Generic

In press

Waples, R. S., M. M. McClure, T. C. Wainwright, P. McElhany, P. W. Lawson. In press. Integrating evolutionary and ecological considerations in recovery planning for Pacific salmon. Cambridge University Press

2009

Steel, E. A., T. J. Beechie, M. H. Ruckelshaus, A. H. Fullerton, P. McElhany, P. Roni. 2009. Mind the gap: Uncertainty and model communication between managers and scientists. American Fisheries Society Symposium. 71 357-372 pp.

2008

Tolimieri, N., M. E. Clarke, H. Singh, C. Goldfinger. 2008. Development of the SeaBED AUV to monitor populations of westcoast groundfish in untrawlable habitat: an example with rosethorn rockfish, Sebastes helvomaculatus. Alaska Sea Grant College Program, University of Alaska Fairbanks, 129-141 pp.

Journal Article

In press

Ashe, E., D. P. Noren, R. Williams. In press. Animal Behaviour And Protected Areas: Habitat Conservation For An Endangered Killer Whale Population. Animal Conservation.

Barnas, K., S. L. Katz. In press. Evaluating restoration implementation across spatial scales in the Columbia River Basin: Do local people know local restoration actions better? Fisheries.

Chittaro, P. M., I. C. Kaplan, A. A. Keller, P. S. Levin. In press. Trade-offs between species conservation and the size of marine protected areas. Conservation Biology.

Daly, E. A., R. D. Brodeur, L. A. Weitkamp. In press. Ontogenetic shifts in diets of juvenile and subadult coho (Oncorhynchus kisutch) and Chinook salmon (O. tshawytchsa) in coastal marine waters: Important for marine survival? Transactions of the American Fisheries Society, 138:1420-1438.

Doctor, K. K., R. Hilborn, M. Rowse, T. Quinn. In press. 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.

Eldridge, W. H., J. J. Hard, K. A. Naish. In press. Fishery-induced evolution in Chinook salmon: the role of harvest gear, location and genetic correlations among life history traits. Ecological Applications.

Ford MJ and Williamson KS. 2009. The Aunt and Uncle Effect RevisitedThe Effect of Biased Parentage Assignment on Fitness Estimation in a Supplemented Salmon Population. Journal of Heredity. DOI: 10.1093/jhered/esp068

Fullerton, A. H., E. A. Steel, Y. Caras, I. A. Lange. In press. Effects of Spatial Pattern and Economic Uncertainties on Freshwater Habitat Restoration Planning: a Simulation Exercise. Restoration Ecology.

Harvey, C. J. In press. Effects of temperature change on demersal fishes in the California Current: a bioenergetics approach. Canadian Journal of Fisheries and Aquatic Sciences, 66(9):1449-1461.

Krahn, M. M., M. B. Hanson, G. S. Schorr, C. K. Emmons, D. G. Burrows, J. L. Bolton, R. W. Baird, G. M. Ylitalo. In press. Effects of age, sex and reproductive status on persistent organic pollutant concentrations in "Southern Resident" killer whales. Marine Pollution Bulletin.

Lawson, P. W. In press. What are we missing? Butterflies, flowers, and salmon models. American Fisheries Society Symposium, 71:33-44.

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.

Parsons, K. M., K. C. Balcomb III, J. K. Ford, J. W. Durban. In press. The social dynamics of the southern resident killer whales and implications for the conservation of this endangered population. Animal Behavior.

Semmens, B., E. J. Ward, J. W. Moore, C. T. Darimont. In press. Quantifying Inter-And-Intra Population Niche Variability Using Hierarchical Bayesian Stable Isotope Mixing Models. PLoS ONE, 4(7):e6187.

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.

Tyson, R., C. E. Jordan, J. Hebert. In press. Modelling anguilliform swimming at intermediate Reynolds number: A review and new approach using the immersed boundary method. Computer Methods in Applied Mechanics and Engineering.

Waples, R. S., C. Do. In press. Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: A largely untapped resource for applied conservation and evolutionphic molecular markers: An evaluation of precision and bias. Evolutionary Applications.

Ward, E. J., H. Chirakkal, M. Gonzalez-Suarez, D. Aurioles-Gamboa, E. E. Holmes, L. Gerber. In press. APPLYING MULTIVARIATE-STATE-SPACE MODELS TO DETECT SPATIAL CLUSTERING OF CALIFORNIA SEA LIONS IN THE GULF OF CALIFORNIA, MEXICO.

Weitkamp, L. A. In press. Marine distributions of coho and Chinook Salmon inferred from coded wire tag recoveries. Transactions of the American Fisheries Society.

White, C. K., C. J. Harvey, M. Ebener. In press. Relationships between stable isotope signatures of parasitic sea lamprey and their hosts. Transactions of the American Fisheries Society.

Williams, G. D., K. S. Andrews, D. Farrer, P. S. Levin. In press. Catch Rates And Population Demographics Of Bluntnose Sixgill Sharks. Transactions of the American Fisheries Society.

Williamson, K. S., B. May. In press. Mitochondrial DNA haplotype diversity in apparent XY-female Fall- and Spring-Run Chinook Salmon in California's Central Valley. Transactions of the American Fisheries Society.

Winans, G. A., P. B. Aebersold, S. A. Lowe. In press. Genetic variability of sablefish Anaplopoma fimbria from California to the Bering Sea.

2009

Allendorf, F. W., J. J. Hard. 2009. Human-induced evolution caused by unnatural selection through harvest of wild animals. Proceedings of the National Academy of Sciences, USA, 106(Supplement 1):9987-9994.

Andrews, K. S., G. D. Williams, D. Farrer, N. Tolimieri, C. J. Harvey, G. Bargmann, P. S. Levin. 2009. Diel activity patterns of sixgill sharks Hexanchus griseus: the ups-and-downs of an apex predator. Animal Behavior, 78(2009):525-536.

Berejikian, B. A., D. M. Van Doornik, J. A. Scheurer, R. Bush. 2009. Reproductive behavior and relative reproductive success of natural - and - hatchery - origin Hood Canal summer chum slamon (Oncorhynchus keta). Canadian Journal of Fisheries and Aquatic Sciences, 66:781789.

Berntson, E. A., P. Moran. 2009. The utility and limitations of genetic data for stock identification and management of North Pacific rockfish (Sebastes spp.). Reviews in Fish Biology and Fisheries, 19(2):233-247.

Buhle, E., K. K. Holsman, M. D. Scheuerell, A. Albaugh. 2009. Using an unplanned experiment to evaluate the effects of hatcheries and environmental variation on threatened populations of wild coho salmon (Oncorhynchus kisutch). Biological Conservation, 142:2449-2455.

Chittaro, P. M., R. J. Finley, P. S. Levin. 2009. Spatial and temporal patterns in the contribution of fish from their juvenile habitats. Oecologia, 160:49-61.

Fullerton, A. H., A. Steel, Y. Caras, M. B. Sheer, P. Olson, J. Kaje. 2009. Putting watershed restoration in context: alternative future scenarios influence management outcomes. Ecological Applications, 19(1):218-235.

Good, T. P., J. A. June, M. A. Etnier, G. Broadhurst. 2009. Ghosts Of The Salish Sea: Threats To Marine Birds In Puget Sound And The Northwest Straits From Derelict Fishing Gear. Marine Ornithology, 37:67-76.

Grim, K. C., M. J. Wolfe, M. Edwards, J. Kaufman, S. Onjukka, P. Moran, J. C. Wolf. 2009. Epizootic ameloblastomas in Chinook salmon (Oncorhynchus tshawytscha) of the Northwestern United States. Veterinary Pathology, 46:622-635.

Honea, J., J. Jorgensen, M. McClure, T. Cooney, K. Engie, & R. Hilborn. 2009. Evaluating habitat effects on population status: Influence of habitat restoration on spring-run Chinook salmon. Freshwater Biology 54:1576-1592.

Jorgensen, J., J. Honea, M. McClure, T. Cooney, D. Holzer, & K. Engie. 2009. Linking landscape-level change to habitat quality: an evaluation of restoration actions on freshwater habitat of spring-run Chinook salmon. Freshwater Biology 54:1560-1575.

Kendall, N.W., J. J. Hard, and T. P. Quinn. 2009. Quantifying six decades of fishery selection for size and age at maturity in sockeye salmon. Evolutionary Applications 2:523-536.

Naiman, R. J., J. M. Helfield, K. K. Bartz, D. C. Drake, J. M. Honea. 2009. Pacific Salmon, Marine-Derived Nutrients and the Characteristics of Aquatic and Riparian Ecosystems. American Fisheries Society Symposium, 69:395-425.

Noren, D. P., L. Rea, T. R. Loughlin. 2009. A model to predict fasting capacities and utilization of body energy stores in weaned Steller sea lions (Eumetopias jubatus) during periods of reduced prey availability. Canadian Journal of Zoology, 87:852-864.

Noren, D. P., A. H. Johnson, D. Rehder, A. Larson. 2009. Close approaches by vessels elicit surface active behaviors by Southern Resident killer whales. Endangered Species Research, 8(3):179-192.

Plummer, M.L. 2009. Assessing benefit transfer for the valuation of ecosystem services. Frontiers in Ecology and the Environment 7(1): 3845.

Purcell, M., A. L. Murray, A. Elz, L. K. Park, S. V. Marcquenski, J. R. Winton, S. W. Alcorn, R. J. Pascho, D. G. Elliott. 2008. Decreased mortality of Lake Michigan Chinook salmon (Oncorhynchus tshawytscha) following bacterial kidney disease challenge: evidence for pathogen-driven selection? # Journal of Aquatic Animal Health, 20:225-235.

Ruckelshaus, M. H., A. Guerry. 2009. Valuing marine ecosystems? Marine Scientist, 26:26-29.

Sanderson, BL, KA Barnas, M Rub. 2009. Non-indigenous species of the Pacific Northwest: an overlooked risk to endangered salmon? BioScience 59: 245-256.

Steel, E. A., A. H. Fullerton, Y. Caras, M. B. Sheer, P. Olson, D. Jensen, J. Burke, M. T. Maher, P. McElhany. 2009. A spatially explicit decision support system for managing wide-ranging species. Ecology and Society, 13(2):50.

Teel, D.J., C. Baker, D.R. Kuligowski, T.A. Friesen, and B. Shields. 2009. Genetic Stock Composition of Subyearling Chinook Salmon in Seasonal Floodplain Wetlands of the Lower Willamette River. Transactions of the American Fisheries Society 138:211-217

Tolimieri, N., K. S. Andrews, G. D. Williams, S. L. Katz, P. S. Levin. 2009. Home range size and patterns of space use for lingcod, copper rockfish and quillback rockfish in Puget Sound in relation to diel and tidal cycles. Marine Ecology Progress Series, 380:229-243.

S. Tucker, M. Trudel, D.W. Welch, J.R. Candy, J.F.T. Morris, M.E. Thiess, C. Wallace, D.J. Teel, W. Crawford, E.V. Farley Jr., T.D. Beacham. 2009. Seasonal Stock-Specific Migrations of Juvenile Sockeye Salmon along the West Coast of North America: Implications for Growth. Transactions of the American Fisheries Society 138:1458-1480

Ward, E. J., E. E. Holmes, K. C. Balcomb III. 2009. Evidence of reproductive senescence and prey limitation in killer whales. Journal of Animal Ecology.

Ward, E. J., E. E. Holmes. 2009. The Role Of Menopause And Reproductive Senescence In A Long-Lived Social Mammal. Frontiers in Zoology.

Williams, R., D. P. Noren. 2009. Swimming speed, respiration rate and estimated cost of transport in adult killer whales. Marine Mammal Science.

2008

Anderson, E. C., R. S. Waples, and S. T. Kalinowski. 2008. An improved method for predicting the accuracy of genetic stock identification. Can. J. Fish. Aquat. Sci. 65:14751486.

Angilletta Jr., M. J., E. A. Steel, K. K. Bartz, J. G. Kingsolver, M. D. Scheuerell, B. R. Beckman, L. G. Crozier. 2008. Big dams and salmon evolution: changes in thermal regimes and their potential evolutionary consequences. Evolutionary Applications, 1(2):286-299.

Araki, H., B. A. Berejikian, M. J. Ford, M. Blouin. 2008. Fitness of hatchery-reared salmonids in the wild. Evolutionary Applications, 1:342-355.

Courbois, J., S. L. Katz, D. J. Isaak, A. Steel, R. F. Thurow, M. Rub, T. Olsen, C. E. Jordan. 2008. Evaluating probability sampling strategies for estimating redd counts: an example with Chinook salmon. Canadian Journal of Fisheries and Aquatic Sciences.

Crozier, L. G., A. P. Hendry, P. W. Lawson, T. P. Quinn, N. Mantua, J. Battin, R. G. Shaw, R. B. Huey. 2008. Evolutionary responses to climate change for organisms with complex life histories: evolution and plasticity in Pacific salmon. Evolutionary Applications, 1(1):252-270.

Ellner, S. P. and E. E. Holmes. 2008. Resolving the debate on when extinction risk is predictable. Ecology Letters 11: E1E5.

Ford MJ, Hard JJ, Boelts B, LaHood E, Miller J. 2008. Estimates of natural selection in a salmon population in captive and natural environments. Conservation Biology 22:783-794

Fullerton, A. H., D. Jensen, E. A. Steel, D. Miller, P. McElhany. 2008. How Certain Are Salmon Recovery Forecasts? A Watershed-Scale Sensitivity Analysis. Environmental Modeling and Assessment.

Good, T. P., J. R. Davies, B. J. Burke, M. H. Ruckelshaus. 2008. Incorporating catastrophic risk assessments into setting conservation goals for Pacific salmon. Ecological Applications 18(1): 246-257.

Hard, J. J., M. R. Gross, M. Heino, R. Hilborn, R. G. Kope, R. Law, and J. D. Reynolds. 2008. Evolutionary consequences of fishing and their implications for salmon. Evolutionary Applications 1(2):388-408.

Harvey, C. J., M. Ebener, C. K. White. 2008. Spatial and ontogenetic variability of sea lamprey diets in Lake Superior. Journal of Great Lakes Research, 34(3):434-449.

Harvey, C. J., K. Gross, V. H. Simon, J. Hastie. 2008. Trophic and fishery interactions between Pacific hake and rockfish: effect on rockfish population rebuilding times. Marine Ecology Progress Series, 365:165-176.

Herman, D. P., C. O. Matkin, G. M. Ylitalo, J. W. Durban, M. B. Hanson, M. E. Dahlheim, J. M. Straley, P. R. Wade, K. L. Tilbury, R. H. Boyer, R. W. Pearce, M. M. Krahn. 2008. Assessing the age-distributions of killer whale (Orcinus orca) populations from the composition of endogenous fatty acids in their outer-blubber layers. Marine Ecology Progress Series, 372:289-302.

Hess, J. E., B. J. Swalla, P. Moran. 2008. New Molecular markers to genetically differentiate populations of Didemnum vexilluman (Kott, 2002) - an invasive ascidian species. Aquatic Invasions, 4(2):299-310.

Holt, M.M., Noren, D., Veirs, V., Emmons, C., and Veirs, S. 2009. (Published online 22 Dec 2008). Speaking up: Killer whales (Orcinus orca) increase their call amplitude in response to vessel noise. Journal of the Acoustical Society of America (JASA) Express Letters. 125: EL27-EL32.

Jacobson, K.C., D. Teel, D.M. VanDoornik and E. Casillas. 2008. Parasite associated mortality of juvenile Pacific salmon caused by the trematode Nanophyetus salmincola during early marine residence. Marine Ecology Progress Series 354:235-244.

LaHood ES, Miller JJ, Apland C, Ford MJ (2008) A Rapid, Ethanol-Free Fish Tissue Collection Method for Molecular Genetic Analyses. Transactions of the American Fisheries Society: Vol. 137, No. 4 pp. 11041107

McClure, M. M., F. Utter, C. Baldwin, R. W. Carmichael, P. Hassemer, P. Howell, P. Spruell, T. Cooney, H. Schaller, C. Petrosky. 2008. Evolutionary Effects of Alternative Artificial Propagation Programs: Implications for the Viability of Endgered Anadromous Salmonids. Evolutionary Applications.

McClure, M. M., S. M. Carlson, T. J. Beechie, G. R. Pess, J. C. Jorgensen, S. M. Sogard, S. E. Sultan, D. M. Holzer, J. Travis, B. L. Sanderson, M. E. Power, R. W. Carmichael. 2008. Evolutionary consequences of habitat loss for Pacific anadromous salmonids. Evolutionary Applications.

