Northwest Science Center publications relevant to protected fish science – 2005-2015

Bartz, K. K., M. J. Ford, T. J. Beechie, K. L. Fresh, G. R. Pess, M. Rowse, M. B. Sheer, R. Kennedy. In press. Trends in developed cover adjacent to habitat for threatened salmon in Puget Sound, Washington, U.S.A. PLoS ONE.

Clements, W. H., D. R. Kashian, P. M. Kiffney, R. E. Zuellig. In press. Perspectives on the context-dependent responses of stream benthic communities to contaminants and other anthropogenic stressors. Freshwater Biology.

Conway-Cranos, L., P. Kiffney, N. S. Banas, M. Plummer, S. M. Naman, J. Bucci, M. Ruck, P. MacCready. In press. Stable isotopes and oceanographic modeling reveal spatial and trophic connectivity between terrestrial, estuarine and marine environments in Puget Sound, WA. Marine Ecology Progress Series.

Faber-Hammond, J., R. B. Phillips, L. K. Park. In press. The Sockeye Salmon Neo-Y Chromosome is a Fusion between the Coho Y Chromosome and the Long Arm of Rainbow Trout Omy2. Cytogenetic and genome research, 136(1):69-74.

Fisch, K.M., C.C. Kozfkay, J.A. Ivy, O.A. Ryder, and R.S. Waples. 2015. Fish hatchery genetic management techniques: integrating theory with implementation. N. Am. J. Aquaculture. (in press).

Flagg, T. A. In press. Balancing conservation and harvest objectives a review of considerations for management of salmon hatcheries in the Pacific Northwest. North American Journal of Aquaculture.

Ford, M. J., T. N. Pearsons, A. R. Murdoch. In press. The relative spawning success of early maturing resident Chinook salmon in a natural river system. Transactions of the American Fisheries Society.

Ford, M. J., A. R. Murdoch, M. P. Hughes. In press. Using parentage analysis to estimate rates of straying and homing in Chinook salmon. Molecular Ecology.

Hess, J. E., R. D. Vetter, P. Moran. In press. A steep genetic cline in yellowtail rockfish, Sebastes flavidus, suggests regional isolation across the Cape Mendocino faunal break. Canadian Journal of Fisheries and Aquatic Sciences.

McElhany, P., K. A. Avery, N. J. Yoder, C. Busack, B. Thompson. In press. Dealing with Uncertainty in Ecosystem Models: Lessons from a Complex Salmon Model. Ecological Applications.

McIntyre, J. K., J. W. Davis, R. C. Edmunds, J. Incardona, N. L. Scholz, J. Stark. 2015. Soil bioretention protects juvenile salmon and their prey from the toxic impacts of urban stormwater runoff. Chemosphere, In press.

McKinney, G., M. Hale, G. W. Goetz, M. Gribskov, F. P. Thrower, K. M. Nichols. In press. Ontogenetic changes in embryonic and brain gene expression in progeny produced from migratory and resident Oncorhynchus mykiss. Molecular Ecology.

Roni, P., T. J. Beechie, C. E. Jordan, G. R. Pess. In press. Basin scale monitoring of river restoration: recommendations from case studies in the Pacific Northwest USA. In Fish habitat management. AFS Symposium 78. American Fisheries Society. Bethesda, Maryland.

Scheuerell, M. D., E. Buhle, B. X. Semmens, M. J. Ford, T. Cooney, R. W. Carmichael. In press. Analyzing large-scale conservation interventions with Bayesian hierarchical models: A case study of supplementing threatened Pacific salmon. Ecology and Evolution.

See, K. E., E. E. Holmes. In press. Reducing bias and improving precision in species extinction forecasts. Ecological Applications.

Steel, E. A., P. McElhany, N. J. Yoder, M. D. Purser, K. Malone, B. E. Thompsen, K. A. Avery, D. Jensen, G. Blair, C. Busack, M. D. Bowen, J. Hubble, T. Kantz. In press. Making the best use of modeled data: Multiple approaches to sensitivity analysis of a fish-habitat model. Fisheries.

Teel, D. J., B. J. Burke, D. R. Kuligowski, C. A. Morgan, D. M. Van Doornik. In press. Genetic identification of Chinook Salmon: Stock-specific distributions of juveniles along the Washington and Oregon coast. Marine and Coastal Fisheries.

Thorson, J. T., J. Cope, K. Kleisner, J. F. Samhouri, A. O. Shelton, E. J. Ward. In press. Giants' shoulders 15 years later: Lessons, challenges, and guidelines in fisheries meta-analysis. Fish and Fisheries. doi:DOI: 10.1111/faf.12061

Dietrich, J. P., S. A. Strickland, G. P. Hutchinson, A. L. Van Gaest, A. B. Krupkin, G. M. Ylitalo, M. R. Arkoosh. 2015. Assimilation efficiency of PBDE congeners in Chinook salmon. Environmental Science & Technology. doi:10.1021/es5057038

Dittman, A. H., T. N. Pearsons, D. May, R. Couture, D. L. Noakes. 2015. Imprinting of hatchery-reared salmon to targeted spawning locations: A new embryonic imprinting paradigm for hatchery programs. Fisheries, 40(3):114-123.

