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Fish Science Dept.
Phil Roger, Manager
(503) 731-1301
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Technical Reports and Research
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 indicates
research done at the Hagerman Genetics Lab.
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2012 Reports
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Age and Length Composition of Columbia Basin Chinook, Sockeye,
and Steelhead at Bonneville Dam in 2012: WEEKLY UPDATE
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Updated Weekly
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John Whiteaker and Jeffrey K. Fryer
Age and length composition of representative samples of adult Columbia Basin chinook
(Oncorhynchus tshawytscha), sockeye (O. nerka), and steelhead salmon
(O. mykiss). Gathered results contribute to an ongoing database for age class
structure of Columbia Basin salmon populations.
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Genetic Evaluation of Steelhead Trout (Oncorhynchus mykiss)
in the Rock Creek Watershed of the Middle Columbia River Basin
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04/13/2012
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Andrew P. Matala
Comparative population structure for Rock Creek within the Columbia River Basin
Steelhead Trout (Oncorhynchus mykiss) SNP baseline.
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Upstream Migration Timing of Columbia Basin Chinook and Sockeye
Salmon and Steelhead in 2010
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03/31/2012
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Jeffrey K. Fryer, Ph.D., John M. Whiteaker and Denise Kelsey
A total of 2,559 Chinook salmon, 870 sockeye salmon, and 1,708 steelhead, were tracked
migrating up the Columbia River. Data collected from the upstream migration of these
fish species were used to 1) compare detection rates, 2) evaluate migration speed
and timing, and 3) estimate abundance of different species.
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2011 Spring Chinook Escapement to the Upper Basin of the
Klickitat River Based on DIDSON Sonar Counts
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2/17/2012
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Peter F. Galbreath, Peter E. Barber and Chris R. Fredericksen
A Dual-Frequency Identification Sonar (DIDSON) sonar was operated at the Castile
Falls Fishway to estimate of 2011 spring Chinook Oncorhynchus tshawytscha escapement
to the upper basin of the Klickitat River. While technical problems limited the
time period during which files were recorded, expansion of the observed count from
the sonar files that were obtained yields an estimate for total escapement of 38
fish.
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Integrated forecasts of fall Chinook salmon returns to the
Pacific northwest
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In Press
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Saang-Yoon Hyun, Rishi Sharma, John K. Carlile, James G. Norris,
Gayle Brown, Ryan J. Briscoe, Diana Dobson
Traditional preseason forecast of run needs to improve in bias and measure of uncertainty.
Preseason forecast made by February does not reflect ocean conditions during the
return year. Another forecast is made using ocean fishery data to detect ocean conditions
in return year. Preseason and ocean fishery forecasts are blended, and the resultant
forecast outperforms. The combined forecast can be made during ocean fishing season,
prior to in-season forecast.
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Linkages between life history type and migration pathways
in freshwater and marine environments for Chinook salmon, Oncorhynchus tshawytscha
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In Press
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Rishi Sharma and Thomas P. Quinn
We used a pair-wise design based on coded wire tagging data to compare the marine
distributions of stream- and ocean-type Chinook salmon from a suite of rivers producing
both forms. These findings have important implications for our understanding of
these life history types, and also for the conservation and management of declining,
threatened, or endangered stream-type Chinook salmon populations in the US and Canada.
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Relating Spatial and Temporal Scales of Climate and Ocean
Variability to Survival of Pacific Northwest Chinook
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In Press
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Rishi Sharma, Luis Vélez-Espino, Alex Wertheimer, Nathan Mantua,
Robert Francis
Pacific Northwest Chinook, Oncorhynchus tshawytscha, have exhibited a high
degree of variability in smolt-to-adult survival over the past three decades. This
variability is summarized for twenty two Pacific Northwest stocks and analyzed using
Generalized Linear Modeling techniques. Results indicate that survival can be grouped
into eight distinct regional clusters: (1) Alaska, Northern BC and North Georgia
Strait; (2) Georgia Strait; (3) Lower Fraser River and West Coast Vancouver Island;
(4) Puget Sound and Hood Canal; (5) Lower Columbia Tules; (6) Columbia Upriver Brights,
Willamette and Cowlitz; (7) Oregon and Washington Coastal; and (8) Klamath River
and Columbia River Summers. Further analysis for stocks within each of the eight
regions indicates that local ocean conditions following the outmigration of smolts
from freshwater to marine areas had a significant effect on survival for the majority
of the stock groups analyzed. Our analyses of the data indicate that Pacific Northwest
Chinook survival covaries on a spatial scale of 350-450 km. Lagged time series models
are presented that link large-scale tropical Pacific conditions, intermediate-basin
scale northeastern Pacific conditions, and local sea surface temperatures to survival
of Pacific Northwest stocks.
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2011 Reports
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Accounting for Tag Loss and its Uncertainty in a Mark–Recapture
Study with a Mixture of Single and Double Tags
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12/27/2011
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Saang-Yoon Hyun, Joel H. Reynolds and Peter Galbreath
Mark–recapture is often used to estimate the abundance of fish populations. Unless
accounted for in the estimation, tag loss will cause mark–recapture methods to overestimate
the true abundance of a closed population and to underestimate the associated uncertainty.
Current methods of accounting for tag loss require allmarked individuals to be double-tagged.We
present a newmodel that fully accounts for tag loss and allows for the use of a
mixture of single- and double-tagged individuals, thus simplifying implementation
in the field.
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Estimating critical abundance thresholds in exploited populations:
a simulation approach based on species resilience to disturbance
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12/01/2011
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Rishi Sharma and Scott Raborn
Managers of exploited species too often assume that populations can be maintained
at equilibrium abundances that will provide maximum yield. Most evidence to date
suggests that populations seldom adhere to equilibria, but rather fluctuate stochastically
between bounds. The last decade has revealed the consequences of not incorporating
uncertainty around point estimates of equilibria, which has led to the decline of
several fisheries. We used the sample importance re-sampling (SIR) algorithm to
exhibit the uncertainties in point estimates generated by models for management
of two salmon populations and one whale population. We then incorporated the cumulative
uncertainties of each system into a simulation technique similar to population viability
analyses (PVA) to provide decision support for establishing threshold abundances
of each exploited population.
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Age And Length Composition Of Columbai Basin Chinook And
Sockeye Salmon and Steelhead At Bonneville Dam in 2010
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12/16/2011
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Jeffrey K. Fryer, Ph.D., Denise Kelsey, Holly Ballantyne and John
M. Whiteaker
The Columbia River Inter-Tribal Fish Commission (CRITFC) conducts a field study
at Bonneville Dam which first began in 1985 to assess the age, length-at-age, and
stock composition of adult Pacific salmon migrating up the Columbia River. Adult
spring, summer and fall Chinook salmon (Oncorhynchus tshawytscha), sockeye salmon
(O. nerka) and steelhead (O. mykiss) were collected, sampled for scales and additional
biological data, PIT tagged Chinook, steelhead and sockeye, revived and released.
Caudal fin clips were also taken from Chinook, steelhead and sockeye for genetic
analysis. Scales were examined to esti¬mate age composition; the results contributed
to an ongoing database for age structure of Columbia Basin salmon runs. Based on
scale pattern analysis of our sample, four-year-olds were the most abundant age
group for spring Chinook salmon comprising 91.6% of the run. Four-year-olds were
the most abundant age class for the summer Chinook making up 70.1% of the run, while
three-year-olds were the most abundant for fall Chinook, at 53.6%. Four-year-olds
were the most abundant age group for sockeye salmon comprising 92.9% of the run,
and four-year-olds were the most abundant in the steelhead run comprising 44.2%
of the run. The unageable freshwater-, but ageable saltwater-winters (r.X) steelhead
were a large proportion of run at 22.7%. Using adipose fin clips, scale patterns,
and dorsal fin condition for classification, the steelhead migration consisted of
64.1% hatchery- and 35.9% natural-origin steelhead. A-run steelhead, less than 78cm
in length, comprised 80.2% of the steelhead run. B-run fish, equal to or greater
than 78cm, comprised 17.8% of the run.