Naish, K. A., and J. J. Hard. 2008. Bridging the gap between the genotype and the phenotype: linking genetic variation, selection and adaptation in fishes. Fish and Fisheries 9:396-422.

Narum, S. R., T. L. Schultz, D. M. Van Doornik, and D. J. Teel. 2008. Localized genetic structure persists in wild populations of Chinook salmon in the John Day River despite gene flow from outside sources. Transactions of the American Fisheries Society 137:1650-1656.

Neely, K. G., J. M. Myers, J. J. Hard, and K. D. Shearer. 2008. Comparison of growth, feed intake, and nutrient efficiency in a selected strain of coho salmon (Oncorhynchus kisutch) and its source stock. Aquaculture 283 (2008):134-140.

Pess, G. R., M. L. McHenry, T. J. Beechie, and J. Davies. 2008. Biological impacts of the Elwha River dams and potential salmonid responses to dam removal. Northwest Science 82 (Special Issue):72-90.

Ruckelshaus, M. H., T. Klinger, N. Knowlton, D. Demaster, E. Sala. 2008. Marine Ecosystem-Based Management in Practice: Scientific and Governance Challenges. Bioscience, 58:53-63.

Stephenson, J. J., M. R. Campbell, J. E. Hess, C. Kozfkay, A. P. Matala, M. V. McPhee, P. Moran, S. R. Narum, M. M. Paquin, O. Schlei, M. P. Small, D. M. Van Doornik, J. K. Wenburg. 2008. A centralized model for creating shared, standarized, microsatellite data that simplifies inter-laboratory collaboration. Conservation Genetics, 10:1145-1149.

Swanson, P., B. Campbell, K. D. Shearer, J. Dickey, B. R. Beckman, D. A. Larsen, L. K. Park, B. Berijikian. 2008. Application of Reproductive Technologies to Captive Breeding Programs for Converservation of Imperiled Stocks of Pacific Salmon. Cybium, 32(2, suppl.):279-282.

Thrower, F. P., and J. J. Hard. 2009. Effects of a single event of close inbreeding on growth and survival in steelhead. Conservation Genetics 10:1299-1307.

Van Doornik, D. M., S. J. Parker, S. R. Millard, E. A. Berntson, P. Moran. 2008. Multiple paternity is prevalent in Pacific ocean perch (sebastes alutus) off the Oregon coast, and is associated with female age. Environmental Biology of Fishes, 83:269-275.

Waples, R. S., and C. Do. 2008. LDNE: A program for estimating effective population size from data on linkage disequilibrium. Mol. Ecol. Resources 8:753-756.

G. A. Winans, M. L. McHenry, J. Baker, A. Elz, A. Goodbla, E. Iwamoto, D. R. Kuligowski, K. M. Miller, M. P. Small, P. Spruell, D. M. Van Doornik. 2008. Northwest Science 82: 128-140.

2007

Andrews, K. S., P. S. Levin, S. L. Katz, D. Farrer, V. Gallucci, G. Bargmann. 2007. Acoustic monitoring of sixgill shark movements in Puget Sound: evidence for localized movement. Canadian Journal of Zoology, 85(11):1136-1143.

Battin, J., M. W. Wiley, M. H. Ruckelshaus, R. N. Palmer, E. Korb, K. K. Bartz, H. Imaki. 2007. Projected impacts of future climate change on salmon habitat restoration actions in a Puget Sound river. Proceedings of the National Academy of Sciences, 104:6720-6725.

Brodeur, R. D., E. A. Daly, M. V. Sturdevant, T. W. Miller, J. H. Moss, M. Thiess, M. Trudel, L. A. Weitkamp, J. L. Armstrong, E. C. Norton. 2007. Regional comparisons of juvenile salmon feeding in coastal marine waters off the West Coast of North America. American Fisheries Society Symposium, 57:183-203.

Davies, Jeremy R., Kerry M. Lagueux, Beth Sanderson, and Timothy J. Beechie, 2007. Modeling Stream Channel Characteristics From Drainage-Enforced DEMs in Puget Sound, Washington, USA. Journal of the American Water Resources Association (JAWRA) 43(2):414-426.

Good, T. P., M. M. McClure, B. P. Sandford, K. Barnas, D. M. Marsh, B. A. Ryan, E. Casillas. 2007. Quantifying the effect of Caspian tern predation on endangered and threatened Pacific salmonids in the Columbia River. Endangered Species Research, 3:11-21.

Good, T. P., T. J. Beechie, P. McElhany, M. M. McClure, M. H. Ruckelshaus. 2007. Recovery planning for Endangered Species Act-listed Pacific salmon: Using science to inform goals and strategies. Fisheries, 32:426-440.

Gustafson, R. G., R. S. Waples, J. M. Myers, L. A. Weitkamp, G. J. Bryant, O. W. Johnson, J. J. Hard. 2007. Pacific salmon extinctions: quantifying lost and remaining diversity. Conservation Biology, 21(4):1009-1020. (Appendix S1 | Appendix S2 | Appendix S3)

Hall, J.E., D.M. Holzer, and T.J. Beechie. 2007. Predicting river floodplain and lateral channel migration for salmon habitat conservation. Journal of the American Water Resources Association. 43(3):786-797.

Hauser, D. D., M. G. Logsdon, E. E. Holmes, G. R. VanBlaricom, R. W. Osborne. 2007. Summer distribution patterns of Southern resident killer whales (Orcinus orca): core areas and spatial segregation of social groups. Marine Ecology Progress Series, 351:301-310.

Herman, D. P., G. M. Ylitalo, C. O. Matkin, J. W. Durban, M. B. Hanson, M. E. Dahlheim, J. M. Straley, K. L. Tilbury, M. M. Krahn. 2007. Assessing the age-distributions of killer whale (Orcinus orca) populations from the composition of endogenous fatty acids in their outer-blubber layers. Scientific Committee of the International Whaling Commission.

Hoekstra, J. M., K. K. Bartz, M. H. Ruckelshaus, J. M. Moslemi, T. K. Harms. 2007. Quantitative threat analysis for management of an imperiled species-Chinook salmon (Oncorhynchus tshawytscha). Ecological Applications, 17:2061-2073.

Holmes, E. E., J. L. Sabo, S. V. Viscido, W. Fagan. 2007. A Statistical Approach to quasi-extinction forecasting. Ecology Letters, 10:1182--1198.

Katz, S.L., Barnas, K., Hicks,. R., Cowen, J. & Jenkinson, R., 2007. Freshwater habitat restoration actions in the Pacific Northwest: A 10 year census. Restoration Ecology 15:506-515.

Krahn, M. M., M. B. Hanson, R. W. Baird, R. H. Boyer, D. G. Burrows, C. K. Emmons, J. K. Ford, L. L. Jones, D. P. Noren, P. S. Ross, G. S. Schorr, T. K. Collier. 2007. Persistent organic pollutants and stable isotope ratios in biopsy samples (2004-2006) from Southern Resident killer whales. Marine Pollution Bulletin, 54(12):1903-1911.

Lefebvre, K. A., D. P. Noren, I. R. Schultz, S. M. Bogard, B. L. Eberhart. 2007. Uptake, tissue distribution and excretion of domoic acid after oral exposure in coho salmon (Oncorhynchus kisutch). Aquatic Toxicology, 81:266-274.

McClure, M. M., M. H. Ruckelshaus. 2007. Collaborative science: moving ecosystem-based management forward in Puget Sound. Fisheries.

McMillan, J. R., S. L. Katz, G. R. Pess. 2007. Observational Evidence of Spatial and Temporal Structure in a Sympatric Anadromous (Winter Steelhead) and Resident Rainbow Trout Mating System on the Olympic Peninsula, Washington. Transactions of the American Fisheries Society, 136(3):736-748.

Plummer, M. 2007. Welcome to the Data-Poor Real World: Incorporating Benefit-Cost Principles into Environmental Policymaking. Research in Law and Economics, 23:103-130.

Sepez, J. A., K. C. Norman, R. Felthoven. 2007. A Quantitative Model for Ranking and Selecting Communities Most Involved in Commercial Fisheries. National Association for the Practice of Anthropology Bulletin, (28)43-57.

Tabor, R. A., B. A. Footen, K. L. Fresh, M. T. Celedonia, F. Mejial, D. L. Lowe, L. K. Park. 2007. Predation of juvenile Chinook salmon and other salmonids by smallmouth bass and largemouth bass in the Lake Washington Basin. North American Journal of Fisheries Management, 27(4):1174-1188.

Tolimieri N (2007) Patterns in species richness, species density and evenness in groundfish assemblages on the continental slope of the US Pacific coast. Environmental Biology of Fishes 78:241256.

Van Doornik, D. M., D. J. Teel, D. R. Kuligowski, C. A. Morgan, and E. Casillas. 2007. Genetic analyses provide insight into the early ocean stock distribution and survival of juvenile coho salmon off the coasts of Washington and Oregon. North American Journal of Fisheries Management 27:220-237.

2006

Bartz, K. K., K. M. Lagueux, M. D. Scheuerell, T. J. Beechie, A. D. Haas, M. H. Ruckelshaus. 2006. Translating restoration scenarios into habitat conditions: an initial step in evaluating recovery strategies for Chinook salmon (Oncorhynchus tshawytscha). Canadian Journal of Fisheries and Aquatic Sciences, 63:1578-1595.

Beechie, T. J., M. Liermann, M. M. Pollock, S. Baker, J. R. Davies. 2006. Channel pattern and river-floodplain dynamics in forested mountain river systems. Geomorphology, 78(1-2):124-141.

Beechie, T.J., M. Ruckelshaus, E. Buhle, A. Fullerton, L. Holsinger. 2006. Hydrologic regime and the conservation of salmon life history diversity. Biological Conservation 130(4):560-572.

Ellis, J., T. P. Good. 2006. Nest attributes, aggression, and breeding success of gulls in single and mixed species subcolonies. Condor, (108)211-219.

Fagan, W., E. E. Holmes. 2006. Quantifying the extinction vortex. Ecology Letters, 9:51-60.

Ford MJ, Fuss H, Boelts B, LaHood, E, Hard J, Miller J. 2006. Changes in run timing and natural smolt production in a naturally spawning coho salmon (Oncorhynchus kisutch) stream after 60 years of intensive hatchery supplementation. Canadian Journal of Fisheries and Aquatic Sciences 63:2343-2355.

Fullerton, A.H., T.J. Beechie, S.E. Baker, J.E. Hall, and K.A. Barnas. 2006.0Regional Patterns of Riparian Characteristics in the Interior Columbia River Basin, Northwestern USA: Applications for Restoration Planning. Landscape Ecology 21:1347-1360.

Gustafson, R. G., E. Iwamoto. 2006. A DNA-based identification key to Pacific Northwest freshwater mussel glochidia: importance to salmonid and mussel conservation. Northwest Science, 79(4):233-245.

Hard, J. J., D. G. Elliott, R. J. Pascho, D. M. Chase, L. K. Park, J. R. Winton, D. E. Campton. 2006. Genetic effects of ELISA-based segregation for control of bacterial kidney disease in Chinook salmon (Oncorhynchus tshawytscha). Canadian Journal of Fisheries and Aquatic Sciences, 63:2793-2808.

Hard, J. J., L. S. Mills, J. M. Peek. 2006. Genetic implications of reduced survival of male red deer (Cervus elaphus) under harvest. Wildlife Biology, 12(4):427-441.

Harvey, C. J., N. Tolimieri, P. S. Levin. 2006. Changes in body size, abundance, and energy allocation in rockfish assemblages of the northeast Pacific. Ecological Applications, 16:1502-1515.

Jenkinson, R., K. Barnas, J. Braatne, E. S. Bernhardt, M. A. Palmer, J. D. AllanNRRSS. 2006. Stream restoration databases and case studies: A guide to information resources and their utility in advancing the science and practice of restoration. Restoration Ecology, 14:177-186.

Kiffney, P. M., C. M. Greene, J. R. Davies, J. E. Hall. 2006. Tributary streams create spatial discontinuities in habitat, biological productivity, and diversity in mainstem rivers. Canadian Journal of Fisheries and Aquatic Sciences.

Kope, R. 2006. Cumulative effects of multiple sources of bias in estimating spawner-recruit parameters with application to harvested stocks of Chinook salmon (Oncorhynchus tshawytscha. Fisheries Research. 82: 101-110.

Mangel, M., P. S. Levin, A. Patil. 2006. Using life history and persistence criteria to prioritize habitats for management and conservation. Ecological Applications, 16:797-806.

P. Moran, D. J. Teel, E. S. LaHood, J. Drake, S. Kalinowski. 2006. Standardising multi-laboratory microsatellite data in Pacific salmon: an historical view of the future. Ecology of Freshwater Fish 15(4):597-605

Ruesink, J. L., B. E. Feist, C. J. Harvey, J. S. Hong, A. C. Trimble, L. M. Wisehart. 2006. Changes in productivity associated with four introduced species: ecosystem transformation of a "pristine" estuary. Marine Ecology Progress Series, 311:203-215.

Scheuerell, M. D., R. Hilborn, M. H. Ruckelshaus, K. K. Bartz, K. M. Lagueux, A. D. Haas, K. Rawson. 2006. The Shiraz model: a tool for incorporating fish-habitat relationships in conservation planning. Canadian Journal of Fisheries and Aquatic Sciences, 63:1596-1607.

Schwenke, P. L., J. G. Rhydderch, M. J. Ford, A. R. Marshall, L. K. Park. 2006. Forensic identification of endangered Chinook Salmon (Onchorhynchus tshawytscha ) using a multilocus SNP assay. Conservation Genetics, 7(6):983-989.

Sepez, J. A., K. C. Norman, B. D. Tilt, A. Poole. 2006. Fish scales: scale and method in social science research for North Pacific and west coast fishing communities. Human Organization, 65(3).

Sheer, M.B. and E.A. Steel. 2006. Lost watersheds: barriers, aquatic habitat connectivity and salmon persistence in the Willamette and Lower Columbia basins. Transactions of the American Fisheries Society 135(6):1654-1669.

Smith, C. T., L. K. Park, D. M. Van Doornik, L. W. Seeb, J. E. Seeb. 2006. Characterization of 19 single nucleotide polymorphism markers for coho salmon. Molecular Ecology Notes, 6:715-720.

Tolimieri N, Levin PS (2006) Assemblage structure of eastern Pacific groundfishes on the U.S. continental slope in relation to physical and environmental variables. Transactions of the American Fisheries Society 135: 115-130.

Wilson, A. B. 2006. Genetic signature of recent glaciation on populations of nearshore marine fishes (Syngnathidae: Syngnathyus). Molecular Ecology, 15:1857-1871.

Zagzebski, K. A., F. M. D. Gulland, M. Haulena, M.E. Lander, D. J. Greig, L. J. Gage, M. B. Hanson, P. K. Yochem, and B. S. Stewart. 2006. Twenty-Five Years of Rehabilitation of Odontocetes Stranded in Central and Northern California, 1977 to 2002. Aquatic Mammals, 32(3):334-344.

2005

Baird, R. W., M. B. Hanson, L. M. Dill. 2005. Factors influencing the diving behaviour of fish-eating killer whales: sex differences and diel and interannual variation in diving rates. Canadian Journal of Zoology, 83:257-267.

Berejikian, B. A., D. M. Van Doornik, A. LaRae, E. P. Tezak, J. Lee. 2005. The effects of exercise on behavior and reproductive success of captively reared steelhead. Transactions of the American Fisheries Society, 134:1236-1252.

Bernhardt, E. S., M. A. Palmer, J. D. Allan, G. Alexander, K. Barnas, S. Brooks, J. Carr, S. Clayton, C. Dahm, J. Follstad-Shah, D. Galat, S. Gloss, P. Goodwin, D. Hart, B. Hassett, R. Jenkinson, S. L. Katz, G. M. Kondolf, P. S. Lake, R. Lave, J. L. Meyer, T. K. O'Donnell, L. Pagano, B. Powell, E. Sudduth. 2005. Synthesizing U.S. river restoration efforts. Science, 308(5722):636-637.

Bilby, R. E., W. Ehinger, T. P. Quinn, G. Volkhardt, K. Krueger, D. E. Seiler, G. R. Pess, C. E. Jordan, D. Poon. 2005. Study evaluates fish response to management actions. Western Forester, 50(2):14-15.

Devlin, R. H., L. K. Park, D. M. Sakhrani, J. Baker, A. R. Marshall, E. LaHood, S. E. Kolesar, M. R. Mayo, C. Biagi, M. Uh. 2005. Variation of Y-chromosome DNA markers in Chinook salmon (Oncorhynchus tshawytscha) populations. Canadian Journal of Fisheries and Aquatic Sciences, 62:1386-1399.