Doctor, K. K., B. A. Berejikian, G. A. Winans, D. M. Van Doornik. 2015. Evidence of between-population variation in morphology and thermal plasticity of agonistic behavior in two genetically distinct populations of steelhead. Environmental Biology of Fishes. doi:10.1007/s10641-015-0399-z

Fullerton, A. H., C. E. Torgersen, J. J. Lawler, R. N. Faux, E. A. Steel, T. J. Beechie, J. L. Ebersole, S. G. Leibowitz. 2015. Rethinking the longitudinal stream temperature paradigm: region-wide comparison of thermal infrared imagery reveals unexpected complexity of river temperatures. Hydrological Processes. doi:10.1002/hyp.10506

Hard, J. J., J. M. Myers, E. J. Connor, R. A. Hayman, R. G. Kope, G. Lucchetti, A. R. Marshall, G. R. Pess, and B. E. Thompson. 2014. Viability Criteria for Steelhead Within the Puget Sound Distinct Population Segment. U.S. Dep. Commer., NOAA Tech. Memo. NMFS-NWFSC-XXX, 390 p.

Hecht, B. C., J. J. Hard, F. P. Thrower, K. M. Nichols. 2015. Quantitative genetics of migration related traits in rainbow and steelhead trout. Genes, Genomes, Genetics, G3 g3.114.016469; Early Online March 16, 2015. doi:10.1534/g3.114.016469

Johnson, G. E., G. R. Ploskey, N. K. Sather, D. J. Teel. 2015. Residence times of juvenile salmon and steelhead in off-channel tidal freshwater habitats, Columbia River, USA. Canadian Journal of Fisheries and Aquatic Sciences, 72:684-696.

Kendall, N., J. R. McMillan, M. R. Sloat, T. W. Buehrens, T. P. Quinn, G. R. Pess, K. V. Kuzischchin, M. M. McClure, R. W. Zabel. 2015. Anadromy and residency in steelhead and rainbow trout Oncorhynchus mykiss: a review of the processes and patterns. Canadian Journal of Fisheries and Aquatic Sciences, 72(3):319-342. doi:10.1139/cjfas-2014-0192

Magie, R. J., M. S. Morris, J. P. Bender, B. F. Jonasson, B. P. Sandford, R. D. Ledgerwood. 2015. Development of a passive integrated transponder (PIT) tag detection system for adult salmonids in the lower Columbia River, 2013. Report of the Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service. Seattle, Washington.

Moser, M. L., P. R. Almeida, P. S. Kemp, P. W. Sorensen. 2015. Lamprey spawning migration. Pages 215-263 in Docker, M. F. (Ed.) Lampreys: biology, conservation and control. Springer-Verlag, New York.

Myers, J. M., J. J. Hard, E. J. Connor, R. A. Hayman, R. G. Kope, G. Lucchetti, A. R. Marshall, G. R. Pess, and B. E. Thompson. 2015. Identifying historical populations of steelhead within the Puget Sound Distinct Population Segment. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-128, 155 p.

Sandell, T. A., D. J. Teel, J. Fisher, B. R. Beckman, K. C. Jacobson. 2015. Infections by Renibacterium salmoninarum and Nanophyetus salmincola Chapin are associated with reduced growth of juvenile Chinook salmon, Oncorhynchus tshawytscha (Walbaum), in the Northeast Pacific Ocean. Journal of Fish Diseases, 38(4):365-378.

Scholz, N.L., McIntyre, J.K. 2015. Chemical pollution. In: Conservation of Freshwater Fishes. G.P. Closs, M. Krkosek, and J.D. Olden (eds.). Cambridge University Press, Cambridge. In press.

Scholz, N. L., Incardona, J.P. 2015. Scaling PAH toxicity to fish early life stages. Environmental Toxicology and Chemistry, 34:459-461.

Thorson, J. T., O. Jensen, R. Hilborn. 2015. Probability of stochastic depletion: an easily interpreted diagnostic for stock assessment modelling and fisheries management. International Council for the Exploration of the Sea Techniques in Marine Environmental Sciences, 72(2):428-435. doi:10.1093/icesjms/fsu127

Thorson, J. T., A. C. Hicks, R. D. Methot. 2015. Random effect estimation of time-varying factors in Stock Synthesis. ICES Journal of Marine Science, 72(1):178-185. doi:10.1093/icesjms/fst211

Trainer, V. L., J. Hardy. 2015. Integrative monitoring of marine and freshwater harmful algae in Washington State for public health protection. Toxins.

Trainer, V.L. and Yoshida, T. (Eds.) 2014. Proceedings of the Workshop on Economic Impacts of Harmful Algal Blooms on Fisheries and Aquaculture. PICES Sci. Rep. No. 47, 85 pp.

Tucker, S., M. E. Thiess, J. F. Morris, D. L. Mackas, W. T. Peterson, J. R. Candy, T. D. Beacham, E. Iwamoto, D. J. Teel, M. Trudel. 2015. Coastal distribution and consequent factors influencing production of endangered Snake River sockeye Salmon. Transactions of the American Fisheries Society, 144(1):107-123.

Van Daele, M. B., C. T. Robbins, B. X. Semmens, E. J. Ward, L. J. Van Daele, W. B. Leacock. 2015. Salmon consumption by Kodiak brown bears (Ursus arctos middendorffi) with ecosystem management implications. Canadian Journal of Zoology.