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Sea Lion Monitoring and Non-Lethal Hazing
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12/15/2011
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Douglas R. Hatch and John M. Whiteaker
The intent and focus of this project is to address marine mammal predation on Columbia
River salmonids. This is a new and growing impact to salmonids particularly in the
last several years (Pinniped Task Force 2007). To date, most of the attention has
focused on the area just below Bonneville Dam, where salmon are concentrated before
they enter the fish ladders and where visual estimates of predation rates are easier
to develop (Stansell et al. 2011). However, there are anecdotal reports of extensive
sea lion predation in areas below the dam that are not visible from the dam. This
unaccounted for predation may be greater than the observed predation.
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Age And Length Composition Of Columbai Basin Chinook And
Sockeye Salmon and Steelhead At Bonneville Dam in 2009
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11/16/2011
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Jeffrey K. Fryer, Ph.D., Denise Kelsey, Holly Ballantyne and John
M. Whiteaker
The Columbia River Inter-Tribal Fish Commission (CRITFC) conducts a field study
at Bonneville Dam which first began in 1985 to assess the age, length-at-age, and
stock composition of adult Pacific salmon migrating up the Columbia River. Adult
spring, summer and fall Chinook salmon (Oncorhynchus tshawytscha), sockeye salmon
(O. nerka) and steelhead (O. mykiss) were collected, sampled for scales and additional
biological data, PIT tagged Chinook, steelhead and sockeye, revived and released.
Caudal fin clips were also taken from Chinook, steelhead and sockeye for genetic
analysis. Scales were examined to esti¬mate age composition; the results contributed
to an ongoing database for age structure of Columbia Basin salmon runs. A new Bonneville
Dam fish trap configuration biased our Chinook sample in 2009 resulting in the proportion
of smaller one-ocean Chinook sampled being higher than in the population as a whole.
It is unknown whether the trap configuration affected other age classes or other
species. Based on scale pattern analysis of our biased sample, three-year-olds were
the most abundant age group for spring Chinook salmon comprising 48.5% of the run
(see trap bias section). Three-year-olds were the most abundant age class for the
summer Chinook making up 37.3% of the run, while four-year-olds were the most abundant
for fall Chinook, at 57.5%. Three-year-olds were the most abundant age group for
sockeye salmon comprising 79.8% of the run, and three-year-olds were the most abundant
in steelhead comprising 50.8% of the run. A large percentage of the steelhead run
(23.0%) had scales that could only be aged for saltwater winters. Using adipose
fin clips, scale patterns, and dorsal fin condition for classification, the steelhead
migration consisted of 73.8% hatchery- and 26.2% natural-origin steelhead. A-run
steelhead, less than 78cm in length, comprised 92.2% of the steelhead run. B-run
fish, equal to or greater than 78cm, comprised 7.8% of the run.
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Introgressive Hybridization Among Major Columbia River Chinook
Salmon (Oncorhynchus tshawytscha) Lineages Within The Klickitat River Due
To Hatchery Practices
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11/01/2011
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Jon E. Hess, Andrew P. Matala, Joseph S. Zendt, Chris R. Frederiksen,
Bill Sharp, Shawn R. Narum
We characterized an introgression event that likely occurred in the 1980’s due to
hatchery broodstock practices and explains the intermediate phylogenetic status
of Klickitat R. spring-run Chinook salmon relative to the major lineages in the
Columbia River Basin.
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Genetic Stock Structure, Relative Productivity and Migration
(Gene Flow) of White Sturgeon Among Bonneville, The Dalles, John Day and McNary
Reservoirs in the Lower Mid-Columbia River Region
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10/31/2011
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Andrew P. Matala and Blaine Parker
Comparative population structure for white sturgeon spawning aggregates within four
mid-Columbia impoundments.
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Upstream Migration Timing of Columbia Basin Chinook and Sockeye
Salmon and Steelhead in 2009
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10/07/2011
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Jeffrey K. Fryer, Ph.D., Denise Kelsey, Jacinda Mainord and John
M. Whiteaker
In 2009 we sampled sockeye and Chinook salmon as well as steelhead at the Bonneville
Dam Adult Fish Facility. Fish were measured for length and scales collected for
later analysis for age and the fish were tagged with Passive Integrated Transponder
(PIT). These fish were tracked upstream as they passed through sites with PIT tag
antennas, including fish ladders at dams, juvenile bypasses, hatcheries, weirs as
well as in-stream antennas. Approximately one third of the steelhead and Chinook
were tagged with a 20mm PIT tag (model TX1420SST), the remainder, as well as all
sockeye, were tagged with a standard 12.5 mm tag (model TX1411SST). Total numbers
of fish tracked upstream were 925 spring Chinook, 907 summer Chinook, and 1109 fall
Chinook salmon, 2474 steelhead, and 807 sockeye salmon.
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Limiting Factors of the Abundance of Okanagan and Wenatchee
Sockeye Salmon in 2010
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6/30/2011
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Jeffrey K. Fryer, Howie Wright, Skyeler Folks, and Kim Hyatt
A total of 913 sockeye salmon, Oncorhynchus nerka, were PIT tagged at Bonneville
Dam in 2010. These fish were tracked upstream using data from detection arrays within
fish ladders at Bonneville, McNary, Priest Rapids, Rock Island, Rocky Reach, Wells,
Ice Harbor, Lower Granite, and Tumwater dams as well as in-river arrays in the Wenatchee
and Okanagan basins.
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Resolving Adaptive and Demographic Divergence among Chinook Salmon Populations in the Columbia River Basin
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6/17/2011
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Andrew Matala, Shawn R. Narum and Jon E. Hess
This article explores local genetic adaptation as a process shaping the population structure and distinct biological attributes for the three lineages of Chinook salmon in the Columbia Basin.
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A Computer Program for Calculating the Fluvial Distance Between
Sites in the Columbia River Basin
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6/10/2011
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David Graves
Describes the Pairwise Stream Distance Application, a tool developed to resolve
the fluvial distance of the shortest path between pairs of sites in the Columbia
River basin.
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Single-Nucleotide Polymorphism (SNP) Loci Correlated with
Run Timing in Adult Chinook Salmon from the Columbia River Basin
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6/01/2011
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Jon E. Hess, Shawn R. Narum
We examined 92 single nucleotide polymorphism (SNP) genotypes from adult Chinook
salmon passing Bonneville Dam, and determined which of these SNPs may be useful
in predicting the approximate day of the year these fish will be encountered at
this location in the Columbia River. Our analyses identified three SNPs in genes
that may be associated with adult run timing and these genes have previously been
reported to be involved with the immune system and muscle development.
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The Impact on Coldwater-Fish Populations Of
Interpretative Differences In The Application Of The United States Clean Water Act
1972 By Individual State Legislatures
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6/1/2011
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Dale Alan McCullough
The United States Clean Water Act (CWA) is one of the key legal means in the USA
to 'restore and maintain the chemical, physical and biological integrity of the
nation's waters'. Given the pervasive influence of human development and associated
climate change in increasing water temperatures in streams of the USA, salmonids
are particularly susceptible to reduction in productivity and geographic distribution.
Native and introduced, self-sustaining salmonid populations can be found in most
of the 50 States of the US. Despite this commonly shared resource, the highly similar
temperature sensitivity among salmonids, and the legal imperative under the CWA
to provide full protection to the most sensitive uses, the States supporting these
thermally sensitive species have adopted a wide range of standards.