Harvey, C. J., P. Kareiva. 2005. Community context and the influence of non-indigenous species on juvenile salmon survival in a Columbia River reservoir. Biological Invasions, 7:651-663.

Harvey, C. J. 2005. Effects of El Ni¿o events on energy demand and egg production of rockfish (Scorpaenidae: Sebastes): A bioenergetics approach. Fishery Bulletin, 103(71-83).

Keister, J. E., J. B. Johnson, C. A. Morgan, W. T. Peterson. 2005. Biological indicators of the timing and direction of warm-water advection during the 1997/1998 El Niqo off the central Oregon coast, USA. Marine Ecology Progress Series, 295:43-48.

Kuligowski, D. R., M. J. Ford, B. A. Berejikian. 2005. Breeding structure of steelhead inferred from patterns of genetic relatedness among nests. Transactions of the American Fisheries Society, 134:1202-1212.

Levin, P. S., G. W. Stunz. 2005. Habitat triage for exploited fishes: Can we identify essential "Essential Fish Habitat"? Estuarine, Coastal and Shelf Science, 64:70-78.

Mangel, M., P. S. Levin. 2005. Regime, phase and paradigm shifts: making community ecology the basic science for fisheries. Philosophical Transactions Royal Society of London, (360)95-105.

McClelland, E. K., J. M. Myers, J. J. Hard, L. K. Park, K. A. Naish. 2005. Two generations of outbreeding in coho salmon (Oncorhynchus kisutch): effects on size and growth. Canadian Journal of Fisheries and Aquatic Sciences, 62:2538-2547.

Oosterhout, G. R., C. W. Huntington, T. E. Nickelson, P. W. Lawson. 2005. Potential benefits of a conservation hatchery program for supplementing Oregon coast coho salmon (Oncorhynchus kisutch) populations: a stochastic model investigation. Canadian Journal of Fisheries and Aquatic Sciences, 62:1920-1935.

Phillips, R. B., M. R. Morasch, L. K. Park, K. A. Naish, R. H. Devlin. 2005. Identification of the sex chromosome pair in coho salmon (Oncorhynchus kisutch): lack of conservation of the sex linkage group with chinook salmon (Oncorhynchus tshawytscha). Cytogenetic and genome research, 111:166-170.

Scheuerell, M. D., P. S. Levin, R. W. Zabel, J. G. Williams, B. L. Sanderson. 2005. A new perspective on the importance of marine-derived nutrients to threatened stocks of Pacific salmon (Oncorhynchus sp.). Canadian Journal of Fisheries and Aquatic Sciences, 62(5):961-964.

Tear, T. H., P. Kareiva, P. L. Angermeier, P. Comer, B. Czech, R. Kautz, L. Landon, D. Mehlman, K. Murphy, M. H. Ruckelshaus, J. M. Scott, G. Wilhere. 2005. How much is enough? The recurrent problem of setting measurable objectives in conservation. Bioscience, 55:835-849.

Tolimieri, N., P. S. Levin. 2005. The roles of fishing and climate in the population dynamics of bocaccio rockfish. Ecological Applications, (15)458-468.

Weitkamp, L. A. 2005. Quillfish Ptilichthys goodei, filiform prey for small coho and chinook salmon. Alaska Fishery Research Bulletin, 11:61-65.

2004

Andrews, K. S., T. W. Anderson. 2004. Habitat-dependent recruitment of two temperate reef fishes at multiple spatial scales. Marine Ecology Progress Series, 277:231-244.

Brodeur, R. D., J. P. Fisher, D. J. Teel, R. L. Emmett, E. Casillas, T. W. Miller. 2004. Juvenile salmonid distribution, growth, condition, origin, environmental and species associations in the Northern California Current. Fishery Bulletin, 102:25-46.

Ford, M. J., D. J. Teel, D. M. Van Doornik, D. R. Kuligowski, P. W. Lawson. 2004. Genetic population structure of central Oregon Coast coho salmon (Oncorhynchus kisutch). Conservation Genetics, 5:797-812.

Gharrett, A. J., R. G. Gustafson, P. Johnson, J. L. Nielsen, J. E. Seeb, L. W. Seeb, W. W. Smoker, R. L. Wilmot, S. Keller, G. H. Thorgaard. 2004. Introduction to genetics of subpolar fish and invertebrates. Environmental Biology of Fishes, 69(1-4):1-5.

Good, T. P. 2004. Distribution and abundance patterns in Caribbean rocky intertidal zones. Bulletin of Marine Science, 74:459-468.

Granath, K. L., W. W. Smoker, A. J. Gharrett, J. J. Hard. 2004. Effects on embryo development time and survival of intercrossing three geographically separate populations of Southeast Alaska coho salmon, Oncorhynchus kisutch. Environmental Biology of Fishes, 69:299-306.

Holmes, E. E. 2004. Beyond theory to application and evaluation: diffusion approximations for population viability analysis. Ecological Applications, 14:1272-1293. (Pre-Press Word | PDF | )

Iwamoto, E., M. J. Ford, R. G. Gustafson. 2004. Genetic population structure of Pacific Hake (Merluccius productus) in the Pacific Northwest. Environmental Biology of Fishes, 69:187-199.

Johnson, J. B., K. S. Omland. 2004. Model selection in ecology and evolution. Trends in Ecology and Evolution, 19:101-108.

Johnson, O. W., K. Neely, R. S. Waples. 2004. Lopsided fish in the Snake River Basin - fluctuating asymmetry as a way of assessing impact of hatchery supplementation in chinook salmon, Oncorhynchus tshawytscha. Environmental Biology of Fishes, 69:379-393.

Keith, C., M. A. McCarthy, H. Regan, T. Regan, C. Bowles, C. Drill, C. Craig, B. Pellow, M. Burgman, L. Master, M. H. Ruckelshaus, B. Mackenzie, S. Andelman, P. R. Wade. 2004. Protocols for listing threatened species can forecast extinction. Ecology Letters, 7:1101-1108.

Lawson, P. W., E. A. Logerwell, N. Mantua, R. C. Francis, V. N. Agostini. 2004. Environmental factors influencing freshwater survival and smolt production in Pacific Northwest coho salmon (Oncorhynchus kisutch). Canadian Journal of Fisheries and Aquatic Sciences, 61:360-373.

Levin, P. S. 2004. Can we have our fish and eat them too? Review of A Perfect Ocean (Pauly, D and Maclean, J). American Scientist, 92:89-90.

Levin, P. S., B. F. Kochin. 2004. Publication of marine conservation papers: Is conservation biology too dry? Conservation Biology, 18:1160-1162.

Maniscalco, J. M., K. Wynne, K. W. Pitcher, M. B. Hanson, S. R. Melin, S. Atkinson. 2004. Occurrence of California Sea Lions (Zalophus californianus) in Alaska. Aquatic Mammals, 30:427-433.

McCarthy, M. A., C. Keith, J. Tietjen, M. Burgman, M. Maunder, L. Master, B. W. Brook, G. Mace, H. P. Possingham, R. Medellin, S. Andelman, H. Regan, T. Regan, M. H. Ruckelshaus. 2004. Comparing predictions of extinction risk using models and subjective judgement. Acta Oecologica, 26:67-74.

Noren, D. P., M. Mangel. 2004. Energy reserve allocation in fasting Northern Elephant Seal pups: iner-relationships between body condition and fasting duration. Functional Ecology, 18:223-242.

Purcell, M., G. Mackey, E. LaHood, H. Huber, L. K. Park. 2004. Molecular methods for the genetic identification of salmonid prey from Pacific harbor seal (Phoca vitulina richardsi) scat. Fishery Bulletin, 102:213-220.

Sabo, J. L., E. E. Holmes, P. Kareiva. 2004. The efficacy of simple viability models in ecological risk assessment: Does density dependence matter? Ecology, 85:328-341.

Smoker, W. W., I. A. Wang, A. J. Gharrett, J. J. Hard. 2004. Embryo survival and smolt to adult survival in second-generation outbred coho salmon. Journal of Fish Biology, 65(Supplement A):254-262.

Steel, E. A., B. E. Feist, D. Jenson, G. R. Pess, M. B. Sheer, J. Brauner, R. E. Bilby. 2004. Landscape models to understand steelhead (Oncorhynchus mykiss) distribution and help prioritize barrier removals in the Willamette Basin, OR, U.S.A. Canadian Journal of Fisheries and Aquatic Sciences, 61:999-1011.

Thrower, F. P., J. J. Hard, J. E. Joyce. 2004. Genetic architecture of growth and early life history transitions in anadromous and derived freshwater populations of steelhead. Journal of Fish Biology, 65(Supplement A):286-307.

Tolimieri, N., P. S. Levin. 2004. Differences in responses of chinook salmon to climate shifts: implications for conservation. Environmental Biology of Fishes, 70:155-167.

Waples, R. S., D. J. Teel, J. M. Myers, A. R. Marshall. 2004. Life-history divergence in Chinook salmon: historic contingency and parallel evolution. Evolution, 58(2):386-403. (txt | Excel)

Willis, P. W., B. J. Crespi, L. M. Dill, R. W. Baird, M. B. Hanson. 2004. Natural hybridization between Dall's porpoises (Phocoenoides dalli) and harbour porpoises (Phocoena phocoena). Canadian Journal of Zoology, 82:828-834.

Winans, G. A., M. M. Paquin, D. M. Van Doornik, B. M. Baker, P. J. Thornton, D. Rawding, A. R. Marshall, P. Moran, S. T. Kalinowski. 2004. Genetic stock identification of steelhead in the Columbia River basin: an evaluation of different molecular markers. North American Journal of Fisheries Management, 24:672-685.

2003

Achord, S., P. S. Levin, R. W. Zabel. 2003. Density-dependent mortality in Pacific salmon: the ghost of impacts past? Ecology Letters, 6:335-342.

Baker, J., P. Moran, R. Ladley. 2003. Nuclear DNA identification of migrating bull trout captured at the Puget Sound energy diversion dam on the White River, Washington State. Molecular Ecology, 12:557-561.

Good, T. P., T. K. Harms, M. H. Ruckelshaus. 2003. Misuse of checklist assessments in endangered species recovery efforts. Conservation Ecology, 7(2):12, online .

Holmes, E. E., A. E. York. 2003. Using age structure to detect impacts on threatened populations: A case study with steller sea lions Using age structure to detect impacts on threatened populations: A case study with steller sea lions. Conservation Biology, 17:1794-1806.

Johnson, J. B., J. T. Silverstein, W. R. Wolters, M. Shimizu, W. W. Dickhoff, B. S. Shepherd. 2003. Disparate regulation of insulin-like growth factor-binding proteins in a primitive, ictalurid, teleost (Ictalurus punctatus). General and Comparative Endocrinology, 134:122-130.

Johnson, J. B., A. L. Basolo. 2003. Predator exposure alters female mate choice in the green swordtail. Behavioral Ecology, 14:619-625.

Leslie, H., M. H. Ruckelshaus, I. R. Ball, S. Andelman, H. P. Possingham. 2003. Using siting algorithms in the design of marine reserve networks. Ecological Applications, 13(1 Suppl.):S185-S198.

Levin, P. S. 2003. Regional differences in responses of Pacific Salmon to large-scale climate patterns. Journal of Biogeography, 30:711-717.

Levin, P. S., M. E. Hay. 2003. Selection of estuarine habitats by juvenile gags in experimental mesocosms. Transactions of the American Fisheries Society, 132:76-83.

Logerwell, E. A., N. Mantua, P. W. Lawson, R. C. Francis, V. N. Agostini. 2003. Tracking environmental processes in the coastal zone for understanding and predicting Oregon coho (Oncorhynchus kisutch) marine survival. Fisheries Oceanography, 12:554-568.

McClure, M. M., E. E. Holmes, B. L. Sanderson, C. E. Jordan. 2003. A large-scale, multispecies status assessment: anadromous salmonids in the Columbia River Basin. Ecological Applications, 13:964-989. (Pre-Press Word | PDF)

Moore, S. E., J. M. Grebmeier, J. R. Davies. 2003. Gray whale distribution relative to forage habitat in the northern Bering Sea: current conditions and retrospective summary. Canadian Journal of Zoology, 81:734-742.

Moran, P. 2003. New molecular methods represent a paradigm shift. SETAC Globe, 4:42-43.

Nash, C. E., F. W. Waknitz. 2003. Interactions of Atlantic salmon in the Pacific Northwest: I. Salmon enhancement and the net-pen farming industry. Fisheries Research, 62:237-254.

Noren, D. P., D. E. Crocker, T. M. Williams, D. P. Costa. 2003. Energy reserve utilization in northern elephant seal (Mirounga angustirostris) pups during the postweaning fast: size does matter. Journal of Comparative Physiology, B, 173:443-454.

Roberts, C. M., G. Branch, R. H. Bustamante, J. C. Castilla, J. Dugan, B. S. Halpern, K. D. Lafferty, H. Leslie, J. Lubchenco, D. McArdle, M. H. Ruckelshaus, R. R. Warner. 2003. Application of ecological criteria in selecting marine reserves and developing reserve networks. Ecological Applications, 13:S215-228.

Roberts, C. M., S. Andelman, G. Branch, R. H. Bustamante, J. C. Castilla, J. Dugan, B. S. Halpern, K. D. Lafferty, H. Leslie, J. Lubchenco, D. McArdle, H. P. Possingham, M. H. Ruckelshaus, R. R. Warner. 2003. Ecological criteria for evaluating candidate sites for marine reserves. Ecological Applications (Suppl.), 13(1 ):S199-S214.

Spidle, A. P., S. T. Kalinowski, B. A. Lubinski, D. L. Perkins, K. F. Beland, J. F. Kocik, T. L. King. 2003. Population structure of Atlantic salmon in Maine with reference to populations from Atlantic Canada. Transactions of the American Fisheries Society, 132(2):196-209.

Steel, E. A., L. Johnston, B. E. Feist, G. R. Pess, R. E. Bilby, D. Jensen, T. J. Beechie, J. M. Myers. 2003. Pacific salmon recovery planning and the Salmonid Watershed Analysis Model (SWAM): a broad-scale tool for assisting in the development of habitat recovery plans. Endangered Species Update, 20(1):3-15.

Teel, D. J., D. M. Van Doornik, D. R. Kuligowski, W. S. Grant. 2003. Genetic analysis of juvenile coho salmon (Oncorhynchus kisutch) off Oregon and Washington reveals few Columbia River wild fish. Fishery Bulletin, 101:640-652. (Allele Frequencies | Electroporetic Conditions)

Waknitz, F. W., R. N. Iwamoto, M. S. Strom. 2003. Interactions of Atlantic salmon in the Pacific Northwest: IV. Impacts on the local ecosystems. Fisheries Research, 62:307-328.

Waknitz, F. W. 2003. U.S. salmon-farming sanctions could also hurt commercial fishing. Global Aquaculture Advocate, April 2003:19-20.

Winans, G. A., S. Pollard, D. R. Kuligowski. 2003. Two reproductive life history types of Kokanee, Onchorynchus nerka, exhibit multivariate morphometric and protein genetic differentiation. Environmental Biology of Fishes, 77:87-100.

Zabel, R. W., C. J. Harvey, S. L. Katz, T. P. Good, P. S. Levin. 2003. Ecologically Sustainable Yield. American Scientist, 91:150-157.

2002

Baker, J., P. Bentzen, P. Moran. 2002. Molecular markers distinguish coastal cutthroat trout from coastal rainbow trout/steelhead and their hybrids. Transactions of the American Fisheries Society, 131:404-417.

Clarke, J. A., J. M. Hoekstra, P. D. Boersma, P. Kareiva. 2002. Improving U.S. Endangered Species Act recovery plans: Key findings and recommendations of the SCB recovery plan project. Conservation Biology, 16:1510-1519.

Ford, M. J. 2002. Applications of selective neutrality tests to molecular ecology. Molecular Ecology, 11:1245-1262.

Ford, M. J. 2002. Selection in captivity during supportive breeding may reduce fitness in the wild. Conservation Biology, 16:815-825.

Good, T. P. 2002. Breeding success in the Western Gull x Glaucous-winged Gull complex: The influence of habitat and nest site characteristics. Condor, 104:353-365.

Holmes, E. E. 2002. Compute and Conserve, Book review of Quantitative methods for Conservation Biology. Conservation Biology, 16(1):275-276.

Holmes, E. E., W. Fagan. 2002. Validating population viability analysis for corrupted data sets. Ecology, 83:2379-2386. (PDF | Pre-Press Word)

Johnson, J. B. 2002. Divergent Life Histories Among Populations of the Fish Brachyrhaphis Rhabdophora: Detecting Putative Agents of Selection by Candidate Model Analysis. Oikos, 96:82-91.