Van Doornik, D. M., M. A. Hess, M. A. Johnson, D. J. Teel, T. A. Friesen, J. M. Myers. 2015. Genetic Population Structure of Willamette River Steelhead and the Influence of Introduced Stocks. Transactions of the American Fisheries Society, 144:150-162. doi:10.1080/00028487.2014.982178

Van Doornik, D. M., B. A. Berejikian. 2015. Landscape factors affect the genetic population structure of Oncorhynchus mykiss populations in Hood Canal, Washington. Environmental Biology of Fishes, 98:637-653. doi:10.1007/s10641-014-0301-4

Waples RS, Adams PB, Bohnsack J, Taylor BL. 2015. When is a species threatened or endangered in "all or a significant portion of its range"? Endangered Species Research 27:189-192.

Ward, E. J., J. H. Anderson, T. J. Beechie, G. R. Pess, M. J. Ford. 2015. Increasing hydrologic variability threatens depleted anadromous fish populations. Global Change Biology.

Ward, E. J., J. E. Jannot, Y. Lee, K. Ono, A. O. Shelton, J. T. Thorson. 2015. Using spatiotemporal species distribution models to identify temporally evolving hotspots of species co-occurrence. Ecological Applications.

Weitkamp, L.A., S. A. Hinton, and P. J. Bentley. 2015. Seasonal abundance, size, and host selection of western river (Lampetra ayresii) and Pacific (Entosphenus tridentatus) Lamprey in the Columbia River estuary. Fish. Bull. 113:213-226.

Westley, P. A., A. H. Dittman, E. J. Ward, T. Quinn. 2015. Signals of climate, density-dependence, and human disturbance in Pacific salmon dispersal. Ecology.

Anderson, J. H., G. R. Pess, R. W. Carmichael, M. J. Ford, T. Cooney, C. Baldwin, M. M. McClure. 2014. Planning Pacific salmon and steelhead reintroductions aimed at long-term viability and recovery. North American Journal of Fisheries Management, 34(1):72-93.

Anlauf-Dunn, K., E. J. Ward, M. Strickland. 2014. Habitat connectivity, complexity and quality: Predicting adult coho salmon occupancy and abundance. Canadian Journal of Fisheries and Aquatic Sciences.

Banas, N. S., L. Conway-Cranos, D. A. Sutherland, P. MacCready, P. Kiffney, M. Plummer. 2014. Patterns of river influence and connectivity among subbasins of Puget Sound, with application to bacterial and nutrient loading. Estuaries and Coasts.

Bangen, S., J. Wheaton, N. Bouwes, C. E. Jordan, C. Volk, M. B. Ward. 2014. Crew variability in topgraphic surveys for monitoring instream fish habitat: a case study from the Columbia River Basin. River research and applications.

Beechie, T. J., G. R. Pess, H. Imaki, A. Martin, J. Alvarez, D. Goodman. 2014. Comparison of potential increases in juvenile salmonid rearing habitat capacity among alternative restoration scenarios, Trinity River, California. Restoration Ecology, Early view.

Beechie, T. J., H. Imaki. 2014. Predicting natural channel patterns based on landscape and geomorphic controls in the Columbia River basin, USA. Water Resources Research, 50(1):1-19.

Bennett, T. R., P. Roni, K. P. Denton, M. McHenry, R. E. Moses. 2014. Nomads no more: Early juvenile coho salmon migrants contribute to the adult return. Ecology of Freshwater Fish, (early view).

Beyer, S. G., S. M. Sogard, C. J. Harvey, J. C. Field. 2014. Variability in rockfish (Sebastes spp.) fecundity: species contrasts, maternal size effects, and spatial differences. Environmental Biology of Fishes.

Bond, M. H., B. R. Beckman, L. Rohrbach, T. P. Quinn. 2014. Differential growth in estuarine and freshwater habitats indicated by plasma IGF1 concentrations and otolith chemistry in Dolly Varden charr Salvelinus malma. Journal of Fish Biology.

Bosley, K. L., T. W. Miller, R. D. Brodeur, K. M. Bosley, A. L. Van Gaest, A. Elz. 2014. Feeding ecology of juvenile rockfishes off Oregon and Washington based on stomach content and stable isotope analyses. Marine Biology, 161(10):2381-2393.

Breckenridge, J. K., S. M. Bollens, G. Rollwagen-Bollens, G. C. Roegner. 2014. Plankton assemblage variability in a river-dominated temperate estuary during late spring (high-flow) and late summer (low-flow) periods. Estuaries and Coasts.

Brette, F., B. Machado, C. Cros, J. Incardona, N. L. Scholz, B. A. Block. 2014. Crude oil impairs cardiac excitation-contraction coupling in fish. Science, 343:772-776.

Brodeur, R. D., J. C. Buchanan, R. L. Emmett. 2014. Pelagic and demersal fish predators on juvenile and adult forage fishes in the California Current: spatial and temporal variations. California Cooperative Oceanic Fisheries Investigations Reports, 55.

Brodeur, R. D., C. Barceló, K. L. Robinson, E. A. Daly, J. J. Ruzicka. 2014. Spatial overlap between forage fishes and the large medusa Chrysaora fuscescens in the northern California Current region. Marine Ecology Progress Series, 510:167-181.

Brynildsrud, O., E. J. Feil, J. Bohlin, S. Castillo-Ramirez, D. Colquhoun, U. McCarthy, I. M. Matejusova, G. D. Wiens, L. D. Rhodes, D. W. Verner-Jeffreys. 2014. Microevolution of Renibacterium salmoninarum: evidence for intercontinental dissemination associated with fish movements. The International Society for Microbial Ecology Journal, 8(4):746-756. doi:10.1038/ismej.2013.186

Buehrens, T. W., P. M. Kiffney, G. R. Pess, T. R. Bennett, S. M. Naman, G. T. Brooks, T. Quinn. 2014. Increasing juvenile coho salmon densities during early recolonization have not affected resident coastal cutthroat trout growth, movement, or survival. North American Journal of Fisheries Management, 34(5):892-907.

Burke, B. J., J. J. Anderson, A. M. Baptista. 2014. Evidence for multiple navigational sensory capabilities by Chinook salmon. Aquatic Biology, 20(1):77-90.

Campbell, L. A., D. L. Bottom, E. C. Volk, I. A. Fleming. 2014. Correspondence between scale morphometrics and scale and otolith chemistry for interpreting

juvenile salmon life histories. Transactions of the American Fisheries Society, 144(1):55-67.

Chamberlin, J. W., T. P. Quinn. 2014. Effects of natal origin on localized distributions of Chinook salmon, Oncorhynchus tshawytscha, in the marine waters of Puget Sound. Fisheries Research, 153:113-122.

Chasco, B., E. J. Ward, C. Rabe, R. Kinzer, J. Vogel, J. A. Hesse, P. Kucera. 2014. Using state-space models to evaluate multiple survey methods: a case study for a threatened population of Chinook salmon (Oncorhynchus tshawytscha) in Johnson Creek, Idaho. North American Journal of Fisheries Management.

Chittaro, P. M., R. W. Zabel, K. Haught, B. L. Sanderson, B. P. Kennedy. 2014. Spatial and temporal patterns of growth and consumption by juvenile spring/summer Chinook salmon Oncorhynchus tshawytscha. Environmental Biology of Fishes, preview online.

Christie, M. R., M. J. Ford, M. Blouin. 2014. On the reproductive success of early-generation hatchery fish in the wild. Evolutionary Applications. doi:DOI: 10.1111/eva.12183

Claiborne, A. M., J. A. Miller, L. A. Weitkamp, D. J. Teel, R. L. Emmett. 2014. Evidence for selective mortality in marine environments: the role of fish migration size, timing, and production type. Marine Ecology Progress Series, 515:187-202.

Cooper, J., S. Diesburg, A. Babej, M. Noon, E. Kahn, M. Puettmann, J. Colt. 2014. Life Cycle Assessment of Products from Alaskan Salmon Byproducts: implications of coproduction, intermittent landings, and storage time. Fisheries Research, 151:26-38. doi:http://dx.doi.org/10.1016/j.fishres.2013.11.015

Craig, B. E., C. A. Simenstad, D. L. Bottom. 2014. Rearing in natural and recovering tidal wetlands enhances growth and life-history diversity of Columbia Estuary tributary coho salmon Oncorhynchus kisutch populations. Journal of Fish Biology, 85(sp1):31-51.

Crozier, L. G., B. J. Burke, B. P. Sandford, G. A. Axel, B. L. Sanderson. 2014. Adult Snake River sockeye salmon passage and survival within and upstream of the FCRPS. Report of the National Marine Fisheries Service to the U.S. Army Corps of Engineers. Portland, Oregon.

Crozier, L. G., D. Dechant, K. Sullivan. 2014. Impacts of climate change on Columbia River salmon: a review of the scientific literature published in 2013. Pages D1-D50 in Endangered Species Act Section 7(a)(2) supplemental biological opinion: consultation on remand for operation of the Federal Columbia River Power System. U.S. National Marine Fisheries Service, Northwest Region.

Crozier, L. G., J. A. Hutchings. 2014. Plastic and evolutionary responses to climate change in fish. Evolutionary Applications, 7(1):68-87.

Cunningham, K. A., S. A. Hayes, A. M. Wargo Rub, C. Reichmuth. 2014. Auditory detection of ultrasonic coded transmitters by seals and sea lions. Journal of the Acoustical Society of America, 135(4):1978-1985.

Daly, E. A., J. A. Scheurer, R. D. Brodeur, L. A. Weitkamp, B. R. Beckman, J. A. Miller. 2014. Juvenile steelhead distribution, migration, growth, and feeding in the Columbia River estuary, plume, and coastal waters. Marine and Coastal Fisheries, 6(1):62-80.

Dietrich, J. P., A. L. Van Gaest, S. A. Strickland, M. R. Arkoosh. 2014. The Impact of Temperature Stress and Pesticide Exposure on Mortality and Disease Susceptibility of Endangered Pacific Salmon. Chemosphere. doi:http://dx.doi.org/10.1016/j.chemosphere.2014.01.079

Dietrich, J. P., A. L. Van Gaest, S. A. Strickland, G. P. Hutchinson, A. B. Krupkin, M. R. Arkoosh. 2014. Toxicity of Forest Fire Retardant Chemicals to Chinook Salmon with Different Life History Strategies and Their Potential to Recover Before Seawater Entry. Science of the Total Environment.

Doctor, K. K., B. A. Berejikian, J. J. Hard, D. M. Van Doornik. 2014. Growth-mediated life history traits of steelhead reveal phenotypic divergence and plastic response to temperature. Transactions of the American Fisheries Society, 143(2):317-333.

East, A., G. R. Pess, J. Bountry, C. Magirl, A. Ritchie, J. Logan, T. Randle, M. Mastin, J. J. Duda, M. Liermann, M. McHenry, T. J. Beechie. 2014. Large-scale dam removal on the Elwha River, Washington, USA: river channel and floodplain geomorphic change. Geomorphology.

Elliott, D. G., G. D. Wiens, K. L. Hammell, L. D. Rhodes. 2014. Vaccination against bacterial kidney disease. In Gudding, R., A. Lillehaug, Ø. Eversen. (Eds.) Fish Vaccination. Wiley-Blackwell.

Ferriss, B., M. Trudel, B. R. Beckman. 2014. Assessing marine pelagic ecosystems: Regional and inter-annual trends in marine growth rates of juvenile salmon off the British Columbia coast. Marine Ecology Progress Series.

Fisher, J. P., L. A. Weitkamp, D. J. Teel, S. A. Hinton, J. A. Orsi, E. Farley, J. F. Morris, M. E. Thiess, R. M. Sweeting, M. Trudel. 2014. Early ocean dispersal patterns of Columbia River Chinook and coho salmon. Transactions of the American Fisheries Society, 143(1):252-272.

Fleming, I. A., D. L. Bottom, K. K. Jones, C. A. Simenstad, J. F. Craig. 2014. Resilience of anadromous and resident salmonid populations. Journal of Fish Biology, 85(sp1):1-7.

Frost, D. A., W. C. McAuley, B. Kluver, M. R. Wastel, D. J. Maynard, T. A. Flagg. 2014. Methods and accuracy of sexing sockeye salmon Oncorhynchus nerka using ultrasound for captive broodstock management. North American Journal of Aquaculture, 76(2):153-158.

Guzman, J. M., J. A. Luckenbach, Y. Yamamoto, P. Swanson. 2014. Expression profiles of Fsh-regulated ovarian genes during oogenesis in coho salmon. PLOS ONE.

Hale, M., J. Colletti, S. A. Gahr, J. Scardina, F. P. Thrower, M. Harmon, M. Carter, R. A. Phillips, G. H. Thorgaard, C. Rexroad III, K. M. Nichols. 2014. Mapping and expression of candidate genes for development rate in rainbow trout (Oncorhynchus mykiss). Journal of Heredity, 105:506520.

Harstad, D. L., D. A. Larsen, B. R. Beckman. 2014. Variation in minijack rate among Columbia River Basin Chinook salmon hatchery populations. Transactions of the American Fisheries Society.

Hecht, B. C., M. Valle, F. P. Thrower, K. M. Nichols. 2014. Divergence in Expression of Candidate Genes for the Smoltification Process Between Juvenile Resident Rainbow and Anadromous Steelhead Trout. Marine Biotechnology, 16:638-656. doi:http://www.springer.com/-/10/7f056b78056e4f9791a54a386b451f8a

Isaak, D. J., E. E. Peterson, J. M. Ver Hoef, S. J. Wenger, J. A. Falke, C. E. Torgersen, C. Sowder, E. A. Steel, M. Fortin, C. E. Jordan, A. S. Ruesch, N. Som, P. Monestiez. 2014. Spatial autocorrelation and statistical analysis on stream networks: overview and applications. WIREs Water.

Johnson, G. E., N. K. Sather, J. R. Skalski, D. J. Teel. 2014. Application of diversity indices to quantify early life-history diversity for Chinook Salmon. Ecological Indicators, 38:170-180.

Johnson, L. L., B. F. Anulacion, M. R. Arkoosh, D. G. Burrows, D. A. da Silva, J. P. Dietrich, M. S. Myers, J. A. Spromberg, G. M. Ylitalo. 2014. Effects of legacy persistent organic pollutants (POPs) in fish. Pages 53-140 in Tierney, K. B. (Ed.) Organic Chemical Toxicology of Fishes. Elsevier, London.

Johnson, R. B., E. L. Kroeger, W. L. Reichert, D. Deavila, M. B. Rust. 2014. Abundance and Origins of Plasma Lipids in Sexually Maturing Female Coho Salmon Oncorhynchus kisutch (Walbaum) in Culture. Aquaculture Research, 45:1771-1781. doi:10.1111/are.12122

Jones, K. K., T. J. Cornwell, D. L. Bottom, L. A. Campbell. 2014. The contribution of estuary-resident life histories to the return of adult Oncorhynchus kisutch. Journal of Fish Biology, 85(sp1):52-80.

Keefer, M. L., C. C. Caudill, M. L. Moser. 2014. Fishway bottleneck relief models: a case study using radio–tagged Pacific lampreys. Transactions of the American Fisheries Society, 143(4):1049-1060.

Kiffney, P. M., E. Buhle, S. M. Naman, G. R. Pess, R. Klett. 2014. Linking resource availability and habitat structure to stream organisms: an experimental and observational assessment. Ecosphere, 5(4):39.

Kline, P., T. A. Flagg. 2014. Putting the Red back in Redfish Lake - Twenty years of progress towards saving the Pacific Northwest's most endangered salmon population. Fisheries.

Kodama, M., M. S. Brieuc, R. H. Devlin, J. J. Hard, K. A. Naish. 2014. Comparative Mapping Between Coho Salmon (Oncorhynchus kisutch) and Three Other Salmonids Suggests a Role for Chromosomal Rearrangements in the Retention of Duplicated Regions Following a Whole Genome Duplication Event. Genes, Genomes, Genetics, 4:1717-1730. doi:10.1534/g3.114.012294

Laetz, C. A., D. H. Baldwin, V. Hebert, J. D. Stark, N. L. Scholz. 2014. Elevated temperatures increase the toxicity of pesticide mixtures to juvenile coho salmon. Aquatic Toxicology, 146:38-44.

Lamb, J. L., B. P. Sandford, G. A. Axel, M. G. Nesbit, B. L. Sanderson. 2014. DRAFT: Monitoring the migrations of wild Snake River spring/summer Chinook salmon juveniles, 2012-2013. Report of the National Marine Fisheries Service to the Bonneville Power Administration. Portland, Oregon.

Landguth, E. L., C. C. Muhlfeld, R. S. Waples, L. Jones, W. H. Lowe, D. Whited, J. Lucotch, H. Neville, G. Luikart. 2014. Combining demographic and genetic factors to assess population vulnerability in stream species. Ecological Applications, 24(6):1505-1524.

Liermann, M., D. Rawding, G. R. Pess, B. Glaser. 2014. The spatial distribution of salmon and steelhead redds and optimal sampling design. Canadian Journal of Fisheries and Aquatic Sciences.

Losee, J., J. Fisher, D. J. Teel, R. Baldwin, D. Marcogliese, K. C. Jacobson. 2014. Growth of Juvenile Coho salmon (Oncorhynchus kisutch) Relates Positively to Species Richness of Trophically Transmitted Parasites. Journal of Fish Biology, 85:1665-1681.

Losee, J., J. A. Miller, W. T. Peterson, D. J. Teel, K. C. Jacobson. 2014. Influence of ocean ecosystem variation on trophic interactions and survival of juvenile coho and Chinook salmon. Canadian Journal of Fisheries and Aquatic Sciences, 71:1747-1757.

Lynch, H., J. T. Thorson, A. O. Shelton. 2014. Dealing with under- and over-dispersed count data in life history, spatial, and community ecology. Ecology, 95(11):31733180. doi:http://dx.doi.org/10.1890/13-1912.1

Macneale, K.H., Spromberg, J.A., Baldwin, D.H., and Scholz, N.L. 2014. A modeled comparison of direct and food web-mediated impacts of common pesticides on Pacific salmon. Public Library of Science ONE, 9: e92436.

Marcogliese, D., K. C. Jacobson. 2014. Parasites as biological tags of marine, freshwater and anadromous fishes in North America from the tropics to the Arctic. Parasitology, (Firstview)1-22.

McIntyre, J.K., Davis, J.W., Incardona, J.P., Stark, J.D., and Scholz, N.L. 2014. Zebrafish and clean water technology: assessing the protective effects of bioinfiltration as a treatment for toxic urban runoff. Science of the Total Environment, 500-501:173-180.

McKinney, G., A. Varian, J. Scardina, K. M. Nichols. 2014. Genetic and morphological divergence in three strains of brook trout commonly stocked in Lake Superior. PLOS ONE.

McMillan, J. R., M. McHenry, G. R. Pess, R. Moses, T. P. Quinn. 2014. Documentation of Unusual, Fall Spawning by Coastal Cutthroat Trout in the Elwha River System, Washington. Transactions of the American Fisheries Society.

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Dittman, A. H., D. May, D. A. Larsen, M. L. Moser, M. Johnston, D. E. Fast. 2010. Homing and spawning site selection by supplemented hatchery- and natural-origin Yakima River spring Chinook salmon. Transactions of the American Fisheries Society, 139(4):1014-1028.

Doctor, K. K., R. Hilborn, M. Rowse, T. Quinn. 2010. Spatial and temporal patterns of upriver migration in populations of sockeye salmon, Oncorhynchus nerka, in the Wood River System, Bristol Bay, Alaska. Transactions of the American Fisheries Society, 139(1):80-91.

Drake, J., E. A. Berntson, J. M. Cope, R. G. Gustafson, E. E. Holmes, P. S. Levin, N. Tolimieri, R. S. Waples, S. Sogard, G. D. Williams. 2010. Status review of five rockfish species in Puget Sound, Washington: Bocaccio (Sebastes paucispinis), canary rockfish (S. pinniger), yelloweye rockfish (S. ruberrimus), greenstriped rockfish (S. elongatus), and redstripe rockfish (S. proriger). U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-108.

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Dumdei, N. D., R. F. Absolon, E. E. Hockersmith, G. A. Axel, M. G. Nesbit, J. L. Lamb, B. J. Burke, K. E. Frick, B. P. Sandford. 2010. Passage behavior and survival of radio-tagged subyearling chinook salmon at Lower Monumental Dam, 2009. Report of the National Marine Fisheries Service to the U.S. Army Corps of Engineers. Walla Walla, Washington.

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Feist, BE, EA Steel, DW Jensen & DND Sather. 2010. Does the scale of our observational window affect our conclusions about correlations between endangered salmon populations and their habitat? Landscape Ecology. 25:727-743.

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Frost, D. A., R. L. McComas, B. P. Sandford. 2010. The effects of a surgically implanted microacoustic tag on growth, survival, behavior, and predation risk on subyearling fall Chinook salmon. Transactions of the American Fisheries Society, 139(4):1192-1197.

Fullerton, A. H., E. A. Steel, Y. Caras, I. A. Lange. 2010. Effects of spatial pattern and economic uncertainties on freshwater habitat restoration planning: a simulation exercise. Restoration Ecology, 18(s2):354-369.

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Goetz, F. W., D. Rosauer, S. Sitar, S. Roberts, R. Johnson, C. Murphy, S. MacKenzie. 2010. A Genetic Basis For The Phenotypic Differentiation Between Siscowet And Lean Lake Trout (Salvelinus namaycush). Molecular Ecology, 19(1):176-96. doi:10.1111/j.1365-294X.2009.04481.x

Good, T. P., J. A. June, M. A. Etnier, G. Broadhurst. 2010. Derelict Fishing Nets In Puget Sound And The Northwest Straits: Patterns And Threats To Marine Fauna. Marine Pollution Bulletin, 60(1):39-50.

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Hanson, M. B., R. W. Baird, J. K. Ford, J. Hempelmann, D. M. Van Doornik, J. R. Candy, C. K. Emmons, G. S. Schorr, B. Gisborne, K. L. Ayers, S. K. Wasser, K. C. Balcomb III, K. Balcomb, J. G. Sneva, M. J. Ford. 2010. Species and stock identification of prey consumed by endangered southern resident killer whales in their summer range. Endangered Species Research, 11(1):69-82.

Harms, J. H., J. R. Wallace, I. J. Stewart. 2010. A Fishery-Independent Estimate of Recent Population Trend For An Overfished U.S. West Coast Groundfish Species, Bocaccio Rockfish (Sebastes paucispinis). Fisheries Research, 106: 298-309.

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Helmuth, B., L. Yamane, K. J. Mach, S. Chhotray, P. S. Levin, S. Woodin. 2010. All Climate Change Is Local: Understanding And Predicting The Effects Of A Changing Planet On Marine Ecosystems. Stanford Journal of Law, Science and Policy, 2:18-35.

Hering, D. K., D. L. Bottom, E. F. Prentice, K. K. Jones, I. A. Fleming. 2010. Tidal movements and residency of subyearling Chinook salmon (Onchorhynchus tschawytcha) in an Oregon salt marsh channel. Canadian Journal of Fisheries and Aquatic Sciences, 67(3):524-533.

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Hockersmith, E. E., G. A. Axel, R. F. Absolon, B. J. Burke, K. E. Frick, J. L. Lamb, M. G. Nesbit, N. D. Dumdei, B. P. Sandford. 2010. Passage behavior and survival for radio-tagged yearling Chinook salmon and juvenile steelhead at Lower Monumental Dam, 2009. Report of the National Marine Fisheries Service to the U.S. Army Corps of Engineers. Walla Walla, Washington.

Horne, P., I. C. Kaplan, K. Marshall, P. S. Levin, C. J. Harvey, A. J. Hermann, E. A. Fulton. 2010. Design and parameterization of a spatially explicity ecosystem model of the central California Current. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-104, 140 p. (PDF | Excel data file)

Johnson, L. L., M. L. Willis, O. P. Olson, R. W. Pearce, C. A. Sloan, G. M. Ylitalo. 2010. Contaminant concentrations in juvenile fall Chinook salmon from Columbia River hatcheries. North American Journal of Aquaculture, 72(1):73-92.

Kaltenberg, A. M., R. L. Emmett, K. J. Benoit-Bird. 2010. Timing of forage fish seasonal appearance in the Columbia River plume and link to ocean conditions. Marine Ecology Progress Series, 419:171-184.

Kaplan, I. C., P. S. Levin, M. Burden, E. A. Fulton. 2010. Fishing Catch Shares in the Face of Global Change: A Framework For Intergrating Cumulative Impacts and Single Species Management. Canadian Journal of Fisheries and Aquatic Sciences, 67:1968-1982.

Kendall, N., A. H. Dittman, T. P. Quinn. 2010. Comparative Maturation Schedules of Two Columbia River Sockeye Salmon, Oncorhynchus nerka, Populations. Endangered Species Research, 13:51-61.

Kiffney, P. M., J. S. Richardson. 2010. Organic matter inputs into headwater streams of southwestern British Columbia as a function of riparian reserves and time since harvesting. Forest Ecology and Management, 260(11):1931-1942.

Kitano, J., S. C. Lema, J. A. Luckenbach, S. Mori, Y. Kawagishi, M. Kusakabe, P. Swanson, C. L. Peichel. 2010. Adaptive Divergence in the Thyroid Hormone Signaling Pathway in the Stickleback Radiation. Current Biology, 20:2124-2130. doi:10.1016/j.cub.2010.10.050

Laikre, L., M. K. Schwartz, R. S. Waples, N. Ryman, GeM Working Group. 2010. Compromising genetic diversity in the wild: unmonitored large-scale release of plants and animals. Trends in Ecology and Evolution, 25(9):520-529.

Laikre, L., F. W. Allendorf, L. C. Aroner, C. S. Baker, D. P. Gregovich, M. M. Hansen, J. A. Jackson, K. C. Kendall, K. S. McKelvey, M. C. Neel, I. Olivieri, N. Ryman, M. K. Schwartz, R. Short Bull, J. B. Stetz, D. A. Tallmon, B. L. Taylor, C. D. Vojta, D. M. Waller, R. S. Waples. 2010. Neglect of genetic diversity in implementation of the Convention on Biological Diversity. Conservation Biology, 24(1):86-88.

Levin, P. S., J. F. Samhouri, M. Damon. 2010. Developing Meaningful Marine Ecosystem Indicators In The Face Of A Changing Climate. Stanford Journal of Law, Science and Policy, 2:37-48.

Levin, P. S., A. Dufault. 2010. Eating Up The Food Web. Fish and Fisheries, 11:307-312.

Liermann, M., R. R. Sharma, C. K. Parken. 2010. Using accessible watershed size to predict management parameters for Chinook salmon, Oncorhynchus tshawytscha, populations with little or no spawner-recruit data: a Bayesian hierarchical modelling approach. Fisheries Management and Ecology, 17(1):40-51.

Luckenbach, J. A., J. T. Dickey, P. Swanson. 2010. Regulation of pituitary GnRH receptor and gonadotropin subunits by IGF1 and GnRH in prepubertal male coho salmon. General and Comparative Endocrinology, 167(3):387-396. doi:10.1016/j.ygcen.2009.09.010

Macneale, K. H., B. L. Sanderson, J. P. Courbois, P. M. Kiffney. 2010. Effects of nonnative brook trout (Salvelinus fontinalis) on threatened juvenile Chinook salmon (Oncorhynchus tshawytscha) in an Idaho stream. Ecology of Freshwater Fish, 19(1):139-152.

Macneale, K. H., P. M. Kiffney, N. L. Scholz. 2010. Pesticides, aquatic food webs, and the conservation of Pacific salmonids. Frontiers in Ecology and the Environment, 8(9):475-482.

Magie, R. J., R. D. Ledgerwood, A. S. Cameron, M. S. Morris, B. P. Sandford, G. M. Matthews. 2010. Detection of PIT-tagged juvenile salmonids in the Columbia River estuary using pair trawls, 2007. Report of the National Marine Fisheries Service to the U.S. Army Corps of Engineers. Walla Walla, Washington.

Magie, R. J., M. S. Morris, R. D. Ledgerwood, A. Cook, B. P. Sandford, G. M. Matthews. 2010. Detection of PIT-tagged juvenile salmonids in the Columbia River estuary using pair-trawls, 2008. Report of the National Marine Fisheries Service to the U.S. Army Corps of Engineers. Walla Walla, Washington.

Magie, R. J., M. S. Morris, A. J. Cook, R. D. Ledgerwood, B. P. Sandford, G. M. Matthews. 2010. Pair-trawl detection of PIT-tagged juvenile salmonids migrating in the Columbia River estuary, 2009. Report of the National Marine Fisheries Service to the Bonneville Power Administration. Portland, Oregon.

Marques, A., M. L. Nunes, S. K. Moore, M. S. Strom. 2010. Climate Change and Seafood Safety: Human Health Implications. Food Research International, 43:1766-1779.

Marsh, D. M., J. R. Harmon, N. N. Paasch, K. L. Thomas, K. W. McIntyre, W. D. Muir, W. P. Connor. 2010. A study to understand the early life history of Snake River fall Chinook salmon, 2006. Report of the National Marine Fisheries Service to the U.S. Army Corps of Engineers. Walla Walla, Washington.

Marsh, D. M., W. D. Muir, B. P. Sandford, D. Elliott, L. Applegate, C. McKibben, S. Mosterd, S. Badil, J. Woodson. 2010. Alternative barging strategies to improve survival of transported juvenile salmonids, 2008. Report of the National Marine Fisheries Service to the U.S. Army Corps of Engineers. Walla Walla, Washington.

Marsh, D. M., N. N. Paasch, K. W. McIntyre, B. P. Sandford, W. D. Muir, G. M. Matthews. 2010. Latent mortality associated with passage through Snake River dams: 2009 tagging activities and final report for the 2006 juvenile migration year. Report of the National Marine Fisheries Service to the Bonneville Power Administration. Portland, Oregon.

Marsh, D. M., B. P. Sandford, S. G. Smith, G. M. Matthews, W. D. Muir. 2010. Transportation of Columbia River salmonids from McNary Dam: final adult returns from the 2002-2004 hatchery spring Chinook and 2003-2005 hatchery steelhead juvenile migrations. Report of the National Marine Fisheries Service to the U.S. Army Corps of Engineers. Walla Walla, Washington.

Marsh, D. M., K. W. McIntyre, B. P. Sandford, S. G. Smith, W. D. Muir, G. M. Matthews. 2010. Transportation of Snake River fall Chinook salmon 2008: final report for the 2004 juvenile migration. Report of the National Marine Fisheries Service to the U.S. Army Corps of Engineers. Walla Walla, Washington.

McComas, R. L., C. D. Magie, B. P. Sandford, J. W. Ferguson, D. M. Katz. 2010. Biological design criteria for fish passage facilities: high-velocity flume development and improved wet-separator efficiency, 2000. Report of the National Marine Fisheries Service to the U.S. Army Corps of Engineers. Walla Walla, Washington.

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