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ANALYTICAL APPROACHES: Comparison of FST Outlier Tests
for SNP Loci Under Selection
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2/6/2011
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Shawn R. Narum, Jon E. Hess
In this study, we evaluated multiple outlier tests that identify genetic markers
under selection and their type I (false positive) and type II (false negative) error
rates in a series of simulated data sets. Results indicate that error rates can
be relatively high for certain methods, and that outliers should be interpreted
cautiously until validated with further testing.
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Comparison of SNPs and Microsatellites for
Fine-Scale Application of Genetic Stock Identification of Chinook Salmon in the
Columbia River Basin.
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1/10/2011
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J. E. Hess, A.P. Matala, Shawn R. Narum
We tested performance of 13 microsatellite vs. 92 SNP loci in a fine scale application
of genetic stock identification (GSI), using a new baseline for Chinook salmon consisting
of 49 collections (n = 4014) distributed across the Columbia River Basin. Both marker
types appear highly useful for GSI applications in the Columbia River Basin.
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Development of 54 novel Single-Nucleotide Polymorphism
(SNP) Assays For Sockeye and Coho Salmon and Assessment of Available SNPs to Differentiate
Stocks Within the Columbia River
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2/17/2011
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Nathan R. Campbell, Shawn R. Narum
This study describes discovery and development of novel SNP markers for sockeye
and coho salmon. Markers were tested in key populations and appear highly informative
to distinguish population structure within each species.
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2010 Annual Report: Genetic Assessment of Columbia River
Stocks.
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3/31/2011
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Jon Hess, Nate Campbell, Andrew Matala, Shawn Narum
This is the 2nd year of a project that combines four inter-related studies from
the Fish & Wildlife Program Accords that address these current and future objectives:
1) discover and evaluate SNP markers in salmon and steelhead; 2) expand and create
genetic baselines for multiple species (Chinook, steelhead, sockeye, and coho);
3) implement Genetic Stock Identification (GSI) programs for mainstem Chinook fisheries
and 4) GSI of fish passing Bonneville Dam (steelhead and Chinook).
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2010 Spring Chinook Escapement to the Upper Basin of the
Klickitat River Based on DIDSON Sonar Counts
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1/10/2011
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Peter F. Galbreath, Peter E. Barber, Chris R. Frederiksen, Robert
B. Lessard
A Dual-Frequency Identification Sonar (DIDSON) sonar was deployed to observe fish
passage through the Castile Falls Fishway on the Klickitat River, and to obtain
an estimate of spring Chinook escapement to the upper basin. The DIDSON continuously
recorded sequential 1-hour files from late May until late September 2010.
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2010 Reports
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2009 Draft Annual Report: Steelhead Kelt Reconditioning and
Reproductive Success
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6/29/2010
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Ryan Bransteter, Jeff Stephenson, Andrew Pierce, Douglas R. Hatch
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2009 Annual Report: Genetic Assessment of Columbia River
Stocks
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2/16/2010
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Shawn Narum, Nate Campbell, Andrew Matala, Jon Hess
This project combines four inter-related studies from the Fish & Wildlife Program
Accords that address these current and future objectives: 1) discover and evaluate
SNP markers in salmon and steelhead; 2) expand and create genetic baselines for
multiple species (Chinook, steelhead, sockeye, and coho); 3) implement Genetic Stock
Identification (GSI) programs for mainstem Chinook fisheries and 4) GSI of fish
passing Bonneville Dam (steelhead and Chinook).
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Are coldwater fish populations of the United
States actually being protected by temperature standards?
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12/1/2010
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Dale Alan McCullough
Realization of the goals of the Clean Water Act depend upon effective and clear
federal and state laws, EPA technical guidance, monitoring, enforcement, and BMPs.
A review of the legal and technical framework for protection of coldwater fish reveals
many weaknesses that leave salmonids vulnerable, but notable successes in standards
development can be offered.
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High-Throughput SNP Genotyping in Salmon and Steelhead
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1/1/2010
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Shawn Narum, Nathan Campbell, Yong Yi
Fluidigm technology is being used to characterize genetic variation in Columbia
River populations to better understand diversity, adaptation, and dispersal in natural
populations of salmon.
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Studies into Factors Limiting the Abundance of Okanagan and
Wenatchee Sockeye Salmon
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10/15/2010
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Jeffrey K. Fryer, (see report)
This report summarizes results of adult sockeye PIT and acoustic tagging programs
to assess the survival of Wenatchee and Okanogan sockeye salmon on their upstream
in 2009.
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Using Hierarchical Models to Estimate Effects
of Ocean Anomalies on Northwest Pacific Chinook salmon Oncorhynchus tshawytscha
recruitment
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1/1/2011
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Rishi Sharma, Marin Liermann
The high variability in survival over the past three decades of north-west Pacific
Chinook salmon Oncorhynchus tshawytscha is summarized for 24 stocks and analyzed
using hierarchical Bayesian models.
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Relationships between Growth and Disease Resistance
in Rainbow Trout, Oncorhynchus mykiss (Walbaum)
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4/1/2010
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Ken Overturf, 4 co-authors(see report)
Rainbow trout from 23 families were evaluated for growth and resistance to the bacterial
coldwater disease (BCWD) caused by Flavobacterium psychrophilum and infectious
haematopoietic necrosis (IHN) caused by IHN virus. Significant positive correlations
were found for end body weight and resistance to IHN (P < 0.05) and for early body
weight and resistance to BCWD (P < 0.1). However, no significant correlations were
detected between resistance to both pathogens or disease resistance and overall
genetic diversity or diversity within the major histocompatibility locus.
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Examining Genetic Lineages of Chinook Salmon in
the Columbia River Basin
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9/22/2010
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Shawn R. Narum, Jon E. Hess, Andrew P. Matala
Results from 13 microsatellite loci confirm those of previous studies that three
major lineages of Chinook salmon persist in the drainage, representing two interior
life histories (ocean and stream types) and one lineage in the lower Columbia River.
Novel observations of introgression were noted in specific collections, including
three from the lower Columbia River (Sandy River, Kalama Hatchery, and Lewis Hatchery)
and one stream-type population (Klickitat River). The stream-type lineage typically
had a lower effective population size than did the other lineages.
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Adaptation of Redband Trout in Desert and Montane
Environments
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9/30/2010
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Shawn R. Narum, Nathan R. Campbell, Christine C. Kozfkay, Kevin
A. Meyer
To explore whether local adaptation has occurred in redband trout (Oncorhynchus mykiss
gairdneri) occupying differing climate regimes, we used a limited genome
scan approach to test for candidate markers under selection in populations occurring
in desert and montane streams. Results of this study imply that many genes are involved
in the adaptation of redband trout to differing environments, and selection acts
to reinforce localization.
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Sequence Divergence of Heat Shock Genes Within
and Among 3 Oncorhynchids
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9/22/2010
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Shawn R. Narum, Nathan R. Campbell
Heat shock proteins (Hsps) are induced in response to high temperatures and other
stressors, and sequence variation plays a role in regulation of expression of these
genes. Our results indicate that Hsp genes may be locally adapted in O. clarki,
whereas higher Hsp polymorphism is necessary for O. mykiss and O. tshawytscha
and variation at the sequence level may have important evolutionary consequences
for these species.
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Observations of Fish Behavior Recorded by a DIDSON Sonar
Concurrent with Blasting Events During Renovation of the Lyle Falls Fish Ladder
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9/1/2010
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Peter F. Galbreath, Shane Keep, Joseph Zendt, Chris R. Frederiksen
A Dual-Frequency Identification Sonar (DIDSON) sonar was deployed to record fish
behavior within the trap of the Lyle Falls Fish Ladder during periods when rock
blasting events occurred – events associated with renovation/construction
activities.
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2009 Spring Chinook Escapement to the Upper Basin of the
Klickitat River Based on DIDSON Sonar Counts
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3/1/2010
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Peter F. Galbreath, Chris R. Frederiksen, Peter E. Barber, Saan-
Yoon Hyun
A Dual-Frequency Identification Sonar (DIDSON) sonar was deployed to observe fish
passage through the Castile Falls Fishway on the Klickitat River, and to obtain
an estimate of spring Chinook escapement to the upper basin. The DIDSON continuously
recorded sequential 1-hour files from late May until late September 2009.
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2009 Reports
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A Centralized Model for Creating Shared, Standardized,
Microsatellite Data that Simplifies Inter-Laboratory Collaboration
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10/22/2008
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Jeff J. Stephenson, 12 co-authors(see report)
This study demonstrates an efficient model for standardizing microsatellite DNA
data among laboratories studying Oncorhynchus mykiss. Following this central
model, we have currently standardized 298 alleles from throughout the species native
range.
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Quantitative PCR assessment of Microsatellite
and SNP Genotyping with Variable Quality DNA Extracts
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8/23/2008
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Nathan R. Campbell, Shawn R. Narum
In this study we developed eight quantitative PCR (qPCR) assays to evaluate the
starting copy number of nuclear and mitochondrial DNA fragments ranging from 75
to 350 base-pairs in DNA extracts from Chinook salmon tissues with varying quality.
Samples were genotyped with 13 microsatellite and 29 SNP assays and average genotyping
success for good, intermediate, and poor quality samples was 96%, 24%, and 24% for
microsatellite loci, and 98%, 97%, and 79% for SNPs, respectively. As measured by
qPCR, good quality samples had a consistently high number of starting copies across
all fragment sizes with little change between the smallest and largest size. In
contrast, the intermediate and poor quality samples displayed decreases in starting
copy number as fragment size increased, and was most pronounced with poor samples.
Logistic regression of genotyping success by starting copy number indicated that
in order to achieve at least 90% genotyping success, approximately 1,000 starting
copies of nuclear DNA are necessary for microsatellite loci, and as few as 14 starting
copies for SNP assays (but we recommend at least 50 copies to reduce genotyping
error). While these guidelines apply specifically to Chinook salmon and the genetic
markers included in this study, the principles are transferable to other species
and markers due to the underlying process associated with template quantity and
PCR amplification.
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Characterization of 22 Novel Single
Nucleotide Polymorphism Markers in Steelhead and Rainbow Trout
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1/1/2009
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Nathan R. Campbell, Ken Overturf, Shawn R. Narum
A total of 98 nucleotide polymorphisms were discovered during sequencing and 22
were developed into 5' exonuclease assays (Taqman assays). Genotypes from TaqMan
assays were compared to sequence data from individuals in the ascertainment panel
to confirm proper allele designations.
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Field Report: 2009 Pinniped Management Activies at Bonneville
Dam
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12/10/2009
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Robin Brown, 5 co-authors(see report)
Summary of pinniped management at Bonneville Dam in 2009.
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A Field Study to Investigate Repeat Homing in Pacific
Lampreys
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12/1/2009
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Douglas R. Hatch, John M. Whiteaker
Pacific lamprey in the Columbia River did not repeat home following displacement
downstream.
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An Evaluation of CRITFC-Coordinated Habitat Restoration Projects
and Limiting Factors to Salmon and Steelhead in the Columbia Basin
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12/1/2009
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David Graves
A GIS-based approach to compare the location of habitat restoration efforts and
limiting factors for populations of salmon and steelhead within the Columbia Basin.
This document illustrates the shortcomings to a standard overlay approach and a
discussion of issues of scale of an analysis.
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Survival, Maturation, Ocean Distribution and Recruitment
of Pacific Northwest Chinook Salmon (Oncorhynchus tshawytscha) in Relation
to Environmental Factors, and Implications for Management
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1/1/2009
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Rishi Sharma
This dissertation discusses three facets of Pacific Northwest (PNW) Chinook salmon,
Oncorhynchus tshawytscha, ecology that are relevant to current management
models used for this species: 1) life history and migration pathways, 2) the impacts
of spatial and temporal variability on PNW Chinook survival and maturation as determined
using coded wire tags, and 3) the relationship between recruitment variability and
environmental variation, explored via development of a new age-structured model.
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The Use of Generalized Additive Models for Forecasting the
Abundance of Queets River Coho Salmon
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4/20/2009
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Shizen Wang, Gary Morishima, Rishi Sharma, Larry Gilbertson
We examined three types of models for preseason forecasting of the abundance of
Queets River coho salmon Oncorhynchus kisutch: (1) a simple model in which
estimates of smolt production are multiplied by projected marine survival rates,
(2) a Ricker spawner–recruitment model, and (3) a regression model relating
log-transformed adult recruitment to smolt production.
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Age and Length Composition of Columbia Basin Chinook and
Sockeye Salmon and Steelhead at Bonneville Dam in 2008
|
5/15/2009
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Charles Torbek, Jacinda Mainord, John Whiteaker, Jeffrey Fryer,
Ph.D.
A field study at Bonneville Dam in 2008 to assess the age, length-at-age and stock
composition of adult Pacific salmon migrating up the Columbia River. These data
were then used to predict the 2008 Chinook salmon run. Adult spring, summer and
fall Chinook salmon (Oncorhynchus tshawytscha), sockeye salmon (O. nerka)
and summer-run steelhead (O. mykiss) were collected, sampled for scales and
additional biological data, revived and released.
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Estimation of Mid-Columbia summer Chinook salmon Escapement
and Age Composition using PIT tags in 2008
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5/11/2009
|
Jeffrey Fryer
A total of 663 spring Chinook, 913 summer Chinook, and 1285 fall Chinook were tracked
migrating up the Columbia River. Data collected from the upstream migration of these
fish were used to (1) compare detection rates of different PIT tag models, (2) evaluate
migration speed and timing, and (3) estimate abundance of different species.
|
Use of PIT Tags to Determine Upstream Migratory Timing and
Survival of Columbia Basin Sockeye Salmon in 2008
|
1/31/2009
|
Jeffrey Fryer
A total of 1133 sockeye salmon, Oncorhynchus nerka, were PIT-tagged at Bonneville
Dam in 2008, 824 with 12.5 mm PIT tags (model TX1411SST) and 309 with 8.5 mm PIT
tags (model TXP148511B). These fish were tracked upstream using detections within
fish ladders at Bonneville, McNary, Priest Rapids, Rock Island, Rocky Reach, Wells,
Ice Harbor, Lower Granite, and Tumwater Dams.
|
|
Ocean Harvest Real-Time Forecasts of Fall Chinook Salmon
(Oncorhynchus tshawytscha) Returns to the Columbia River
|
4/24/2009
|
Saang-Yoon Hyun, Rishi Sharma
Forecasts of fall Chinook salmon runs to the Columbia River are a critical management
component for harvest decisions and monitoring abundance trends. For the forecast
importance, preseason forecasts of fall Chinook salmon runs have been made annually,
using historical sibling runs. However their accuracy has not been consistent over
years, and further uncertainty of preseason forecasts has not been measured. The
main motivation of this study is to improve the traditional forecast methods. We
noted that catch and effort data from ocean troll fisheries during May – July
have not been incorporated to the traditional preseason forecasts that are made
before February or March. Such data could be available on a real-time basis, and
thus incorporation of those data would enable us to make the real-time forecasts
of fish runs.
|
|
Research in Thermal Biology: Burning Questions for Coldwater
Stream Fishes
|
1/1/2009
|
Dale A. McCullough, 14 co-authors (see report)
Given the many biological scales at which water temperature effects have been studied,
and the growing need to integrate knowledge from multiple disciplines of thermal
biology to fully protect beneficial uses, we held that a survey of the most promising
recent developments and an expression of some of the remaining unanswered questions
with significant management implications would best be approached collectively by
a diverse research community.
|
|
2008 Reports
|
|
Localized Genetic Structure Persists in Wild Populations
of Chinook Salmon in the John Day River Despite Gene Flow from Outside Sources
|
11/20/2008
|
Shawn R. Narum, Terra L. Schultz, Donald M. Van Doornik, David
Teel
Samples of Chinook salmon Oncorhynchus tshawytscha collected from four spawning
areas in the John Day River, Oregon (n = 330), were genotyped with 13 microsatellite
loci to test for bottlenecks and temporal stability within sites as well as genetic
differentiation among sites, and to estimate gene flow from outside populations.
The evidence presented here elucidates the balance of philopatry and dispersal acting
to maintain genetic diversity and localized structure among the Chinook salmon of
the John Day River.
|
|
Field Report: 2008 Pinniped Management Activies at Bonneville
Dam
|
9/23/2008
|
Robin Brown, Steve Jefferies, Doug Hatch, Bryan Wright
Summary of pinniped management at Bonneville Dam in 2008.
|
|
Differentiating Salmon Populations at Broad and Fine
Geographical Scales with Microsatellites and Single Nucleotide Polymorphisms
|
1/1/2008
|
Shawn R. Narum, 16 co-authors (see report)
Single nucleotide polymorphisms (SNPs) are appealing genetic markers due to several
beneficial attributes, but uncertainty remains about how many of these bi-allelic
markers are necessary to have sufficient power to differentiate populations, a task
now generally accomplished with highly polymorphic microsatellite markers. In this
study, we tested the utility of 37 SNPs and 13 microsatellites for differentiating
29 broadly distributed populations of Chinook salmon (n=2783). Information content
of all loci was determined by In and G'ST, and the top 12 markers ranked by In were
microsatellites, but the 6 highest, and 7 of the top 10 G'STranked markers, were
SNPs.
|
Procedures for Estimating Tag Loss Rate and Spawning Escapement
in a Mark-Recapture Study of Metolius River Kokanee Oncorhynchus nerka
|
8/4/2008
|
Peter F. Galbreath, Saang-Yoon Hyun
Mark-Recapture/Resight procedures were used to estimate the 2007 spawning escapement
of kokanee Oncorhynchus nerka migrating from Lake Billy Chinook into the
Metolius River, Jefferson County, Oregon. An initial analysis of data, which included
an adjustment for a presumed 25% tag loss rate (without confidence limits), provided
an escapement estimate of 101,854 ± 11,151 (±10.9%; 95% confidence interval).
|
Influence of Landscape on Resident and Anadromous Life History
Types of Oncorhynchus mykiss
|
1/1/2008
|
Shawn R. Narum, Joseph S. Zendt, David Graves, William R. Sharp
Landscape features can significantly influence genetic and life history diverstiy
of rainbow/steelhead trout, Oncorhynchus mykiss. In this study, heterozygosity
of 21 populations of O. mykiss from the Pacific Northwest, USA, was significantly
negatively correlated with features such as elevation (P=0.0023), upstream distance
(P=0.0129), and precipitation (P=0.0331), and positively correlated with temperature
(P=0.0123).
|
A GIS Analysis of Climate Change and Snowpack on Columbia
Basin Tribal Lands
|
5/27/2008
|
David Graves
A GIS-based analysis to better anticipate changes to snowpack on tribal ceded areas
in the Columbia Basin. This analysis includes the use of contemporary climate data
and projections of 21st century climate change. Contemporary data were examined
to determine the extent of areas near or just above the current mean winter freezing
level, which may transition from snow-dominated to rain-dominated regimes with moderate
warming. A snowpack model was constructed and implemented at monthly time steps
to simulate precipitation, snowpack, and snowmelt over a distributed area during
future climate scenarios.
|
Age and Length Composition of Columbia Basin Chinook and
Sockeye Salmon and Steelhead at Bonneville Dam in 2007
|
4/3/2008
|
John Whiteaker, Jeffrey Fryer
A field study at Bonneville Dam in 2007 to assess the age, length-at-age and stock
composition of adult Pacific salmon migrating up the Columbia River. These data
were then used to predict the 2007 Chinook salmon run. Adult spring, summer and
fall Chinook salmon (Oncorhynchus tshawytscha), sockeye salmon (O. nerka)
and summer-run steelhead (O. mykiss) were collected, sampled for scales and
additional biological data, revived and released.
|
Steelhead Kelt Reconditioning and Reproductive Success -2007
Annual Report
|
5/12/2008
|
Doug Hatch, 13 co-authors (see report)
The annual report of a field study to investigate the reproductive success of hatchery,
wild, and artificially reconditioned kelt steelhead. Three sites were chosen to
provide replicates to evaluate reproductive success of Oncorhynchus mykiss.
Potential adults and progeny were sampled in each drainage and genotyped with 16
microsatellite loci to determine parentage.
|
Use of PIT tags to Determine Upstream Migratory Timing and
Survival of Columbia Basin Sockeye Salmon in 2007
|
1/31/2008
|
Jeffrey Fryer
A total of 509 sockeye salmon, Oncorhynchus nerka, were PIT-tagged at Bonneville
Dam in 2007 and tracked upstream using detections at mainstem dam fish ladders.
Based on these detections, upstream survival steadily declined as the migration
progressed; Bonneville-Rock Island survival declined from over 74% for sockeye salmon
passing Bonneville Dam during June to less then 68% during the first two weeks of
July. There was also a significant linear relationship between decreasing survival
and increasing water temperature. The estimated stock composition of sockeye passing
Bonneville Dam was 85.3% Okanogan and 14.7% Wenatchee.
|
Estimation of Mid-Columbia summer Chinook salmon Escapement
and Age Composition using PIT tags in 2007
|
1/15/2008
|
Jeffrey Fryer
In 2007, a total of 470 summer Chinook salmon (Oncorhynchus tshawytscha)
were PIT tagged at Bonneville Dam between June 16 and July 13. An additional 763
spring Chinook salmon were PIT tagged between April 24 and June 15, while 194 fall
Chinook were PIT tagged between September 13 and October 12. After adding previously
tagged fish, and subtracting fish that likely shed PIT tags, a total of 764 spring
Chinook, 470 summer Chinook, and 194 fall Chinook were tracked upstream.
|
|
2007 Reports
|
|
Reproductive Isolation Following Reintroduction of Chinook
Salmon with alternative Life Histories
|
1/13/2007
|
Shawn R. Narum, William D. Arnsberg, Andre J. Talbot, Madison S.
Powell
We evaluated reproductive isolation of Chinook salmon (Oncorhynchus tshawytscha)
life history types that have been reintroduced to northern Idaho, USA.
|
|
Identification of Novel Single-Nucleotide Polymorphisms
in Chinook Salmon and Variation among Life History Types
|
1/14/2008
|
Nathan R. Campbell, Shawn R. Narum
In this study, we used expressed sequence tags from rainbow trout Oncorhynchus mykiss)
to design primers for amplification of genomic DNA fragments from Chinook salmon
O. tchawytscha. The regions flanking the repeat sequence of published microsatellite
loci in Chinook salmon were also chosen to examine nucleotide variation.
|
|
Impacts of Marker Class Bias Relative to Locus-Specific
Variability on Population Inferences in Chinook Salmon: A Comparison of Single-Nucleotide
Polymorphisms with Short Tandem Repeats and Allozymes
|
11/29/2007
|
Christian T. Smith, 5 co-authors (see report)
We examined 22 allozymes, 9 short tandem repeats (STRs), and 41 SNPs in approximately
1,300 Chinook salmon Oncorhynchus tshawytscha representing 16 collections.
We used plots of the genetic differentiation index FST versus heterozygosity and
sequence criteria to identify SNPs that might be under natural selection.
|
|
Development of a Standardized DNA Database for Chinook
Salmon
|
11/1/2007
|
L. W. Seeb, 19 co-authors (see report)
An international multi-laboratory project was conducted to develop a standardized
DNA database for Chinook salmon (Oncorhynchus tshawytscha).
|
|
Genetic Variation and Structure of Chinook Salmon Life
History Types in the Snake River Life History Types in the Snake River
|
1/1/2007
|
Shawn R. Narum, Jeffrey Stephenson, Matthew R. Campbell
An evaluation of 25 inland populations of Chinook salmon Oncorhynchus tshawytscha
in the Snake River with 13 microsatellite loci to test for contemporary genetic
differentiation at three scales: between life history types, among regions within
life history types, and among populations within regions. Published in Transactions
of the American Fisheries Society.
|
|
Year-To-Year Variability in Ocean Recovery Rate of Columbia
River Upriver Bright Fall Chinook Salmon (Oncorhynchus tshawytscha)
|
1/1/2007
|
Saang-Yoon Hyun, Katherine W. Myers, Andre Talbot
Unusually large returns of several stocks of fall Chinook salmon (Oncorhynchus tshawytscha)
from the U.S. Northwest commonly occurred during the late 1980s. We examined year-to-year
variability in cohort strength of one of these stocks, Upriver Bright (URB) fall
Chinook salmon from the Columbia River Hanford Reach for brood years 1976–99
(recovery years 1979–2002).
|
|
Bayesian Decision Analysis for Status of Snake River Spring-Summer
Chinook Salmon Oncorhynchus tshawytscha Populations at Extinction Risk
|
7/31/2007
|
Saang-Yoon Hyun, Rishi Sharma
The viability of populations was assessed using population trend data and the Diffusion
Approximation (DA) model. Various extinction risk metrics for a population are functions
of the DA model parameters, and thus, estimates of the DA model parameters are key
quantities. Using Bayesian methods, we showed uncertainty in those estimates, and
further proceeded to a decision analysis to assess viability of populations.
|
|
Iteroparity in Complex Mating Systems of Steelhead
Oncorhynchus mykiss (Walbaum)
|
7/9/2007
|
Shawn R. Narum, 4 co-authors (see report)
This study investigated diverse reproductive types in complex mating systems of
steelhead Oncorhynchus mykiss. Postspawned steelhead (kelts) were sampled
during attempted downstream migration over Lower Granite Dam on the Snake River,
U.S.A.
|
|
An Evaluation of the Reproductive Success of Natural-Origin,
Hatchery-Origin and Kelt Steelhead in the Columbia Basin
|
3/1/2007
|
Doug Hatch, 16 co-authors (see report)
The annual report of a field study to investigate the reproductive success of hatchery,
wild, and artificially reconditioned kelt steelhead. Three sites were chosen to
provide replicates to evaluate reproductive success of Oncorhynchus mykiss.
Potential adults and progeny were sampled in each drainage and genotyped with 16
microsatellite loci to determine parentage.
|
|
Age and Length Composition of Columbia Basin Chinook and
Sockeye Salmon and Steelhead at Bonneville Dam in 2006
|
3/12/2007
|
John Whiteaker, Jeffrey Fryer
A field study at Bonneville Dam in 2006 to assess the age, length-at-age and stock
composition of adult Pacific salmon migrating up the Columbia River. These data
were then used to predict the 2007 Chinook salmon run. Adult spring, summer and
fall Chinook salmon (Oncorhynchus tshawytscha), sockeye salmon (O. nerka)
and summer-run steelhead (O. mykiss) were collected, sampled for scales and
additional biological data, revived and released.
|
|
Identification of Columbia Basin Sockeye Salmon Stocks Using
Scale Pattern Analyses in 2006
|
2/27/2007
|
Jeffrey Fryer
In 2006, samples of adult Columbia Basin sockeye salmon Oncorhynchus nerka
were collected at Bonneville Dam on the Columbia River as well as at Tumwater Dam
on the Wenatchee River, and Wells Dam in the mid-Columbia River downstream of the
Okanogan River.
|
|
Estimation of Mid-Columbia Summer Chinook Salmon Escapement
and Age Composition using PIT tags in 2006
|
2/24/2007
|
Jeffrey Fryer
Based on PIT tagged recoveries, 75.3% of summer Chinook salmon passed upstream of
McNary Dam, 69.3% upstream of Rock Island Dam, 33.3% upstream of Wells Dam, and
4.5% upstream of Lower Granite. Over the three weeks of fall Chinook salmon tagging,
47.5% of those fish tagged passed McNary Dam, 5.1% passed Ice Harbor Dam, and 1.0%
passed Rock Island Dam.
|
|
Use of PIT Tags to Determine Upstream Migratory Timing and
Survival of Columbia Basin Sockeye Salmon in 2006
|
2/21/2007
|
Jeffrey Fryer
A total of 503 sockeye salmon, Oncorhynchus nerka, were PIT-tagged at Bonneville
Dam in 2006 and tracked upstream using detections at mainstem dam fish ladders.
|
|
2006 Reports
|
|
An Evaluation of the Clearwater River Supplementation Program
in Western Washington
|
1/18/2006
|
Rishi Sharma, 4 co-authors (see report)
This paper presents preliminary results of a study to evaluate the potential utility
of supplementation of natural origin coho salmon (Oncorhynchus kisutch) on
the Clearwater River, a tributary of the Queets River in western Washington. The
study, initiated in 1984, involves the collection of natural origin brood stock,
rearing in a combination of hatchery and natural environments, and volitional releases,
combined with marking and sampling of natural origin fish.
|
|
2004-2006 US Letter of Agreement (LOA) Chinook Draft Report:
Fixes or alternatives to the Individual Stock Based Management Provisions (ISBM)
|
1/1/2006
|
Rishi Sharma
Submitted as a final report to the U.S. Chinook Technical Committee
|
|
2005 Annual Report: Kelt Reconditioning: A Research Project
to Enhance Iteroparity in Columbia Basin Steelhead (Oncorhynchus mykiss)
|
12/1/2006
|
Ryan Bransetter, 6 co-authors (see report)
|
|
2005-2006 Annual Report: Kelt Reconditioning: A Research
Project to Enhance Iteroparity in Columbia Basin Steelhead (Oncorhynchus mykiss)
|
12/1/2006
|
Ryan Bransetter, 7 co-authors (see report)
A Research Project to Enhance Iteroparity in Columbia Basin Steelhead (Oncorhynchus
mykiss)
|
|
Preseason Forecasts Of Ocean Escapements Of Columbia River
Chinook Salmon (Oncorhynchus tshawytscha) Populations
|
06/30/2006
|
Saang-Yoon Hyun, Stuart Ellis, Phil Roger
|
|
2005 Annual Report: An Evaluation of the Reproductive Success
of Natural-Origin, Hatchery-origin, and Kelt Steelhead in the Columbia Basin
|
3/16/2006
|
Doug Hatch, 15 co-authors (see report)
|
|
Summer Chinook Juvenile Sampling and Adult Monitoring in
the Mid-Columbia
|
10/24/2006
|
Peter F. Galbreath, 4 co-authors (see report)
Summry of results for a project that involved field work in 2004 and 2005 performed
by CRITFC and the Yakama Nation Department of Fisheries. Activities were designed
to describe characteristics of adult escapement, juvenile production and out-migration,
and ocean migration of Mid-Columbia summer (summer/fall ocean-type) Chinook salmon
Oncorhynchus tshawytscha in the Methow River, Okanogan County, Washington.
|
|
Beyond Bonferroni: Less Conservative Analyses for Conservation
Genetics
|
10/1/2006
|
Shawn R. Narum
Determining genetic differentiation between two or more temporally or geographically
distinct sample collections.
|
|
Identification Of Columbia Basin Sockeye Salmon Stocks In
2005
|
4/5/2006
|
Jeffrey Fryer
In 2005, samples of adult Columbia Basin sockeye salmon Oncorhynchus nerka
were collected at Bonneville Dam, Tumwater Dam, and Wells Dam. Age composition was
estimated from the sampled sockeye salmon passing the three dams.
|
|
Small-Scale Genetic Structure and Variation in Steelhead
of the Grande Ronde River, Oregon, USA
|
1/1/2006
|
Shawn R. Narum, Steve Boe, Paul Moran, Matt Powell
Patterns of genetic variation in summer-run steelhead Oncorhynchus mykiss
from the Grande Ronde River, Oregon, were evaluated with 20 microsatellite loci
to determine the level of fine-scale genetic structure and influences from hatchery-reared
stocks. Included were temporal collections of three wild populations (Lookingglass
Creek, Catherine Creek, and the upper Grande Ronde River) and one hatchery population
(Wallowa Hatchery).
|
|
altered Flood Control, Climate Change, and Rebuilding Pacific
Northwest Salmon Stocks
|
3/24/2006
|
Kyle Dittmer
Moving the mainstem Columbia and Snake Rivers back toward natural conditions will
promote integrated ecosystems. altered flood control operations, plus earlier reservoir
refill, creates a more natural peaking flow regime that is more harmonious with
the salmon's life cycle than current Federal operations can provide, while still
protecting down river communities. altered flood control can achieve immediate benefits
to depressed salmon populations and may be a more timely measure while the region
debates the issue of bypassing the four Lower Snake dams.
|
|
Age And Length Composition Of Columbia Basin Chinook And
Sockeye Salmon And Steelhead At Bonneville Dam In 2005
|
4/6/2006
|
John Whiteaker, Jeffrey K. Fryer, Ph.D., Jermiah Doyle
In continuation of the Stock Assessment Project, the Columbia River Inter-Tribal
Fish Commission (CRITFC) conducted a field study at Bonneville Dam in 2005 to assess
the age, length-at-age and stock composition of adult Pacific salmon migrating up
the Columbia River.
|
|
Monitoring Fine Sediment: Grande Ronde and John Day Rivers
|
9/1/2006
|
Dale A. McCullough, Ph.D., M. Jonas Greene
Fine sediment trends were evaluated by monitoring percentage surface fine sediment
as well as fine sediment infiltration into cleaned spawning gravels embedded into
spawning reaches in plastic buckets.
|
|
Microsatellites Reveal Population Substructure of Klickitat
River Native Steelhead and Genetic Divergence from an Introduced Stock
|
1/18/2006
|
Shawn R. Narum, 4 co-authors (see report)
An analysis of 446 individuals at nine microsatellite loci to determine the local
population structure of naturally produced steelhead Oncorhynchus mykiss
and genetic differentiation from introduced hatchery strain steelhead in the Klickitat
River of the Pacific Northwest.
|
|
2005 Reports
|
|
A Quantitative Framework for the Analysis of Habitat and
Hatchery Practices on Pacific salmon
|
1/1/2005
|
Rishi Sharma, Andrew B. Cooper, Ray Hilborn
We developed a model to capture the interaction of two factors (habitat and hatchery
indicators) on salmon abundance, and provide a framework for evaluating alternative
restoration actions for salmon in the northwestern United States, assuming speci€c
ocean conditions and harvest rates.
|
|
Using Simulation Techniques to Estimate Management Parameters
on Snake River Steelhead: Declines in Productivity Make Rebuilding Difficult
|
3/17/2005
|
Henry Yuen, Rishi Sharma
We collected adult and juvenile spawner recruit data on wild summer steelhead Oncorhynchus
mykiss for the Snake River and estimated parameters for €sheries management
by partitioning the data into predam and postdam periods and €tting the Ricker
and Beverton–Holt models to those time series.
|
|
Documenting the Existing Individual Stock Based Management
(ISBM) Provision of the Chinook chapter of the Pacific Salmon Treaty: Data, Methods,
User Guide and Limitations
|
1/1/2005
|
Rishi Sharma
This report documents the source of data that is used to compute the ISBM indices
for each of the stocks identified in the Chinook chapter and the algorithms used
in computing the indices pre- and post-season for each of these stocks, and the
procedures used in the extracting the data from the Chinook Technical Committee’s
Chinook model or from coded wire tag (CWT) data.
|
|
Validation of a Long-Range Dual Frequency Identification Sonar
(DIDSON-LR) for Fish Passage Enumeration in the Methow River
|
11/1/2005
|
Peter F. Galbreath, Peter E. Barber
A DIDSON-LR was operated in parallel with visual observations to validate reliability
of the instrument to enumerate fish passage in an open river.
|
|
A Statistical Model for In-Season Forecasts of Sockeye Salmon
(Oncorhynchus nerka) Returns to the Bristol Bay Districts of Alaska
|
1/1/2005
|
Saang-Yoon Hyun, Ray Hillborn, James J. Anderson, Billy Ernst
Developed a model for in-season age-specific forecasts of salmon returns using preseason
return forecasts, age composition of in-season returns, cumulative in-season returns
by fishing district, and age composition and an index of abundance from an in-season
test fishery.
|
|
Age and Length Composition of Columbia Basin Chinook, Sockeye,
and Coho Salmon at Bonneville Dam in 2004
|
3/31/2005
|
Donette P. Miranda, John Whiteaker, Jeffrey K. Fryer, Ph.D.
In continuation of the Stock Assessment Project, CRITFC conducted a field study
at Bonneville Dam in 2004 to assess the age, length-at-age and stock composition
of Pacific salmon migrating up the Columbia River, and to predict the 2005 Chinook
salmon run.
|
|
Identification of Columbia Basin Sockeye Salmon Stocks in
2004
|
4/8/2005
|
Jeffrey K. Fryer
Results of studies performed on samples of adult Columbia Basin sockeye salmon,
Oncorhynchus nerka, collected at Bonneville Dam as well as at Tumwater Dam
on the Wenatchee River and Wells Dam in the mid-Columbia River downstream of the
Okanogan River.
|
|
2004 Reports
|
|
Kelt Reconditioning: A Research Project to Enhance Iteroparity
in Columbia Basin Steelhead (Oncorhynchus mykiss) - 2004 Annual Report
|
11/1/2004
|
Douglas Hatch, 6 co-authors (see report)
To test kelt steelhead reconditioning as a potential recovery tool, we captured
wild emigrating steelhead kelts from the Yakima River and evaluated reconditioning
(short and long-term) success and diet formulations at Prosser Hatchery on the Yakima
River. In total, 899 kelts were collected for reconditioning at Prosser Hatchery.
Captive specimens Captured kelts were separated into two experimental groups: short-term
and long-term reconditioning.
|
|
Three Genetic Stocks of Upriver Bright Fall Chinook Salmon
Detected in the Columbia River Basin, USA
|
1/1/2004
|
Shawn R. Narum, 4 co-authors (see report)
In order to detect stock structure in the Columbia River basin, we analyzed 694
upriver bright fall Chinook salmon samples from seven locations at seven microsatellite
loci.
|
|
Genetic Divergence of Sympatric Resident and Anadromous Forms
of Oncorhynchus mykiss in the Walla Walla River, U.S.A.
|
8/1/2004
|
S. R. Narum, C. Contor, A. Talbot, M. S. Powell
Genetic structure and gene flow were examined among anadromous (steelhead), resident
(rainbow trout), and mixed Oncorhynchus mykiss life-history forms collected
from the major drainages the mainstem Walla Walla River and the Touchet River within
the Walla Walla River sub-basin, Washington, U.S.A.
|
|
A Distinctive Microsatellite Locus That Differentiates Ocean-Type
from Stream-Type Chinook Salmon in the Interior Columbia River Basin
|
7/1/2004
|
Shawn R. Narum, Madison S. Powell, Andre J. Talbot
Chinook salmon Oncorhynchus tshawytscha display two life history strategies
that are referred to as ocean type and stream type. Ocean-type Chinook salmon typically
differ from stream-type fish in juvenile migration timing, adult spawning location,
and run timing. Spatial and temporal separation during spawning can lead to reproductive
isolation and genetic divergence between the two life history strategies.
|
|
Age and Length Composition of Columbia Basin Chinook, Sockeye,
and Coho Salmon at Bonneville Dam in 2003
|
3/31/2004
|
Donette P. Miranda, John Whiteaker, Jeffrey K. Fryer, Ph.D.
In continuation of the Stock Assessment Project, CRITFC conducted a field study
at Bonneville Dam in 2003 to assess the age, length-at-age and stock composition
of Pacific salmon migrating up the Columbia River, and to predict the 2004 Chinook
salmon run.
|
|
Identification of Columbia Basin Sockeye Salmon Stocks in
2003
|
3/18/2004
|
Jeffrey Fryer
Results of studys performed on samples of adult Columbia Basin sockeye salmon, Oncorhynchus
nerka, which were collected at Bonneville Dam as well as at Tumwater Dam
on the Wenatchee River and Wells Dam in the mid-Columbia River downstream of the
Okanogan River.
|
|
2003 Reports
|
|
Beliefs, Values, and Technical Assessment in Environmental
Management: Contaminated Sediments in Puget Sound
|
1/1/2003
|
Thomas M. Leschine, Kent A. Lind, Rishi Sharma
This article examines the use of principles of risk assessment in Washington State’s
development of management standards for contaminated sediments in Puget Sound. It
asks whether and how the use of a mixed quantitative-qualitative hazard assessment
approach for contaminated-site ranking, coupled with a strategy of separating technical
assessment from consideration of social and economic factors in management decisions
on a site-by-site basis, helped foster accord on the management approach selected
by the Washington Department of Ecology.
|
|
Evaluate Steelhead (Oncorhynchus mykiss) Kelt Outmigration
from Lower Granite Dam to Bonneville Dam and Test the Use of Transportation to Increase
Returns of Repeat Spawners
|
10/9/2003
|
Douglas Hatch, Ryan Branstetter, Shawn Narum
A field study was conducted at Lower Granite Dam, Washington; in the spring of 2002
to identify and enumerate kelt steelhead collected in the juvenile bypass system
and evaluate their age-structure, and genetic profiles. We also investigated kelt
steelhead migration rates, routes, and survival as well as compared return rates
of transported verse in-river migration strategies.
|
|
Kelt Reconditioning: A Research Project to Enhance Iteroparity
in Columbia Basin Steelhead (Oncorhynchus mykiss) - 2002 Annual Report
|
7/9/2003
|
Douglas Hatch, 5 co-authors (see report)
To test kelt steelhead reconditioning as a potential recovery tool, we captured
wild emigrating steelhead kelts from the Yakima River and evaluated reconditioning
(short and long-term) success and diet formulations at Prosser Hatchery on the Yakima
River. In total, 899 kelts were collected for reconditioning at Prosser Hatchery.
Captured kelts were separated into two experimental groups: short-term and long-term
reconditioning.
|
|
Tribal Energy Vision
|
5/1/2003
|
Tom Foley Consulting, Rob Lothrop
This energy vision develops a set of resources that can be developed to meet future
needs in a wise and economic manner while taking pressure off of the Columbia River
hydroelectric system. It promotes the development of resources on reservations and
other tribal lands to meet this vision.
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Development of a Stock Assessment and Research Plan for Mid-Columbia
River Summer Chinook Salmon
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5/1/2003
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Danielle F. Evenson, Andre J. Talbot
Available data pertinent to mid-Columbia summer chinook were collected, summarized,
and analyzed to identify information gaps necessary to develop a comprehensive stock
assessment and to propose areas for further research that will help evaluate current
escapement goals and guide future management plans.
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Idenitification of Columbia Basin Sockeye Salmon Stocks Using
Scale Pattern Analyses in 2002
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4/20/2003
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Jeffrey Fryer, Denise A. Kelsey
Results of studys performed on samples of adult Columbia Basin sockeye salmon, Oncorhynchus
nerka, which were collected at Bonneville Dam as well as at Tumwater Dam
on the Wenatchee River and Wells Dam in the mid-Columbia River downstream of the
Okanogan River.
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Age and Length Composition of Columbia Basin Chinook, Sockeye,
and Coho Salmon at Bonneville Dam in 2002
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3/20/2003
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Denise A. Kelsey, Jeffrey Fryer
Age and length composition of representative samples of adult Columbia Basin chinook
(Oncorhynchus tshawytscha), sockeye (O. nerka), and coho salmon (O.
kisutch). Gathered results contribute to an ongoing database for age class
structure of Columbia Basin salmon populations.
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2002 Reports
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2001 Reports
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~ pre-2001 Reports
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Monitoring Fine Sediment Grande Ronde and John Day Rivers:
Annual Report for 1999
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1/1/2000
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Jonathan J. Rhodes, Jonas M. Greene, Michael D. Purser
The project was initiated to monitor surface fine sediment levels and overwinter
intrusion of fine sediment in spring chinook salmon spawning habitat in the North
Fork John Day (NFJDR) and Grande Ronde Rivers, for five years. The project is also
investigating the potential relationship between surface fine levels and overwinter
sedimentation.
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Age and Length Composition of Columbia Basin Chinook, Sockeye,
and Coho Salmon at Bonneville Dam in 1999
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12/14/1999
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Rian C. Hooff, Amy Ritchie, Jeff Fryer, John Whiteaker
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Age and Length Composition of Columbia Basin Chinook, Sockeye,
and Coho Salmon at Bonneville Dam in 1998
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3/31/1999
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Rian C. Hooff, Amy Ritchie, John Netto
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Monitoring of Streambank Stability and Streamside Vegetation
in a Livestock Exclosure on the Warm Springs River, Oregon: Comparison of Ground-Based
Surveys with Aerial Photographic Analysis
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3/16/1999
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Dale A. McCullough, Ph.D.
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A Review and Synthesis of Effects of alterations to the Water
Temperature Regime on Freshwater Life Stages of Salmonids, with Special Reference
to Chinook Salmon
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2/22/1999
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Dale A. McCullough, Ph.D.
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Evaluation of Deschutes River Fall Chinook Salmon
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7/1/1996
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Roy E. Beaty
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A Monitoring Strategy for Application to Salmon-Bearing Watersheds
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6/4/1996
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Dale A. McCullough, F. A. Espinosa, Jr.
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Framework for Estimating Salmon Survival as a Function of
Habitat Condition
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8/19/1997
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Michael L. Cuenco, Ph.D., Dale A. McCullough
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A Comparison and Evaluation of Existing Land Management Plans
Affecting Spawning and Rearing Habitat of Snake River Basin Salmon Species Listed
Under the Endangered Species Act
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9/1/1995
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Jonathan J. Rhodes
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A Coarse Screening Process for Evaluation of the Effects
of Land Management Activities on Salmon Spawning and Rearing Habitat in ESA Consulation
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12/1/1994
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Jonathan J. Rhodes, Dale A. McCullough, F. A. Espinosa, Jr.
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A Fish Consumption Survey of the Umatilla, Nez Perce, Yakama,
and Warm Springs Tribes of the Columbia River Basin
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10/1/1994
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Columbia River Inter-Tribal Fish Commission
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A Systems Classification of Watersheds and Streams
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1/1/1988
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Dale A. McCullough
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Tribal scientists doing fish monitoring beneath the White Bluffs at the Hanford
Reach of the Columbia River.
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