Johnson, J. B. 2002. Evolution after the flood: Phylogeography of the desert fish Utah chub. Evolution, 56:948-960.

Kalinowski, S. T., P. W. Hedrick. 2002. Estimation of linkage disequilibrium for loci with multiple alleles: basic approach and an application using data from bighorn sheep. Heredity, 87:698-708.

Kalinowski, S. T. 2002. Evolutionary and statistical properties of three genetic distances. Molecular Ecology, 11:1263-1273.

Kalinowski, S. T. 2002. How many alleles per locus should be used to estimate genetic distances? Heredity, 88:62-65.

Kalinowski, S. T., P. W. Hedrick. 2002. Inbreeding depression in captive bighorn sheep. Animal Conservation, 4:319-324.

Kalinowski, S. T., R. S. Waples. 2002. Relationship of effective to census size in fluctuating populations. Conservation Biology, 16:129-136.

Katz, S. L. 2002. Design of heterothermic muscle in fish. Journal of Experimental Biology, 205:2251-2266.

Kuligowski, D. R., G. A. Winans. 2002. Inorganic pyrophosphatase: A new polymorphic allozyme locus in Pacific salmon. Biochemical Genetics, 40:379-385.

LaHood, E., P. Moran, J. Olsen, W. S. Grant, L. K. Park. 2002. Microsatellite allele ladders in two species of Pacific salmon: preparation and field-test results. Molecular Ecology Notes, 2:187-190.

Levin, P. S., J. A. Coyer, R. Petrik, T. P. Good. 2002. Community-wide effects of non-indigenous species on temperate reefs. Ecology, 83:3182-3193.

Levin, P. S., M. E. Hay. 2002. Fish-seaweed association on temperate reefs: do small-scale experiments predict large-scale patterns. Marine Ecology Progress Series, 232:239-246.

Levin, P. S., J. Ellis, R. Petrik, M. E. Hay. 2002. Indirect effects of feral horses on estuarine communities. Conservation Biology, 16:1364-1371.

Levin, P. S., J. G. Williams. 2002. Interspecific effects of artificially propagated fish: an additional conservation risk for salmon. Conservation Biology, 16:1581-1587.

Levin, P. S., S. Achord, B. E. Feist, R. W. Zabel. 2002. Non-indigenous brook trout and the demise of threatened Snake River salmon: a forgotten threat? Proceedings of the Royal Society of London. Series B, 269:1663-1670.

Levin, P. S., D. A. Levin. 2002. The real biodiversity crisis. American Scientist, 90:6-8.

Mathisen, O. A., N. J. Sands, N. Haubenstock. 2002. Trophic ranking of the biota in Iliamna Lake, Alaska. Verh Internat Verein Limnol, 28:1060-1065.

Moore, S. E., W. A. Watkins, M. A. Daher, J. R. Davies, M. E. Dahlheim. 2002. Blue Whale Habitat Associations in the Northwest Pacific: analysis of remotely-sensed data using a Geographic Information System. Oceanography, 15(3):20-25.

Moran, P. 2002. Current conservation genetics: building an ecological approach to the synthesis of molecular and quantitative genetic methods. Ecology of Freshwater Fish, 11:30-55.

Moran, P., J. Baker. 2002. Polymerase Chain Reaction Inhibition in Historical Fish Scale Mounting Cards. Transactions of the American Fisheries Society, 131:109-119.

Naish, K. A., L. K. Park. 2002. Linkage relationships for 35 new microsatellite loci in chinook salmon Oncorhynchus tshawytscha. Animal Genetics, 33:316-318.

Ruckelshaus, M. H., P. S. Levin, J. B. Johnson, P. Kareiva. 2002. The Pacific salmon wars: what science brings to the challenge of recovering species. Annual Review of Ecology and Systematics, 33:665-706.

Stunz, G. W., T. J. Minello, P. S. Levin. 2002. A comparison of early juvenile red drum densities among various habitat types in Galveston Bay, Texas. Estuaries, 25:76-85.

Stunz, G. W., T. J. Minello, P. S. Levin. 2002. Growth of newly settled red drum Sciaenops ocellatus in different estuarine habitat types. Marine Ecology Progress Series, 238:227-236.

Tolimieri, N., O. Haine, J. Montgomery, A. Jeffs. 2002. Ambient sound as a navigational cue for larval reef fish. Bioacousitics, 12:214-217.

Van Doornik, D. M., M. J. Ford, D. J. Teel. 2002. Patterns of temporal genetic variation in coho salmon: Estimates of the effective proportion of 2-year-olds in natural and hatchery populations. Transactions of the American Fisheries Society, 131:1007-1019.

Waknitz, F. W. 2002. Farms first, hatcheries next? Alaska Fisherman's Journal, Sept 2002:4.

Wang, S. Z., J. J. Hard, F. Utter. 2002. Genetic variation and fitness in salmonids. Conservation Genetics, 3:321-333.

Weitkamp, L. A., K. Neely. 2002. Coho salmon (Oncorhynchus kisutch) ocean migration patterns: insight from marine coded-wire tag recoveries. Canadian Journal of Fisheries and Aquatic Sciences, 59:1100-1115.

Zabel, R. W., P. S. Levin. 2002. Simple assumptions on age composition lead to erroneous conclusions on the nature of density dependence in age-structured populations. Oecologia, 133:349-355.

2001

Berejikian, B. A., E. P. Tezak, L. K. Park, E. LaHood, S. L. Schroder, E. Beall. 2001. Male competition and breeding success in captively reared and wild coho salmon (Oncorhynchus kisutch). Canadian Journal of Fisheries and Aquatic Sciences, 58:804-810.

Berejikian, B. A., E. P. Tezak, L. K. Park, S. L. Schroder, E. Beall, E. LaHood. 2001. Male dominance and spawning behavior of captively reared and wild coho salmon (Oncorhynchus kisutch). Canadian Journal of Fisheries and Aquatic Sciences, 58:804-810.

Boersma, P. D., P. Kareiva, W. Fagan, J. Clark, J. M. Hoekstra. 2001. How Good Are Endangered Species Recovery Plans? Bioscience, 51:643-649.

Ford, M. J. 2001. Molecular Evolution of Transferrin: Evidence for Positive Selection in Salmonids. Molecular Biology and Evolution, 18:639-647.

Gustafson, R. G., R. S. Waples, S. T. Kalinowski, G. A. Winans. 2001. Evolution of sockeye salmon ecotypes. Science, 291:251-252.

Gutierrez-Espeleta, G. A., P. W. Hedrick, S. T. Kalinowski, W. M. Boyce. 2001. Is the decline of desert bighorn sheep from infectious disease the result of low MHC variation? Heredity, 86:439-450.

Holmes, E. E. 2001. Estimating risks in declining populations with poor data. Proceedings of the National Academy of Sciences, USA, 98:5072-5077.

Johnson, J. B. 2001. Adaptive Life-History Evolution in the Livebearing Fish Brachyrhaphis Rhabdophora: Genetic Basis for Parallel Divergence in Age and Size at Maturity and a Test of Predator- Induced Plasticity. Evolution, 55:1486-1491.

Johnson, J. B. 2001. Hierarchical Organization of Genetic Variation in the Costa Rican Livebearing Fish Brachyrhaphis Rhabdophora (Poeciliidae). Biological Journal of the Linnean Society, 72:519-527.

King, T. L., S. T. Kalinowski, W. B. Schill, A. P. Spidle, B. A. Lubinski. 2001. Population structure of Atlantic salmon (Salmo salar L.): a rangewide perspective from microsatellite DNA variation. Molecular Ecology, 10:807-821.

Levin, P. S., N. Tolimieri. 2001. Differences in the impacts of dams on the dynamics of salmon populations. Animal Conservation, 4(4):291-299.

Levin, P. S., M. H. Schiewe. 2001. Preserving salmon biodiversity. American Scientist, 89:220-227.

Levin, P. S., R. W. Zabel, J. G. Williams. 2001. The road to extinction is paved with good intentions: negative effects of fish hatcheries on threatened salmon. Proceedings of the Royal Society of London. Series B, 268:1153-1158.

McClure, M. M., T. Cooney, M. Marvier. 2001. Assessing the role of dams in salmon recovery. Hydro-Review, 20:36?45.

Myers, J. M., W. K. Hershberger, A. M. Saxton, R. N. Iwamoto. 2001. Estimates of genetic and phenotypic parameters for length and weight of marine net-pen reared coho salmon (Onchorhynchus kisutch Walbaum). Aquaculture Research, 32:277-285.

Myers, J. M., P. O. Heggelund, G. Hudson, R. N. Iwamoto. 2001. Genetics and broodstock management of coho salmon. Aquaculture, 197:43-62.

Stunz, G. W., P. S. Levin, T. J. Minello. 2001. Selection of estuarine nursery habitats by wild-caught and hatchery-reared juvenile red drum in laboratory mesocosms. Environmental Biology of Fishes, 61:305-313.

Wang, S. Z., J. J. Hard, F. Utter. 2001. Salmonid inbreeding: a review. Reviews in Fish Biology and Fisheries, 11:301-319.

Waples, R. S., R. G. Gustafson, L. A. Weitkamp, J. M. Myers, O. W. Johnson, P. J. Busby, J. J. Hard, G. J. Bryant, F. W. Waknitz, K. Neely, D. J. Teel, W. S. Grant, G. A. Winans, S. Phelps, A. R. Marshall, B. M. Baker. 2001. Characterizing Diversity in Salmon From the Pacific Northwest. Journal of Fish Biology, 59(Suppl. A):1-41.

Winans, G. A., D. Viele, A. Grover, M. Palmer-Zwahlen, D. J. Teel, D. M. Van Doornik. 2001. An Update of Genetic Stock Identification of Chinook Salmon in the Pacific Northwest: Test Fisheries in California. Reviews in Fisheries Science, 9(4):213-237.

2000

Ford, M. J. 2000. Effects of natural selection on patterns of DNA sequence variation at the transferrin, somatolactin, and p53 genes within and among chinook salmon (Oncorhynchus tshawytscha) populations. Molecular Ecology, 9:843-855.

Gutierrez-Espeleta, G. A., S. T. Kalinowski, W. M. Boyce, P. W. Hedrick. 2000. Genetic variation and population structure in desert bighorn sheep: implications for conservation. Conservation Genetics, 1:3-15.

Hard, J. J., B. A. Berejikian, E. P. Tezak, S. L. Schroder, C. M. Knudsen, L. T. Parker. 2000. Evidence for morphometric differentiation of wild and captively reared adult coho salmon (Oncorhynchus kisutch Walbaum): a geometric analysis. Environmental Biology of Fishes, 58:61-73.

Hard, J. J., L. Connell, W. K. Hershberger, L. W. Harrell. 2000. Genetic variation in mortality of chinook salmon (Oncorhynchus tshawytscha) during a bloom of the marine alga Heterosigma akashiwo. Journal of Fish Biology, 56:1387-1397.

Hedrick, P. W., S. T. Kalinowski. 2000. Inbreeding depression in conservation biology. Annual Review of Ecology and Systematics, 31:139-162.

Kalinowski, S. T., P. W. Hedrick, P. S. Miller. 2000. A careful look at inbreeding depression in the Speke's gazelle captive breeding program. Conservation Biology, 14:1375-1384.

Kareiva, P., P. S. Levin, M. M. McClure. 2000. Letter: Many plans, one bottom line: save endangered salmon. Science, 289:2281-2282.

Levin, P. S., N. Tolimieri, M. Nicklin, P. F. Sale. 2000. Integrating individual behavior and population ecology: the potential for habitat-dependent population regulation in a reef fish. Behavioral Ecology, 11:565-571.

Myers, J. M., R. N. Iwamoto, D. J. Teel, D. M. Van Doornik, W. K. Hershberger. 2000. Coho salmon broodstock development---1977 to 1998. Ten generations of systematic selective breeding. Bulletin of National Research Institute of Aquaculture, Supplement, 1:63-70.

Teel, D. J., G. B. Milner, G. A. Winans, W. S. Grant. 2000. Genetic population structure and origin of life-history types in chinook salmon in British Columbia, Canada. Transactions of the American Fisheries Society, 129:194-209.

Winans, G. A., S. Urawa. 2000. Allozyme variability of Oncorhynchus nerka in Japan. Ichthyological Research, 47(4):343-352.

1999

Bergstrom, C. T., P. McElhany, L. Real. 1999. Transmission bottlenecks as determinants of virulence in rapidly evolving pathogens. Proceedings of the National Academy of Sciences, USA, 96:5095-5100.

Ford, M. J., P. J. Thornton, L. K. Park. 1999. Natural selection promotes divergence of transferrin among salmonid species. Molecular Ecology, 8:1055-1061.

Gustafson, R. G., G. A. Winans. 1999. Distribution and population genetic structure of river-/sea-type sockeye salmon in western North America. Ecology of Freshwater Fish, 8:181-193.

Gutierrez-Espeleta, G. A., S. T. Kalinowski, W. M. Boyce, P. W. Hedrick. 1999. Genetic variation in desert bighorn sheep. Desert Bighorn Council Transactions, 42:1-10.

Hard, J. J., W. R. Heard. 1999. Analysis of straying variation in Atlantic hatchery chinook salmon (Oncorhynchus tshawytscha) following transplantation. Canadian Journal of Fisheries and Aquatic Sciences, 56:578-589.

Hard, J. J., G. A. Winans, J. C. Richardson. 1999. Phenotypic and genetic architecture of juvenile morphometry in chinook salmon. Journal of Heredity, 90(6):597-606.

Kalinowski, S. T., P. W. Hedrick. 1999. An improved method for estimating inbreeding depression in pedigrees. Zoo Biology, 17:481-497.

Kalinowski, S. T., P. W. Hedrick. 1999. Detecting inbreeding depression is difficult in captive endangered species. Animal Conservation, 2:131-136.

Kalinowski, S. T., P. W. Hedrick, P. S. Miller. 1999. No inbreeding depression observed in Mexican and red wolf captive breeding programs. Conservation Biology, 13:1371-1377.

Ruckelshaus, M. H., C. Hartway, P. Kareiva. 1999. Dispersal and landscape errors in spatially explicit population models: a reply. Conservation Biology, 13:1223-1224.

Sarder, M. R., D. J. Penman, J. M. Myers, B. J. McAndrew. 1999. Production and propagation of fully inbred clonal lines in the Nile tilapia (Oreochromis niloticus L.). Journal of Experimental Zoology, 284:675-685.

Van Doornik, D. M., G. A. Winans, D. J. Teel. 1999. Allozyme studies of Pacific salmonids with nonlethal sampling of fin tissue. North American Journal of Fisheries Management, 19:678-686.

Wainwright, T. C., R. G. Kope. 1999. Methods of extinction risk assessment developed for U.S. West Coast salmon. ICES Journal of Marine Science, 56:444-448.

1998

Ford, M. J. 1998. Testing models of migration and isolation among populations of Chinook salmon (Oncorhynchus tschawytscha). Evolution, 52:539?57.

Gustafson, R. G., R. D. Turner, R. A. Lutz, R. C. Vrijenhoek. 1998. A new genus and five new species of mussels (Bivalvia, Mytilidae) from deep-sea sulfide/hydrocarbon seeps in the Gulf of Mexico. Malacologia, 40(1-2):63-112.

Hoeh, W. R., M. B. Black, R. G. Gustafson, A. E. Bogan, R. A. Lutz, R. C. Vrijenhoek. 1998. Testing alternative hypotheses of Neotrigonia (Bivalvia : Trigonioida) phylogenetic relationships using cytochrome C oxidase subunit I DNA sequences. Malacologia, 40:267-278.

Kope, R. G., T. C. Wainwright. 1998. Trends in the status of Pacific salmon populations in Washington Oregon, California, and Idaho. North Pacific Anadromous Fish Commission Bulletin, 1:1-12.

Lowe, S. A., D. M. Van Doornik, G. A. Winans. 1998. Geographic variation in genetic and growth patterns of the Atka mackerel in the Aleutian Archipelago. Fishery Bulletin, 96:502-515.

Mahnken, C. V., G. Ruggerone, F. W. Waknitz, T. A. Flagg. 1998. A historical perspective on salmonid production from Pacific Rim hatcheries. North Pacific Anadromous Fish Commission Bulletin, 1:38?53.

Moran, P., D. A. Dightman, L. K. Park. 1998. Nonelectrophoretic genotyping using allele-specific PCR and a dsDNA-specific dye. Biotechniques, 24:206-208, 210, 212.

Nickelson, T. E., P. W. Lawson. 1998. Population viability of coho salmon, Oncorhynchus kisutch, in Oregon coastal basins: application of a habitat-based life cycle model. Canadian Journal of Fisheries and Aquatic Sciences, 55(11):2383-2392.

Ruckelshaus, M. H. 1998. Spatial scale of genetic structure and an indirect estimate of gene flow in eelgrass, Zostera marina. Evolution, 52:330-343.

Van Doornik, D. M., G. A. Winans. 1998. Inheritance of allozymes in coho salmon. Transactions of the American Fisheries Society, 127:833-837.

Winans, G. A., P. B. Aebersold, Y. Ishida, S. Urawa. 1998. Genetic stock identification of chum salmon in highseas test fisheries in the western North Pacific Ocean and Bering Sea. Bulletin - North Pacific Anadromous Fish Commission, 1:220-237.

1997

Berejikian, B. A., E. P. Tezak, S. L. Schroder, C. M. Knudsen, J. J. Hard. 1997. Reproductive behavioral interactions between wild and captively reared coho salmon (Oncorhynchus kisutch). ICES Journal of Marine Science, 54:1040-1050.

Bradshaw, W. E., C. M. Holzapfel, C. A. Kleckner, J. J. Hard. 1997. Heritability of development time and protandry in the pitcher-plant mosquito, Wyeomyia smithii. Ecology, 78:969-976.

Bushek, D., S. K. Allen, K. A. Alcox, R. G. Gustafson, S. E. Ford. 1997. Response of Crassostrea virginica to in vitro cultured Perkinsus marinus: Preliminary comparisons of three inoculation methods. Journal of Shellfish Research, 16:479-485.

Moran, P., D. A. Dightman, R. S. Waples, L. K. Park. 1997. PCR-RFLP analysis reveals substantial population-level variation in the introns of Pacific salmon (Oncorhynchus spp.). Molecular Marine Biology and Biotechnology, 6:315-327.

Ruckelshaus, M. H., C. Hartway, P. Kareiva. 1997. Assessing the data requirements of spatially explicit dispersal models. Conservation Biology, 11:1298-1306.

Takasaki, N., T. Yamaki, M. Hamada, L. K. Park, N. Okada. 1997. The salmon SmaI family of short interspersed repetitive elements (SINEs): interspecific and intraspecific variation of the insertion of SINEs in the genomes of chum and pink salmon. Genetics, 146:369-380.

Weitkamp, L. A. 1997. Artificial propagation and coho salmon along the Oregon coast. Restoration (Oregon Sea Grant), Summer 1997:1-6.

1996

Achord, S., G. M. Matthews, O. W. Johnson, D. M. Marsh. 1996. Use of passive integrated transponder (PIT) tags to monitor migration timing of Snake River chinook salmon smolts. North American Journal of Fisheries Management, 16:302-313.

Maynard, D. J., D. A. Frost, F. W. Waknitz, E. F. Prentice. 1996. Vulnerability of marked age-0 steelhead to a visual predator. Transactions of the American Fisheries Society, 125:330-333.

Park, L. K., P. Moran, D. A. Dightman. 1996. A chinook salmon PCR-RFLP marker in the p53 locus. Animal Genetics, 27:127-128.

Ruckelshaus, M. H. 1996. Estimates of genetic neighborhood parameters from pollen and seed dispersal distributions in a marine angiosperm (Zostera marina L. ). Evolution, 50:856-864.

Takasaki, N., L. K. Park, M. Kaeriyama, A. J. Gharrett, N. Okada. 1996. Characterization of species-specifically amplified SINEs in three salmonid species - Chum salmon, pink salmon, and kokanee: The local environment of the genome may be important for the generation of a dominant source gene at a newly retroposed locus. Journal of Molecular Evolution, 42:103-116.

Van Doornik, D. M., G. B. Milner, G. A. Winans. 1996. Transferrin polymorphism in coho salmon, Oncorhynchus kisutch, and its application to genetic stock identification. Fishery Bulletin, 94:566-575.

Winans, G. A., P. B. Aebersold, R. S. Waples. 1996. Allozyme variability in Oncorhynchus nerka in the Pacific Northwest with special consideration to populations of Redfish Lake, Idaho. Transactions of the American Fisheries Society, 125:645-663.

1995

Flagg, T. A., F. W. Waknitz, D. J. Maynard, G. B. Milner, C. V. Mahnken. 1995. Impact of hatcheries on native coho salmon populations in the lower Columbia River. American Fisheries Society Symposium, 15:366-375.

Hard, J. J. 1995. A quantitative genetic perspective on the conservation of intraspecific diversity. American Fisheries Society Symposium, 17:304-326.

Hard, J. J. 1995. Genetic monitoring of life-history characters in salmon supplementation: problems and opportunities. American Fisheries Society Symposium, 15:212-225.

Hard, J. J. 1995. Science, education, and the fisheries scientist. Fisheries, 20(3):10-16.

Hauser, D., M. Bibert, J. C. Marvaud, M. W. Eklund, M. R. Popoff. 1995. Botulinal neurotoxin C1 complex genes, clostridial neurotoxin homology and genetic transfer in Clostridium botulinum. Toxicon, 33(4):515-526.

Moran, P., I. Kornfield. 1995. Were population bottlenecks associated with the radiation of the Mbuna species flock (Teleostei: Cichlidae) of Lake Malawi? Molecular Biology and Evolution, 12(6):1085-1093.

Park, L. K., P. Moran, D. A. Dightman. 1995. A polymorphism in intron D of the chinook salmon growth hormone 2 gene. Animal Genetics, 26:277-285.

Ruckelshaus, M. H. 1995. Estimates of the mating system and of inbreeding depression in a population of the marine angiosperm Zostera marina L. Marine Biology, 123:583-593.

Van Doornik, D. M., G. B. Milner, G. A. Winans. 1995. An improved method of data collection for transferrin polymorphism in coho salmon (Oncorhynchus kisutch). Biochemical Genetics, 33(7/9):257-260.

Wennergren, U., M. H. Ruckelshaus, P. Kareiva. 1995. The promise and limitations of spatial models in conservation biology. Oikos, 74:349-356.

Winans, G. A., P. B. Aebersold, S. A. Lowe. 1995. Allozyme variation in Atka mackeral, Pleurogrammus monopterygius. Isozyme Bulletin, 28:52.

1994

Hauser, D., M. Bibert, M. W. Eklund, P. Boquet, M. R. Popoff. 1994. Localization of C3 Gener in a transporon-like element in Clostridium botulinum strains C-468, C-stockholm, and D-1873, and characterization of botulinal neurotoxin C1 gene in the mutant CN phage. Journal of Bacteriology, 175:7260-7268.

Park, L. K., P. Moran. 1994. Developments in molecular techniques in fisheries. Reviews in Fish Biology and Fisheries, 4:300-325.

Schemske, D. W., B. C. Husband, M. H. Ruckelshaus, C. Goodwillie, I. M. Parker, J. G. Bishop. 1994. Establishing priorities in plant conservation. Ecology, 75:584-606.

Waples, R. S., C. Do. 1994. Genetic risk associated with supplementation of Pacific salmonids: Captive broodstock programs. Canadian Journal of Fisheries and Aquatic Sciences, 51(Suppl. 1):310-329.

Winans, G. A., P. B. Aebersold, S. Urawa, N. V. Varnavskaya. 1994. Determining continent of origin of chum salmon (Oncorhynchus keta) using genetic stock identification techniques: status of allozyme baseline in Asia. Canadian Journal of Fisheries and Aquatic Sciences, 51(Suppl. 1):95-113.

1993

Park, L. K., M. A. Brainard, D. A. Dightman, G. A. Winans. 1993. Low levels of intraspecific variation in the mitochondrial DNA of chum salmon (Oncorhynchus keta). Molecular Marine Biology and Biotechnology, 2:362-370.

Ruckelshaus, M. H., R. C. Wissmar, C. A. Simenstad. 1993. The importance of autotroph distribution to mussel growth in a well-mixed, temperate estuary. Estuaries, 16:898-912.

Williams, S. L., M. H. Ruckelshaus. 1993. Effects of nitrogen availability and herbivory on the interaction between eelgrass (Zostera marina L. ) and epiphytes. Ecology, 74:904-918.

1992

Cox, P. A., R. H. Laushman, M. H. Ruckelshaus. 1992. Surface and submarine pollination in the seagrass Zostera marina L. Botanical Journal of the Linnean Society, 109:281-291.

Duguay, S. J., L. K. Park, M. Samadpour, W. W. Dickhoff. 1992. Nucleotide sequence and tissue distribution of three insulin-like growth factor I prohormones in salmon. Molec. Endocrinol, 6:1202-1210.

Utter, F., R. S. Waples, D. J. Teel. 1992. Genetic isolation of previously indistinguishable chinook salmon populations of the Snake and Klamath Rivers: Limitations of negative data. Fishery Bulletin, 90:770-777.

1990

Waples, R. S., D. J. Teel. 1990. Conservation genetics of Pacific Salmon I. Temporal changes in allele frequency. Conservation Biology, 4:144-156.

Waples, R. S., G. A. Winans, F. Utter, C. V. Mahnken. 1990. Genetic approaches to the management of Pacific salmon. Fisheries, (15)19-25.

Waples, R. S., P. B. Aebersold. 1990. Treatment of data for duplicated gene loci in mixed-stock fishery analysis. Canadian Journal of Fisheries and Aquatic Sciences, 47:2092-2098.

1989

Dickhoff, W. W., C. V. Mahnken, F. W. Waknitz, W. S. Zaugg, M. G. Bernard, C. V. Sullivan. 1989. Effect of temperature and feeding on smolting and seawater survival of Atlantic salmon (Salmo salar). Aquaculture, 82:93-102.

Humphreys, R. L., G. A. Winans, D. T. Tagami. 1989. Synonymy and life history of the North Pacific Pelagic Armorhead,. Copeia, 1989:142-153.

Utter, F., G. B. Milner, G. Stahl, D. J. Teel. 1989. Genetic population structure of chinook salmon in the Pacific Northwest. Fishery Bulletin, 87:239-264.

Winans, G. A. 1989. Genetic variability in chinook salmon stocks from the Columbia River Basin. North American Journal of Fisheries Management, 9:47-52.

1988

Winans, G. A., L. L. Jones. 1988. Electrophoretic variability in Dall's porpoise (Phocoenoides dalli) in the North Pacific Ocean and Bering Sea. Journal of Mammalogy, 69:14-21.

1987

Utter, F., D. J. Teel, G. B. Milner, D. McIsaac. 1987. Genetic estimates of stock compositions of 1983 chinook salmon harvests off the Washington Coast and the Columbia River. Fishery Bulletin, 85(1):13-23.

Winans, G. A., R. S. Nishioka. 1987. A multivariate description of change in body shape of coho salmon (Oncorhynchus kisutch ) during smoltification. Aquaculture, 66:235-245.

1986

Johnson, O. W., W. W. Dickhoff, F. Utter. 1986. Comparative growth and development of diploid and triploid coho salmon Oncorhynchus kisutch. Aquaculture, 57:329-336.

1985

Milner, G. B., D. J. Teel, F. Utter, G. A. Winans. 1985. A genetic method of stock identification in mixed populations of Pacific salmon. Marine Fisheries Review, 47(1):1-8.

Winans, G. A. 1985. Geographic variation in the Milkfish Chanos chanos II. Multivariate morphological evidence. Copeia, 1985:890-898.

1984

Grant, W. S., D. J. Teel, T. Kobayashi, C. C. Schmitt. 1984. Biochemical population genetics of Pacific halibut (Hippoglossus stenolepis) and comparison to Atlantic halibut (H. hippoglossus). Canadian Journal of Fisheries and Aquatic Sciences, 41:1083-1088.

Kobayashi, T., G. B. Milner, D. J. Teel, F. Utter. 1984. Genetic basis of electrophoretic variation in adenosine deaminase in chinook salmon. Transactions of the American Fisheries Society, 113:86-89.

Winans, G. A. 1984. Multivariate morphometric variability in Pacific salmon: technical demonstration. Canadian Journal of Fisheries and Aquatic Sciences, 41:1150-1159.

1983

Grant, W. S., R. Bakkala, F. Utter, D. J. Teel, T. Kobayashi. 1983. Biochemical genetic population structure of yellowfin sole, Limanda aspera, of the north Pacific Ocean and Bering Sea. Fishery Bulletin, 113:86-89.

1982

Folmar, L. C., W. W. Dickhoff, C. V. Mahnken, F. W. Waknitz. 1982. Stunting and parr-reversion during smoltification of coho salmon (Oncorhynchus kisutch). Aquaculture, 28:91-104.

Giorgi, A. E., G. B. Milner, D. J. Teel. 1982. Polymorphic isozymes in lingcod, Ophiodon elongatus. Isozyme Bulletin, 15:120-121.

Gorbman, A., W. W. Dickhoff, J. L. Mighell, E. F. Prentice, F. W. Waknitz. 1982. Morphological indices of developmental progress in the parr-smolt coho salmon, Oncorhynchus kisutch. Aquaculture, 28:1-20.

Book

In press

Clarke, M. E., N. Tolimieri, H. Singh. In press. Using the Seabed AUV to assess populations of groundfish in untrawlable areas. Springer

Johnson, O. W., M. H. Ruckelshaus, W. S. Grant, F. W. Waknitz, A. M. Garrett, G. J. Bryant, K. Neely, J. J. Hard. In press. Coastwide Status Review of Coastal Cutthroat Trout (Oncorhynchus clarki clarki) by the National Marine Fisheries Service for listing under the Endangered Species Act. The 2005 Coastal Cutthroat Trout Symposium: status, management, biology, and conservation. 2 Oregon Chapter of AFS, Portland, OR

2009

Hinrichsen, R. A. and E. E. Holmes. 2009. Using multivariate state-space models to study spatial structure and dynamics. In Spatial Ecology (editors Robert Stephen Cantrell, Chris Cosner, Shigui Ruan). CRC/Chapman Hall.

Kaplan, I. C., P. S. Levin. 2009. Ecosystem-based management of what? An emerging approach for balancing conflicting objectives in marine resource management. Springer, 736 p.

2002

Neely, K., O. W. Johnson, K. W. Myers, J. J. Hard. (rapporteurs) 2002. Proceedings of the 20th Northeast Pacific Pink and Chum Workshop, Seattle, Washington. 167 p.

1999

Kareiva, P., S. Andelman, D. Doak, B. Elderd, M. Groom, J. M. Hoekstra, L. Hood, F. James, J. Lamoreux, G. LeBuhn, C. McCulloch, J. Regetz, L. Savage, M. H. Ruckelshaus, D. Skelly, H. Wilbur, K. Zamudio, E. Aas. 1999. Using science in habitat conservation plans. American Institute of Biological Sciences, Washington, D.C., vi, 97 p.

1990

Parker, N. C., A. E. Giorgi, R. C. Heidinger, D. B. Jester, E. D. Prince, G. A. Winans. (Eds.) 1990. Fish-marking Techniques. American Fisheries Society Symposium 7. American Fisheries Society, Bethesda, Maryland, xiv, 879 p.

Section

In press

Allendorf, F. W., J. J. Hard. In press. Human-Induced Evolution Caused By Unnatural Selection Through Harvest Of Wild Animals. In In the Light of Evolution III: Two Centuries of Darwin. National Academies Press, Washington, DC.

Burnett, K. M., J. L. Ebersole, R. E. Gresswell, D. P. Larsen, P. W. Lawson, D. J. Miller, J. D. Rodgers, E. A. Steel, D. L. Stevens, C. E. Torgersen. In press. Data and Modeling Tools for Assessing Landscape-Level Influences on Salmonid Population: Examples from Western Oregon. In Sustainability of the Arctic-Yukon-Kuskokwim Salmon Fisheries. AFS.

Hard, J. J. In press. Case study of Pacific salmon. In Dieckmann, U., O. R. Godoe, M. Heino, J. Mork. (Eds.) Fisheries-Induced Adaptive Change. Cambridge University Press, Cambridge, U.K.

Hard, J. J., W. H. Eldridge, K. A. Naish, C. Krueger. In press. Genetic consequences of size-selective fishing: implications for viability of Yukon River Chinook salmon. In Krueger, C., C. E. Zimmerman. (Eds.) Sustainability of the Arctic-Yukon-Kuskokwim Salmon Fisheries: What Do We Know About Salmon Ecology, Management, and Fisheries? American Fisheries Society, Anchorage.

2009

Beechie, T.J., G.R. Pess, M.M. Pollock, M.H. Ruckelshaus, P. Roni. 2009. Chapter 33: Restoring rivers in the 21st century: science challenges in a management context. Pages 695-716. Editors R.J. Beamish and B.J. Rothschild. In The Future of Fisheries Science in North America, Springer, Heidelberg.

Ruckelshaus, M. H., T. E. Essington, P. S. Levin. 2009. Marine Ecosystem Based Management in Practice. Puget Sound, WA, USA. Page 392 in McLeod, K. L., H. Leslie. (Eds.) Ecosystem-Based Management for the Oceans. Island Press, San Francisco, CA.

2008

Johnson, O. W., M. H. Ruckelshaus, W. S. Grant, F. W. Waknitz, A. M. Garrett, G. J. Bryant, K. Neely, and J. J. Hard. 2008. Summary of 1998 coast wide coastal cutthroat trout status review conducted by the National Marine Fisheries Service. Pages 3-4 in P. J. Connolly, T. H. Williams, and R. E. Gresswell, editors. The 2005 coastal cutthroat trout symposium: status, management, biology, and conservation. Oregon Chapter, American Fisheries Society, Portland.

2007

A. R. Kapuscinski, J. J. Hard, R. Neira, K. M. Paulson, A. Ponniah, W. Kamonrat, W. Mwanja, I. A. Fleming, J. Gallardo, R. H. Devlin, and J. Trisak. 2007. Approaches to assessing gene flow. Pp. 112-150 in Kapuscinski, A. R., S. Li, K. R. Hayes, and G. Dana (editors), Environmental Risk Assessment of Genetically Modified Organisms, Vol 3: Methodologies for Transgenic Fish. CABI International, Wallingford, Oxfordshire, UK.

Senanan, W., J. J. Hard, A. Alcivar-Warren, J. Trisak, M. Zakaraia-Ismail, and M. L. Hernandez. 2007. Risk management: Post-approval monitoring and remediation. Pp. 272-290 in Kapuscinski, A. R., S. Li, K. R. Hayes, and G. Dana (editors), Environmental Risk Assessment of Genetically Modified Organisms, Vol 3: Methodologies for Transgenic Fish. CABI International, Wallingford, Oxfordshire, UK.

Waples, R. S., M. J. Ford, and D. Schmitt. 2007. Empirical results of salmon supplementation in the Northeast Pacific: A preliminary assessment. pp. 383-403 in T. M. Bert, ed. Ecological and Genetic Implications of Aquaculture Activities. Kluwer Academic Publishers.

2006

Good, T. P., D. Harstad, C. Hall, C. Maranto, M. Harper, B. A. Ryan. 2006. Predation on juvenile salmonids by Caspian Terns nesting in Potholes Reservoir. In Appendix in Piscivorous Waterbird Research on the Columbia River: draft 2005 season summary.

Plummer, M. 2006. The Grand Unified Theory of Natural Resource Economics: A Special Case. Page 18 in Layton, D. F., R. Halvorsen. (Eds.) Explorations in Environmental & Natural Resource Economics: Essays in Honor of Gardner M. Brown. Edward Elgar.

Ruckelshaus, M. H., D. Darm. 2006. Science and Implementation. Pages 104-126 in Scott, J. M., D. D. Goble, F. W. Davis. (Eds.) The Endangered Species Act at 30: Conserving Biodiversity in Human-Dominated Landscapes. Island Press, Washington, D.C.

2005

Good, T. P., K. Barnas, D. M. Marsh, M. M. McClure, B. A. Ryan, B. P. Sandford, E. Casillas. 2005. Caspian Tern Predation on Juvenile Salmonid Outmigrants in the Columbia River Estuary. In Caspian Tern Management to Reduce Predation of Juvenile Salmonids in the Columbia River Estuary. U.S. Fish and Wildlife Service Migratory Birds and Habitat Programs, Portland, OR.

Plummer, M. 2005. The Economic Evaluation of Stream and Watershed Restoration Projects. Pages 313-330 in Roni, P. (Ed.) Methods for monitoring stream and watershed restoration. American Fisheries Society, Bethesda, Maryland.

Roni, P., M. Liermann, C. E. Jordan, E. A. Steel. 2005. Steps for Designing a Monitoring and Evaluation Program for Aquatic Restoration. Pages 13-34 in Roni, P. (Ed.) Methods for monitoring stream and watershed restoration. American Fisheries Society, Bethesda, Maryland.

2004

Ford, M. J. 2004. Conservation units and preserving diversity. Pages 338-357 in Hendry, A. P., S. C. Stearns. (Eds.) Evolution Illuminated. Salmon and their relatives. Oxford University Press.

Hard, J. J. 2004. Evolution of chinook salmon life history under size-selective harvest. Pages 315-337 in Hendry, A. P., S. C. Stearns. (Eds.) Evolution Illuminated. Salmon and their relatives. Oxford University Press.

Holmes, E. E., B. Semmens. 2004. Population viability analysis for metapopulations: a diffusion approximation approach. Pages 565-598 in Hanski, I., O. E. Gaggiotti. (Eds.) Ecology, Genetics, and Evolution of Metapopulations. Elsevier Press.

Jacobson, K. C., R. E. Baldwin, D. J. Teel. 2004. Parasite community composition: Insights on the ecology and migration of juvenile salmon. Pages 49-51 in Workshop on Application of Stock Identification in defining Marine Distribution and Migration of Salmon. North Pacific Anadromous Fish Commission, Vancouver, BC.

Lundrigan, T. A., P. Moran, D. J. Teel, A. R. Marshall, S. F. Young, D. L. Bottom. 2004. Conservation and genetic stock identification: A study investigating the stock-specific distribution and performance of juvenile chinook salmon in the Columbia River estuary. Pages 70-71 in Workshop on Application of Stock Identification in defining Marine Distribution and Migration of Salmon. North Pacific Anadromous Fish Commission, Vancouver, BC.

Mahnken, C. V., W. T. Fairgrieve, F. W. Waknitz, D. J. Maynard, H. L. Blankenship. 2004. Lessons for marine fish enhancement: experiences with Pacific salmon. Pages 91-105 in Stock Enhancement and Sea Ranching: Developments, Pitfalls and Opportunities. Blackwell, Oxford.

Ruckelshaus, M. H., P. McElhany, M. M. McClure, S. Heppell. 2004. Chinook salmon in Puget Sound: Effects of spatially correlated catastrophes on persistence. Pages 208-218 in Ackakaya, R., M. Burgman, O. Kindvall, C. C. Wood, P. Sjogren-Gulve, J. S. Hatfield, M. A. McCarthy. (Eds.) Species Conservation and Management: Case Studies. Oxford Univ. Press.

Teel, D. J. 2004. Genetic mixed stock analysis of juvenile chinook salmon in coastal areas of western North America. Pages 47-48 in Workshop on Application of Stock Identification in defining Marine Distribution and Migration of Salmon. North Pacific Anadromous Fish Commission, Vancouver, BC.

2003

Payne, J. F., A. Mathieu, T. K. Collier. 2003. Ecotoxicological studies focusing on marine and freshwater fish. Pages 191-224 in Douben, P. E. (Ed.) PAHs: An Ecotoxicological Perspective. John Wiley.

Ruckelshaus, M. H., P. McElhany, M. J. Ford. 2003. Recovering species of conservation concern: Are populations expendable? Pages 305-329 in Kareiva, P., S. A. Levin. (Eds.) The importance of species : perspectives on expendability and triage. Princeton University Press.

Sanderson, B. L., E. A. Steel, T. J. Beechie, G. R. Pess, M. B. Sheer, C. A. Campbell. 2003. Analyses for Phase I recovery planning: setting recovery goals. Pages 18-39 in Beechie, T. J., E. A. Steel, P. Roni, E. Quimby. (Eds.) Ecosystem recovery planning for listed salmon: an integrated assessment approach for salmon habitat. U.S. Dept. Commerce, NOAA Technical Memorandum, NMFS-NWFSC-58, 183 p.

Steel, E. A., M. Liermann, P. McElhany, N. L. Scholz, A. Cullen. 2003. Managing uncertainty in habitat recovery planning. In Beechie, T. J., P. Roni, E. A. Steel, E. Quimby. (Eds.) Ecosystem recovery planning for listed salmon: An integrated assessment approach for salmon habitat. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-58, 183 p.

2002

Good, T. P., J. Fabbri. 2002. Catastrophic risk assessment of Lower Columbia and Willamette River ESUs of threatened Pacific salmon. In Appendix L in Willamette/Lower Columbia Pacific salmonid viability criteria. Willamette/Lower Columbia Technical Recovery Team Report (P. McElhany et al.), December 2, 2002.

Hard, J. J. 2002. Genetic risks of hatchery salmon production to wild salmon. Pages 72-85 in Orr, C., R. Routledge, P. Gallaugher. (Eds.) Hatcheries and the protection of wild salmon. Speaking for the Salmon workshop proceedings. Centre for Coastal Studies and Continuing Studies in Science at Simon Fraser University, Burnaby, B.C.

Hard, J. J. 2002. Inbreeding. Pages 96-110 in Berejikian, B. A. (Ed.) Research on captive broodstock technology for Pacific salmon. Annual Report to Bonneville Power Administration, Project No. 93-56 (Contract No. 00005227).

Hard, J. J. 2002. Update on the status of pink salmon in the Pacific Northwest. Pages 47-51 in Neely, K., O. W. Johnson, K. W. Myers, J. J. Hard. (rapporteurs) Proceedings of the 20th Northeast Pacific Pink and Chum Workshop, Seattle, Washington.

Levin, P. S., C. B. Grimes. 2002. Reef fish ecology and grouper conservation and management. Pages 377-389 in Sale, P. F. (Ed.) Advances in ecology of fishes on coral reefs. Academic Press, San Diego.

Swanson, P., B. Campbell, B. R. Beckman, D. A. Larsen, J. T. Dickey, K. A. Cooper, N. Hodges, P. Kline, K. D. Shearer, D. Venditti, G. A. Winans, G. Young. 2002. Monitoring reproductive development in captive broodstock and anadromous hatchery stocks of Snake River spring chinook salmon during the freshwater phase of adult migration: Progress Report. In Berejikian, B. A. (Ed.) Research on Captive Broodstock Programs for pacific Salmon. Report to Bonneville Power Administration for FY 01. Contract No. 199305600.

2001

Hard, J. J. 2001. Inbreeding. Pages 86-94 in Berejikian, B. A., C. E. Nash. (Eds.) Research on captive broodstock technology for Pacific salmon. Annual Report to Bonneville Power Administration, Project No. 93-56 (Contract No. 00005227).

Johnson, O. W., A. M. Garrett, W. S. Grant, K. Neely, M. H. Ruckelshaus, F. W. Waknitz, J. J. Hard. 2001. Summary of status review of coastal cutthroat trout from the Pacific northwest. Pages 255-257 in Brewin, M. K., A. J. Paul, M. Monita. (Eds.) Bull trout II conference proceedings. Trout Unlimited Canada, Calgary, Alberta.

Kope, R. G. 2001. Pacific Salmon Fisheries. In Steele, J. H., K. K. Turekian, S. A. Thorpe. (Eds.) Encyclopedia of Ocean Sciences. Academic Press, London.

Mathisen, O. A., N. J. Sands. 2001. Density-dependent ocean growth of some Bristol Bay sockeye salmon stocks. Pages 349-362 in Spatial processes and management of fish populations: Proceedings of the 17th Lowell Wakefield Fisheries Symposium, October 27-30, 1999. University of Alaska Sea Grant College Program Report No. 01-02, Anchorage, Alaska.

2000

Hard, J. J., R. G. Kope, W. S. Grant. 2000. Endangered Species Act review of the status of pink salmon from Washington, Oregon, and California. Pages 103-110 in Knudsen, E. E., C. R. Steward, D. D. MacDonald, J. E. Williams, D. W. Reiser. (Eds.) Sustainable Fisheries Management: Pacific Salmon. Lewis Publishers, Boca Raton, FL.

Hard, J. J. 2000. Genetic interactions between wild and cultured salmon. Pages 8-18 in Gallaugher, P., C. Orr. (Eds.) Aquaculture and the protection of wild salmon. Speaking for the Salmon workshop proceedings. Continuing Studies in Science at Simon Fraser University, Burnaby, B.C.

Hard, J. J. 2000. Inbreeding. In Berejikian, B. A. (Ed.) Research on captive broodstock programs for Pacific salmon. Report to Bonneville Power Administration, Contract No. 1999A117859, Proj. No. 199305600 (BPA Report DOE/BP-17859-1), June 2000.

Hard, J. J., W. K. Hershberger. 2000. Research on quantitative genetic consequences of captive broodstock programs for Pacific salmon populations. In Research on captive broodstock technology for Pacific salmon. Annual Report to Bonneville Power Administration, Project No. 93-56 (Contract No. DE-AI79-93BP55064).

Holmes, E. E., P. Kareiva. 2000. Using single species measurements to anticipate community consequences of environmental contaminants. Page 344 in Albers, P., G. Heinz, H. Ohlendorf. (Eds.) Environmental Contaminants and Terrestrial Vertebrates: Effects on Populations, Communities, and Ecosystems. Special Publication of SETAC Press.

Moran, P., D. A. Dightman, L. K. Park. 2000. Nonelectrophoretic genotyping using allele-specific PCR and a dsDNA-specific dye. In Burczak, J. D., E. R. Mardis. (Eds.) Polymorphism Detection and Analysis, BioTechniques Update Series. Eaton Publishing, Nantucket, Massachussets.

Weitkamp, L. A., T. C. Wainwright, G. J. Bryant, D. J. Teel, R. G. Kope. 2000. Review of the status of coho salmon from Washington, Oregon, and California. Pages 111-118 in Knudsen, E. E., C. R. Steward, D. D. MacDonald, J. E. Williams, D. W. Reiser. (Eds.) Sustainable Fisheries Management: Pacific Salmon. Lewis Publishers, Boca Raton, FL.

1999

Hard, J. J. 1999. Status review of pink salmon in the Pacific Northwest. Pages 166-173 in Hawkins, S. (rapporteur) Proceedings of the 19th Northeast Pacific pink and chum salmon workshop.

Kope, R. G. 1999. Pacific Coast Salmon. Pages 149-155 in Our Living Oceans: Report on the status of U. S. living marine resources. U.S. Dept. Commerce, NOAA Tech. Memo. NMFS-F/SPO-41, 301 p.

1998

Roni, P., L. A. Weitkamp, J. Scordino. 1998. Identification of essential fish habitat for salmon in the Pacific northwest: Initial efforts, information needs, and future direction. Pages 93-107 in Fish habitat: essential fish habitat and rehabilitation. American Fisheries Society Symposium 22.

Ruckelshaus, M. H., C. Hays, P. Fiedler, P. Kareiva. 1998. Conservation of species in the sea. Pages 112-156 in Conservation Biology for the Coming Decade. Chapman and Hall, New York.

1997

Carlton, J. C., M. H. Ruckelshaus. 1997. Non-indigenous marine and estuarine invertebrates and plants of Florida. Pages 187-204 in Simberloff, D., T. Brown, D. Schmitz. (Eds.) Non-Indigenous Species in Florida: Patterns, Effects and Management. Island Press, Washington, D. C.

Johnson, O. W., R. S. Waples, T. C. Wainwright, K. Neely, F. W. Waknitz, L. T. Parker. 1997. Summary of the biological status review of Umpqua River sea-run cutthroat trout. Pages 87-102 in Hall, J. R. (Ed.) Sea-Run Cutthroat Trout: Biology, Management, and Future Conservation, proceedings of a symposium. Reedsport, OR, Oct. 12-14, 1995. Oregon Chapter, American Fisheries Society, Corvallis, Oregon.

Kareiva, P., D. Skelly, M. H. Ruckelshaus. 1997. Re-evaluating the use of models to predict the consequences of habitat loss and fragmentation. Pages 156-166 in Pickett, S. T., R. Ostfeld, M. Shachak, G. Likens. (Eds.) The Ecological Basis of Conservation: Heterogeneity, Ecosystems and Biodiversity. Chapman and Hall, NY.

Lawson, P. W. 1997. Interannual variability in growth and survival of chinook and coho salmon. In Emmett, R. L., M. H. Schiewe. (Eds.) Estuarine and ocean survival of Northeastern Pacific salmon: Proceedings of the workshop. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-219.

1996

Hard, J. J., W. K. Hershberger. et al 1996. Research on quantitative genetic consequences of captive broodstock programs for Pacific salmon populations. Pages 8-1 to 8-28 in Swanson, P. (Ed.) Research on Captive Broodstock Technology for Pacific Salmon. Annual Report 1995. BPA Report DOE/BP-55064. Bonneville Power Administration, Portland, Oregon.

1995

Berejikian, B. A., E. P. Tezak, L. K. Park, S. L. Schroder, C. M. Knudsen, J. J. Hard. 1995. Reproductive success of captively reared and wild coho salmon (Oncorhynchus kisutch). In Swanson, P. (Ed.) Captive broodstock evaluation. Report to Bonneville Power Administration, Contract DE-AI79-93BP55064.

Flagg, T. A., F. W. Waknitz, D. J. Maynard, G. B. Milner, C. V. Mahnken. 1995. The effect of hatcheries on native coho salmon populations in the lower Columbia River. Pages 366-375 in Schramm, H. L. Jr., R. G. Piper. (Eds.) Uses and effects of cultured fishes in aquatic ecosystems. American Fisheries Society, Bethesda, MD.

Hard, J. J., W. K. Hershberger. 1995. Quantitative genetic consequences of captive broodstock programs for anadromous Pacific salmon (Oncorhynchus spp.). Pages 2-1 to 2-75 in An assessment of the status of captive broodstock technology for Pacific salmon. Final Report to Bonneville Power Admin., Proj. No. 93-56, Contract No. DE-AI79-93BP55064, June 1995.

1994

Hard, J. J. 1994. Genetics and salmon management: Expanded summary of a panel discussion. Pages 151-163 in Application of DNA technology to the management of Pacific salmon. NOAA Tech. Memo. NMFS-NWFSC-17.

Moran, P. 1994. Overview of commonly used DNA techniques. Pages 15-26 in Application of DNA technology to the management of Pacific salmon. NOAA Tech. Memo. NMFS-NWFSC-17.

Moran, P., E. Bermingham. 1994. Phylogeographic structure of coho salmon populations assessed by mitochondrial DNA. Pages 57-62 in Application of DNA technology to the management of Pacific salmon. NOAA Tech. Memo. NMFS-NWFSC-17.

Park, L. K., P. Moran, D. A. Nickerson. 1994. Application of the oligonucleotide ligation assay to the study of chinook salmon populations in the Snake River. Pages 91-97 in Park, L. K., P. Moran, R. S. Waples. (Eds.) Application of DNA technology to the management of Pacific salmon: Proceedings of the workshop. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-17.

Park, L. K. 1994. Introduction to DNA basics. Pages 3-13 in Application of DNA technology to the management of Pacific salmon. NOAA Tech. Memo. NMFS-NWFSC-17.

Ruckelshaus, M. H. 1994. The importance of ecological and genetic attributes of marine plant populations to restoration of nearshore habitats. In Wyllie-Echeverria, T., A. M. Olson, M. J. Hershman. (Eds.) Seagrass Science and Policy in the Pacific Northwest. EPA 910/R-94-004.

1993

Johnson, O. W., D. J. Maynard, G. B. Milner, F. W. Waknitz. 1993. Genetic considerations in the status review of lower Columbia River coho salmon. Pages 161-181 in Coho Salmon Workshop. Coast Bastion Inn, Nanamio, British Columbia.

1990

Ruckelshaus, M. H., R. C. Wissmar, C. A. Simenstad. 1990. Sources and Fates of organic matter: utilization of eelgrass carbon by estuarine bivalves. Pages 13-20 in Merkel, K. W., R. S. Hoffman. (Eds.) Proc. Calif. Eelgrass Symp. Sweetwater River Press, CA.

1988

Ruckelshaus, M. H., R. C. Wissmar, C. A. Simenstad. 1988. Mussel growth and estuarine habitat quality. Pages 463-472 in Proc. First Annual Meeting Puget Sound Research. Vol. I. Puget Sound Water Quality Authority, WA.

1987

Utter, F., P. B. Aebersold, G. A. Winans. 1987. Interpreting genetic variation detected by electrophoresis. Pages 21-45 in Ryman, N., F. Utter. (Eds.) Population Genetics and Fishery Management. Univ. Wash. Press, Seattle, WA.

1985

Malins, D. C., B. B. McCain, M. M. Krahn, M. S. Myers, J. E. Stein, W. T. Roubal, D. W. Brown, U. Varanasi, H. O. Hodgins, S. Chan. 1985. Occurrence of hepatic neoplasms and other lesions in bottom-dwelling fish and relationships to pollution in Puget Sound, Washington. Pages 399-414 in Jolly, R. L., R. J. Bull, W. P. Davis, S. L. Katz, M. H. Roberts Jr., V. A. Jacobs. (Eds.) Effects, Vol. 5. Lewis Publishers, Inc., Chelsea, Michigan.

1984

Utter, F., P. B. Aebersold, J. H. Helle, G. A. Winans. 1984. Genetic characteristics of populations on the southeastern range of sockeye salmon. Pages 17-32 in Walton, J. M., D. B. Houston. (Eds.) Proc. Oympic Wild Fish Conf. Peninsula College, Port Angeles, WA.

Contract Report

2007

Beamer, E. M., C. A. Rice, R. Henderson, K. L. Fresh, M. Rowse. 2007. Taxonomic Composition of Fish assemblages, and Density and Size of Juvenile Chinook Salmon in the Greater Skagit River Estuary: Field Sampling and Data Summary Report. Report to the Seattle District of the U.S. Army Corps of Engineers.

Murdoch, A., Pearsons, T., Maitland, T., Ford, M., and Williamson, K. 2007. Monitoring the reproductive success of naturally spawning hatchery and natural spring Chinook salmon in the Wenatchee River. BPA Project No. 2003-039-00. Bonneville Power Administration, Portland, Oregon., Department of Energy, Bonneville Power Administration. Available: http://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P103928

2005

Hard, J.J., and K.A. Naish. 2005. Evaluate effects of inbreeding and inbreeding depression. In B.A. Berejikian (editor), Research on captive broodstock programs for Pacific salmon, 2004-2005 Annual report, Project No. 199305600, p. 138-160. Available Bonneville Power Administration (BPA Report DOE/BP-00017690-1, 162 electronic pages), Environment Fish and Wildlife, P.O. Box 3621, Portland, OR 97208.

Murdoch, A. R., T. N. Pearsons, T. W. Maitland, M. J. Ford, K. Williamson. 2005. Monitoring the reproductive success of naturally spawning hatchery and natural spring Chinook salmon in the Wenatchee River. Report to the Department of Energy, Bonneville Power Administration.

2004

Berejikian, B. A., J. A. Scheurer, J. Lee, D. M. Van Doornik, E. Volk, T. Johnson. 2004. Evaluation of conservation hatchery rearing and release strategies for steelhead recovery in the Hamma Hamma River. Annual Report to the Hatchery Scientific Review Group, IAC Grant #01-042, 33 p.

Hard, J.J., and K.A. Naish. 2004. Evaluate effects of inbreeding and inbreeding depression. In B.A. Berejikian (editor), Research on captive broodstock programs for Pacific salmon, 2003-2004 Annual report, Project No. 199305600, p.164-189. Available Bonneville Power Administration (BPA Report DOE/BP-00005227-4, 190 electronic pages), Environment Fish and Wildlife, P.O. Box 3621, Portland, OR 97208.

Roegner, G. C., D. L. Bottom, A. M. Baptista, J. Burke, S. A. Hinton, D. A. Jay, C. A. Simenstad, E. Casillas, K. K. Jones. 2004. Estuarine habitat and juvenile salmon: current and historical linkages in the lower Columbia River and estuary, 2002. Report of Research by Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration to the U.S. Army Corps of Engineers, Portland District, Contract W66QKZ20374382.

2003

Berejikian, B. A., J. A. Scheurer, J. Lee, D. M. Van Doornik, E. Volk, T. Johnson, R. Endicott. 2003. Evaluation of conservation hatchery rearing and release strategies for steelhead recovery in the Hamma Hamma River. Annual Report to the Hatchery Scientific Review Group, IAC Grant #01-042, 25 p.

McComas, R. L., B. P. Sandford, C. D. Magie, J. W. Ferguson, D. M. Katz, M. Plummer. 2003. Evaluation of a prototype high-velocity flume separator at Ice Harbor Dam, 1999. Report of Research by Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration to the U.S. Army Corps of Engineers, Walla Walla District, vi, 76 p.

2002

Berejikian, B. A., D. M. Van Doornik, E. Volk, T. Johnson, J. Lee, J. Atkins, R. Endicott. 2002. Evaluation of conservation hatchery rearing and release strategies for steelhead recovery in the Hamma Hamma River. Annual report to the Hatchery Scientific Review Group, IAC Grant #01-042, 25 p.

2001

Berejikian, B. A., D. M. Van Doornik, E. Volk, T. Johnson, B. Smith, R. Endicott. 2001. Evaluation of conservation hatchery rearing and release strategies for steelhead recovery in the Hamma Hamma River. Annual report to the Hatchery Scientific Review Group, IAC Grant #01-042, 21 p.

Bottom, D. L., C. A. Simenstad, A. M. Baptista, D. A. Jay, J. Burke, K. K. Jones, E. Casillas, M. H. Schiewe. 2001. Salmon at river's end: the role of the estuary in the decline and recovery of Columbia River salmon. Report to the U.S. Department of Energy, Bonneville Power Administration, Contract 98-AI06603, 255 p. plus appendix.

1999

Waples, R. S., P. Moran. 1999. Genetic monitoring and evaluation program for supplemented populations of salmon and steelhead in the Snake River basin. Report to the Technical Progress Report submitted to Bonneville Power Administration (Oct 1999).

1997

Waples, R. S., P. B. Aebersold, G. A. Winans. 1997. Population genetic structure and life history variability in Oncorhynchus nerka from the Snake River Basin. Final report of research to the Bonneville Power Administration, Contract DE-AI79-93BP05326, 104 p.

1996

Roni, P., L. A. Weitkamp. 1996. Environmental monitoring of the Manchester Naval Fuel Pier replacement, Puget Sound, Washington, 1991-1994. Report to the U.S. Department of Navy, Naval Facilities Engineering Command, Western Division, Contract N62474-91-MP-00758, 40 p. plus appendices.

1995

Stuehrenberg, L. C., D. Smith, O. W. Johnson. 1995. Evaluation of factors affecting collection efficiency estimates of chinook salmon and steelhead smolts at McNary Dam, 1989. Final Report to the Bonneville Power Administration, Contract DE-AI79- 88BP1024, 25 p.

Swanson, P., T. A. Flagg, J. J. Hard, L. W. Harrell, K. D. Shearer, R. J. Pascho, W. K. Hershberger, K. C. Massee, R. W. Hardy. 1995. Research on Captive Broodstock Technology for Pacific Salmon, Annual Report 1995. Report to the Bonneville Power Administration, Contract 1993BP55064, Project No. 199305600, 220 p. (BPA Report DOE/BP-55064-2)

1994

Prentice, E. F., D. J. Maynard, S. L. Downing, D. A. Frost, M. S. Kellett, D. A. Bruland, P. Sparks-Mcconkey, F. W. Waknitz, R. N. Iwamoto, K. W. McIntyre, N. N. Paasch. 1994. A study to determine the biological feasibility of a new fish tagging system (1990-93). Report to the Bonneville Power Administration, Contract DE-AI79-84BP11982, 250 p.

Weitkamp, L. A. 1994. Environmental monitoring of the Manchester Naval fuel pier replacement, Puget Sound, Washington., Contract Contract N62474-91-MP-00758, 92 p.

1993

Prentice, E. F., D. J. Maynard, P. Sparks-Mcconkey, C. S. McCutcheon, D. Neff, W. Steffens, F. W. Waknitz, A. L. Jensen, L. C. Stuehrenberg, S. L. Downing, B. P. Sandford, T. W. Newcomb. 1993. A study to determine the biological feasibility of a new fish tagging system. Report to the Bonneville Power Administration, Contract DE-AI79-84BP11982, 182 p.

Waples, R. S., O. W. Johnson, P. B. Aebersold, C. K. Shiflett, D. M. Van Doornik, D. J. Teel, A. E. Cook. 1993. A genetic monitoring and evaluation program for supplemented populations of salmon and steelhead in the Snake River basin. Annual Report of Research to the Bonneville Power Administration, Portland, Oregon, Contract DE-A179-89BP00911, Project No. 89-096.

Weitkamp, L. A., D. B. Dey. 1993. Environmental monitoring of the Manchester Naval Fuel Pier replacement, Puget Sound, Washington, 1992. Report to the Department of Navy, Contract N62474-91-MP-00758, 62 p.

1991

Waples, R. S., D. J. Teel, P. B. Aebersold. 1991. A genetic monitoring and evaluation program for supplemented populations of salmon and steelhead in the Snake River basin. Annual report of research to the Bonneville Power Administration, Contract DE-A179-89BP00911, Project No. 89-096.

1986

Milner, G. B., D. J. Teel, P. B. Aebersold, F. Utter. 1986. Genetic stock identification. Annual report of research to the Bonneville Power Administration, Contract DE-A179-85BP23520, Project No. 85-84.

1983

Milner, G. B., D. J. Teel, F. Utter. 1983. Genetic stock identification study. Final Report of Research by NOAA, NWAFC to the Bonneville Power Administration, Seattle, WA, Contract DE-A179-82BP28044M001.

1981

Milner, G. B., D. J. Teel, F. Utter, C. L. Burley. 1981. Columbia River stock identification study: Validation of genetic method. Final Report of Research by NOAA, NWAFC to the Bonneville Power Administration, Seattle, WA, Contract DE-A179-80BP18488.

1980

Milner, G. B., D. J. Teel, F. Utter. 1980. Columbia River stock identification study. Final Report of Research by NOAA, NWAFC to the U.S. Fish and Wildlife Service, Seattle, WA, Contract 14-16-0001-6438.

1979

Milner, G. B., D. J. Teel. 1979. Columbia River stock identification study. Annual report of research by NOAA, NWAFC to the U.S. Fish and Wildlife Service, Seattle, WA, Contract 14-16-0001-6438.

Milner, G. B., D. J. Teel, F. Utter. 1979. Electrophoretic survey of protein genetic variation in eight strains of rainbow trout (Salmon gairdneri) from the U.S. Fish and Wildlife Service Genetic Laboratory. Final Report of Research by NOAA, NWAFC to the U.S. Fish and Wildlife Service, Seattle, WA, Contract Contract No. 14-16-0009-79-911.

Technical Memorandum

2009

Currens, K., R. Fuerstenberg, W. Graeber, K. Rawson, M. H. Ruckelshaus, N. J. Sands, J. Scott. 2009. Identification of an independent population of sockeye salmon in Lake Ozette, Washington. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-96, 18 p.

Rawson, K., N. J. Sands, K. P. Currens, W. H. Graeber, M. H. Ruckelshaus, R. R. Fuerstenberg, J. B. Scott. 2009. Viability criteria for the Lake Ozette sockeye salmon evolutionarily significant unit. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-99, 38 p.

Sands, N. J., K. Rawson, K. Currens, W. Graeber, M. H. Ruckelshaus, R. Fuerstenberg, J. Scott. 2009. Determination of independent populations and viability criteria for the Hood Canal summer chum salmon evolutionarily significant unit. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-101, 58 p.

2008

Holt, M. M. 2008. Sound exposure and Southern Resident killer whales (Orcinus orca): A review of current knowledge and data gaps. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-89, 59 p.

Levin, P. S., M. J. Fogarty, G. C. Matlock, M. Ernst. 2008. Integrated ecosystem assessments. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-92, 20 p.

Wainwright, T. C., M. W. Chilcote, P. W. Lawson, T. E. Nickelson, C. W. Huntington, J. S. Mills, K. M. Moores, G. H. Reeves, H. A. Stout, L. A. Weitkamp. 2008. Biological recovery criteria for the Oregon Coast coho salmon evolutionarily significant unit. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-91, 199 p.

2007

Berntson, E. A., P. S. Levin, P. Moran. 2007. Conservation of North Pacific rockfishes: Ecological genetics and stock structure. Proceedings of the workshop March 2-3, 2004, Seattle, Washington. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-80, 80 p.

Brand, E. J., I. C. Kaplan, C. J. Harvey, P. S. Levin, E. A. Fulton, A. J. Hermann, J. C. Field. 2007. A spatially explicit ecosystem model of the California Current's food web and oceanography. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-84, 145 p.

Hard, J. J., J. M. Myers, M. J. Ford, R. G. Kope, G. R. Pess, R. S. Waples, G. A. Winans, B. A. Berejikian, F. W. Waknitz, P. B. Adams, P. A. Bisson, D. E. Campton, R. Reisenbichler. 2007. Status review of Puget Sound steelhead (Oncorhynchus mykiss). U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-81, 117 p.

Lawson, P. W., E. P. Bjorkstedt, M. W. Chilcote, C. W. Huntington, J. S. Mills, K. M. Moores, T. E. Nickelson, G. H. Reeves, H. A. Stout, T. C. Wainwright, L. A. Weitkamp. 2007. Identification of historical populations of coho salmon (Oncorhynchus kisutch) in the Oregon coast evolutionarily significant unit. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-79, 129 p.

Norman, K. C., J. A. Sepez, H. Lazrus, N. Milne, C. Package, S. Russell, K. Grant, R. Petersen Lewis, J. Primo, E. Springer, M. Styles, B. D. Tilt, I. Vaccaro. 2007. Community profiles for West Coast and North Pacific fisheries - Washington, Oregon, California, and other U.S. states. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-85, 602 p.

2006

Gustafson, R. G., J. Drake, M. J. Ford, J. M. Myers, E. E. Holmes, R. S. Waples. 2006. Status review of Cherry Point Pacific herring (Clupea pallasii) and updated status review of the Georgia Basin Pacific herring distinct population segment under the Endangered Species Act. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-76, 182 p.

Myers, J. M., C. Busack, D. Rawding, A. R. Marshall, D. J. Teel, D. M. Van Doornik, M. T. Maher. 2006. Historical population structure of Pacific salmonids in the Willamette River and lower Columbia River basins. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-73, 311 p.

Ruckelshaus, M. H., K. P. Currens, W. H. Graeber, R. R. Fuerstenberg, K. Rawson, N. J. Sands, J. B. Scott. 2006. Independent populations of Chinook salmon in Puget Sound. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-78, 125 p.

2005

Bottom, D. L., C. A. Simenstad, J. Burke, A. M. Baptista, D. A. Jay, K. K. Jones, E. Casillas, M. H. Schiewe. 2005. Salmon at river's end: The role of the estuary in the decline and recovery of Columbia River salmon. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-68, 246 p.

Good, T. P., R. S. Waples, P. Adams. (eds.) 2005. Updated status of Federally listed ESUs of West Coast salmon and steelhead. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-66, 598 p.

Holmes, E. E., W. Fagan, J. J. Rango, A. Folarin, J. A. Sorensen, J. E. Lippe, N. E. McIntyre. 2005. Cross validation of quasi-extinction risks from real time series: An examination of diffusion approximation methods. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-67, 37 p.

2004

Berejikian, B.A., and M.J. Ford. 2004. Review of relative fitness of hatchery and natural salmon. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-61, 28 p.

Ford, M. J., T. A. Lundrigan, P. Moran. 2004. Population genetics of Entiat River spring Chinook salmon. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-60, 45 p. (PDF | Excel Data file)

Krahn, M. M., M. J. Ford, W. F. Perrin, P. R. Wade, R. P. Angliss, M. B. Hanson, B. L. Taylor, G. M. Ylitalo, M. E. Dahlheim, J. E. Stein, R. S. Waples. 2004. 2004 Status Review of Southern Resident Killer Whales (Orcinus orca) under the Endangered Species Act. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-62, 73 p.

Norman, S. A., S. Raverty, B. McLellan, A. Pabst, D. Ketten, M. Fleetwood, J. K. Gaydos, B. Norberg, L. Barre, T. Cox, M. B. Hanson, S. Jeffries. 2004. Multidisciplinary investigation of stranded harbor porpoises (Phocoena phocoena) in Washington State with an assessment of acoustic trauma as a contributory factor (2 May-2 June 2003). U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS F/NWR-7, 118 p.

2002

Krahn, M. M., P. R. Wade, S. T. Kalinowski, M. E. Dahlheim, B. L. Taylor, M. B. Hanson, G. M. Ylitalo, R. P. Angliss, J. E. Stein, R. S. Waples. 2002. Status Review of Southern Resident Killer Whales (Orcinus orca) under the Endangered Species Act. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-54, 133 p.

Mace, P. M., A. W. Bruckner, N. K. Daves, J. D. Field, J. R. Hunter, N. E. Kohler, R. G. Kope, S. S. Lieberman, M. Miller, J. W. Orr, R. S. Otto, T. Smith, N. B. Thompson, J. Lyke, A. G. Blundell. 2002. NMFS / Interagency Working Group Evaluation of CITES Criteria and Guidelines. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-F/SPO-58, 70 p.

Waknitz, F. W., T. J. Tynan, C. E. Nash, R. N. Iwamoto, L. G. Rutter. 2002. Review of Potential Impacts of Atlantic Salmon Culture on Puget Sound Chinook Salmon and Hood Canal Summer-Run Chum Salmon Evolutionarily Significant Units. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-53, 83 p. (PDF | HTML)

2001

Nash, C. E., K. M. Brooks, W. T. Fairgrieve, R. N. Iwamoto, C. V. Mahnken, M. B. Rust, M. S. Strom, F. W. Waknitz. 2001. The net-pen salmon farming industry in the Pacific Northwest. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-49, 125 p. (PDF | HTML)

Stout, H. A., B. B. McCain, R. D. Vetter, T. L. Builder, W. H. Lenarz, L. L. Johnson, R. D. Methot. 2001. Status Review of Copper Rockfish (Sebastes caurinus), Quillback Rockfish (S. maliger), and Brown Rockfish (S. auriculatus) in Puget Sound, Washington. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-46, xxiv, 158 p.

Stout, H. A., R. G. Gustafson, W. H. Lenarz, B. B. McCain, D. M. Van Doornik, T. L. Builder, R. D. Methot. 2001. Status review of Pacific herring in Puget Sound, Washington. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-45, 175 p.

2000

Gustafson, R. G., W. H. Lenarz, B. B. McCain, C. C. Schmitt, W. S. Grant, T. L. Builder, R. D. Methot. 2000. Status review of Pacific hake, Pacific cod, and walleye pollock from Puget Sound, Washington. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-44, 275 p.

McElhany, P., M. H. Ruckelshaus, M. J. Ford, T. C. Wainwright, E. P. Bjorkstedt. 2000. Viable salmon populations and the recovery of evolutionarily significant units. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-42, 156 p.

1999

Johnson, O. W., M. H. Ruckelshaus, W. S. Grant, F. W. Waknitz, A. M. Garrett, G. J. Bryant, K. Neely, J. J. Hard. 1999. Status review of coastal cutthroat trout from Washington, Oregon, and California. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-37, 292 p. (PDF | HTML)

1998

Myers, J. M., R. G. Kope, G. J. Bryant, D. J. Teel, L. J. Lierheimer, T. C. Wainwright, W. S. Grant, F. W. Waknitz, K. Neely, S. Lindley, R. S. Waples. 1998. Status review of Chinook salmon from Washington, Idaho, Oregon, and California. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-35, 443 p. (PDF | HTML)

1997

Gustafson, R. G., T. C. Wainwright, G. A. Winans, F. W. Waknitz, L. T. Parker, R. S. Waples. 1997. Status review of sockeye salmon from Washington and Oregon. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-33, 282 p. (PDF | HTML)

Johnson, O. W., W. S. Grant, R. G. Kope, K. Neely, F. W. Waknitz, R. S. Waples. 1997. Status review of chum salmon from Washington, Idaho. Oregon, and California. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-32, 280 p. (PDF | HTML)

1996

Busby, P. J., T. C. Wainwright, G. J. Bryant, L. J. Lierheimer, R. S. Waples, F. W. Waknitz, I. V. Lagomarsino. 1996. Status Review of West Coast Steelhead from Washington, Idaho, Oregon, and California. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-27, 261 p. (PDF | HTML)

Hard, J. J., R. G. Kope, W. S. Grant, F. W. Waknitz, L. T. Parker, R. S. Waples. 1996. Status review of pink salmon from Washington, Oregon, and California. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-25, 131 p. (PDF | HTML)

1995

Waknitz, F. W., G. M. Matthews, T. C. Wainwright, G. A. Winans. 1995. Status review for mid- Columbia River summer chinook salmon. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-22, 80 p.

Weitkamp, L. A., T. C. Wainwright, G. J. Bryant, G. B. Milner, D. J. Teel, R. G. Kope, R. S. Waples. 1995. Status review of coho salmon from Washington, Oregon, and California. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-24, 258 p. (PDF | HTML)

1994

Johnson, O. W., R. S. Waples, T. C. Wainwright, K. Neely, F. W. Waknitz, L. T. Parker. 1994. Status review for Oregon's Umpqua River sea-run cutthroat trout. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-15, 122 p.

Park, L. K., P. Moran, R. S. Waples. (Eds.) 1994. Application of DNA technology to the management of Pacific salmon: Proceedings of the workshop. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-17.

1993

Busby, P. J., O. W. Johnson, T. C. Wainwright, F. W. Waknitz, R. S. Waples. 1993. Status review for Oregon's Illinois River winter steelhead. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-10, 85 p.

1992

Hard, J. J., R. P. Jones Jr., R. S. Waples. 1992. Pacific Salmon and Artificial Propagation Under the Endangered Species Act. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-2.

1991

Johnson, O. W., T. A. Flagg, D. J. Maynard, G. B. Milner, F. W. Waknitz. 1991. Status review for lower Columbia River coho salmon. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-F/NWC-202, 94 p. (Complete Article (PDF) | Summary (HTML))

Waples, R. S., O. W. Johnson. 1991. Status Review for Snake River Sockeye Salmon. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-F/NWC-195.

1990

Waples, R. S., G. A. Winans, F. Utter, C. V. Mahnken. 1990. Genetic monitoring of Pacific salmon hatcheries. U.S. Dept. of Commerce, NOAA Tech. Memo., Rept NMFS 92.

Report

2009

Waples, R.S., and M.L. Plummer. 2009. Towards a scientific framework for assessing lethal vs non-lethal take of cetaceans. Paper SC/61/O1 presented to the IWC Scientific Committee, June 2009, Madeira. 3pp.

2008

Bromaghin, J. F., R. M. Nielson, and J. J. Hard. 2008. An investigation of the potential effects of selective exploitation on the demography and productivity of Yukon River Chinook Salmon. US Fish and Wildlife Service, Alaska Fisheries Technical Report No. 100, 69 p.

Ford, M. J., K. Williamson. 2008. Report on 2006 White River captive brood pedigree analysis. Report to Grant County Public Utility District Contract Number, 430-2499, Northwest Fisheries Science Center, Conservation Biology, 36 p.

Galbreath, P. F., C. A. Beasley, B. A. Berejikian, R. W. Carmichael, D. E. Fast, M. J. Ford, J. A. Hesse, L. L. McDonald, A. R. Murdoch, C. M. Peven, D. A. Venditti. 2008. Recommendations for Broad Scale Monitoring to Evaluate the Effects of Hatchery Supplementation on the Fitness of Natural Salmon and Steelhead Populations. Final Draft Report of the Ad Hoc Supplementation Monitoring and Evaluation Workgroup. Fish Science Department, Columbia River Inter-Tribal Fish Commission; Quantitative Consultants, Inc.; Northwest Fisheries Science Center, NOAA Fisheries; Oregon Department of Fish and Wildlife; Yakima Klickitat Fisheries Project, Yakima Nation; Department of Fisheries, Nex Perce Tribe; Western Ecosystems Technology, Inc.; Washington Department of Fish and Wildlife; Fisheries Program, Chalan Public Utility District; Idaho Department of Fish and Game.

Levin, P. S., M. J. Fogarty, G. C. Matlock. 2008. Integrated Ecosystem Assessments (White Paper).

2007

Ford, M. J., N. J. Sands, P. McElhany, R. G. Kope, D. Simmons, P. Dygert. 2007. Analyses to Support a Review of an ESA Jeopardy Consultation on Fisheries Impacting Lower Columbia Tule Chinook Salmon. National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division; National Marine Fisheries Service, Northwest Regional Office, Sustainable Fisheries Division.

2005

Hard, J. J., J. M. Myers, M. J. Ford, R. G. Kope, G. R. Pess, R. S. Waples, G. A. Winans, B. A. Berejikian, F. W. Waknitz, P. B. Adams, P. A. Bisson, D. E. Campton, R. Reisenbichler. 2005. Status review update for Puget Sound steelhead. Report submitted to NOAA/NMFS Northwest Regional Office, Seattle, Washington, 26 July 2005, 70 p. + 4 appendices.

Kope, R. G. 2005. Performance of ocean salmon fisheries management relative to National Marine Fisheries Service Endangered Species Act consultation standards. Northwest Fisheries Science Center, Seattle, WA, 28 p.

2003

Myers, J. M., C. Busack, D. Rawding, A. R. Marshall. 2003. Historical population structure of Willamette and Lower Columbia River Basin Pacific salmonids. WLC-TRT Report, NOAA Fisheries Northwest Fisheries Science Center, Seattle. WA.

2002

Baker, J., P. Moran. 2002. Nuclear DNA identification of migrating bull trout captured at the Puget Sound Energy diversion dam on the White River, Washington State. Report to Puyallup Tribal Fisheries

Fuss, H., M. J. Ford. 2002. Differences in natural production between hatchery and wild coho salmon. Annual report to the Hatchery Scientific Work Group, June 2002.

Peek, J. M., M. S. Boyce, E. O. Garton, J. J. Hard, L. S. Mills. 2002. Risks involved in current management of elk in Washington. Final report to Washington Department of Fish and Wildlife and Washington Wildlife Commission, Olympia, Washington, 99 p.

Ruckelshaus, M. H., K. Currens, R. Fuerstenberg, W. Graeber, K. Rawson, N. J. Sands, K. J. Scott. 2002. Planning ranges and preliminary guidelines for the delisting and recovery of the Puget Sound Chinook salmon Evolutionarily Significant Unit. Puget Sound Technical Recovery Team.

2001

Ford, M. J., P. Budy, C. Busack, e. al. 2001. Upper Columbia River Steelhead and Spring Chinook Salmon: Population Structure and Biological Requirements. Final Report, March 2001.

Fuss, H., C. Sharpe, P. Hulett, M. J. Ford, J. J. Hard, E. LaHood. 2001. Differences in natural production between hatchery and wild coho salmon in Minter Creek, Washington. Annual report to the Hatchery Science Review Group, June, 2001..

Ruckelshaus, M. H., e. al. 2001. Independent populations of chinook salmon in Puget Sound. Puget Sound Technical Recovery Team Report, 92 p.

Weitkamp, L. A. 2001. Status review update for lower Columbia River coho. West Coast coho salmon Biological Review Team, 15 Mar. 2001. 52 p.

1999

Teel, D. J., P. A. Crane, C. Guthrie III, A. R. Marshall, D. M. Van Doornik, W. D. Templin, N. V. Varnavskya, L. W. Seeb. 1999. Comprehensive allozyme database discriminates chinook salmon around the Pacific Rim. NPAFC document Doc. 440, Alaska Department of Fish and Game, Division of Commercial Fisheries, 25 p.

1998

Pella, J., M. Masuda, C. Guthrie III, C. Kondzela, A. J. Gharrett, A. Moles, G. A. Winans. 1998. Stock composition of some sockeye salmon, Oncorhynchus nerka, catches in Southeast Alaska, based on incidence of allozyme variants, freshwater ages, and a brain_tissue parasite. NOAA Tech. Report, NMFS 132, 23 p.

Urawa, S., Y. Ueno, Y. Ishida, S. Takagi, G. A. Winans, N. Davis. 1998. Genetic stock identification of young chum salmon in the North Pacific Ocean and adjacent Seas. NPAFC Doc. 336, National Salmon Resources Center, Fisheries Agency of Japan, Toyohira_ku, Sapporo 062_0922, Japan, 9 p.

1997

Urawa, S., Y. Ishida, Y. Ueno, S. Takagi, G. A. Winans, N. Davis. 1997. Genetic stock identification of chum salmon in the north Pacific Ocean and Bering Sea during the winter and summer of 1996. NPAFC Doc. 259, National Salmon Conservation Center, Fisheries Agency of Japan, Toyohira-ku, Sapporo 062, Japan, 11 p.

1994

Weitkamp, L. A. 1994. A review of the effects of dams on the Columbia River estuarine environment, with special reference to salmonids. U.S. Dept. of Energy, Bonneville Power Administration and Coastal Zone and Estuarine Studies Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, ix, 148 p.

1985

Milner, G. B., D. J. Teel. 1985. Genetic variation in steelhead populations of the Snake River. Final Report, NWAFC, CZES, Seattle, WA.

Thesis

2004

Weitkamp, L. A. 2004. Ocean conditions, marine survival, and performance of juvenile chinook (Oncorhynchus tshawytscha) and coho (O. kisutch) salmon in Southeast Alaska. