Estimate CI Estimate CI Estimate CI Estimate CI

Willamette River spring 0.40 0.27–0.55 0.63 0.49–0.76 0.71 0.52–0.81 0.16 0.07–0.23West Cascade tributary fall 0.09 0.02–0.21 0.08 0.03–0.17 0.05 0.00–0.12 0.23 0.14–0.43West Cascade tributary spring 0.02 0.00–0.14 0.16 0.02–0.29 0.17 0.07–0.32 0.06 0.00–0.16Spring Creek tule fall 0.49 0.26–0.55 0.11 0.03–0.16 0.06 0.00–0.12 0.26 0.080–0.31Deschutes River fall 0.00 0.00–0.03 0.00 0.00–0.03 0.01 0.00–0.04 0.03 0.00–0.08Middle and upper Columbia River spring 0.00 0.00–0.00 0.00 0.00–0.04 0.00 0.00–0.00 0.00 0.00–0.00Upper Columbia River summer–fall 0.00 0.00–0.02 0.02 0.00–0.06 0.00 0.00–0.07 0.26 0.14–0.38Snake River fall 0.00 0.00–0.00 0.00 0.00–0.00 0.00 0.00–0.03 0.00 0.00–0.10Snake River Spring 0.00 0.00–0.00 0.00 0.00–0.01 0.00 0.00–0.00 0.00 0.00–0.00

NOTE 215

with results of previous research. Mattson (1962)

reported that in late winter and soon after emergence,

spring Chinook salmon fry began migrating from upper

Willamette River tributaries down the river and past

Willamette Falls. Friesen et al. (2007) found that

during February through late spring, subyearlings were

abundant in shallow nearshore habitat in the lower

main-stem Willamette River; those authors concluded

that the fish were probably representatives of the spring

run from the river’s upper basin. However, our study

provides the first evidence that Willamette River

spring-run Chinook salmon use the seasonal flood-

plains near the convergence of the Willamette and

Columbia rivers. Because our analysis was of small

fish with intact adipose fins and because nearly all

juveniles released from Willamette River basin hatch-

eries during our study were large yearlings marked

with adipose fin clips (PSMFC 2008), we concluded

that the Willamette River spring-run Chinook salmon

sampled in this study were naturally produced fish.

We found that fall Chinook salmon also used lower

Willamette River floodplain areas in winter and spring.

The Spring Creek fall run was the greatest contributor

to our winter 2005 (48%) and wetland spring 2006

(27%) samples. One potential source of these fish is the

upper Willamette River. Fall Chinook salmon were not

historically present above Willamette Falls, but a large

fall-run hatchery program was initiated in the mid-20th

century in the upper Willamette River. Fish from

numerous hatchery sources were used in the program,

mostly tule or early fall stocks whose origins can be

traced to the Spring Creek National Fish Hatchery

stock (Myers et al. 2006). Although the hatchery

program has been discontinued in the upper Willamette

River, a relatively small, naturally spawning fall-run

population has persisted (Friesen et al. 2007). Other

possible sources for the Spring Creek fall-run group in

our samples are the tule populations that exist in the

lower and middle Columbia River (Myers et al. 2006).

Some groups of tule fall Chinook salmon released from

the region’s hatcheries in 2005 and 2006 included

unmarked fish (PSMFC 2008). Therefore, we cannot

be certain that all of the fish we caught from the Spring

Creek fall stock group were naturally produced.

It is noteworthy that both spring and fall subyearling

Chinook salmon from outside the Willamette River are

found in this system’s river and wetland habitats.

Movements of juvenile Chinook salmon into nonnatal

streams have been reported previously (Murray and

Rosenau 1989; Scrivener et al. 1994; Bradford et al.

2001). However, our results provide the first docu-

mentation of such immigration into the Willamette

River from the Columbia River. Some of the nonnatal

fish in our samples may be from west Cascade tributary

populations near the Willamette River. For example,

spring- and fall-run fish are produced in (1) the Sandy

River, which enters the Columbia River a short

distance upstream from its confluence with the Will-

amette River, and (2) the Lewis River, which is directly

across the Columbia River from Multnomah Channel.

However, our estimates of contributions from the upper

Columbia River summer–fall group (26% of the 2006

wetland sample) indicate that subyearlings also entered

our study area from much greater distances. Potential

sources for this stock group are all near or above

Bonneville Dam (rkm 235), including numerous main-

stem and tributary ‘‘upriver bright’’ fall-run and

summer-run populations in the upper Columbia River.

Therefore, it is certain that some of the juvenile

Chinook salmon occupying lower Willamette River

wetland habitats make extensive migrations down the

Columbia River before entering the Willamette River.

Our results provide evidence that floodplain areas in

the lower Willamette River are used by juvenile

Chinook salmon from the upper Willamette River,

lower Columbia River, and upper Columbia River

summer–fall ESUs. Further study is warranted to

evaluate juvenile origins, abundance, behavior, and

residency in the lower Willamette River and to assess

the potential role that the area’s wetland restoration

projects may have in increasing juvenile life history

diversity and assisting in the recovery of specific stocks

of Chinook salmon.

Acknowledgments

This study was funded by Ducks Unlimited, Inc.,

and the U.S. Army Corps of Engineers. We thank Rose

Miranda, Julie Brenton, Andrea Thury, Tommy Butler,

and Paul Turenne for collecting tissue samples in the

field. We also thank Ry Thompson and Chad Smith

from the City of Portland, Bureau of Environmental

Services, for helping sample at Ramsey wetland.

Special thanks to Kirk Schroeder and Ken Kenaston

of the Oregon Department of Fish and Wildlife for

providing baseline tissue samples.

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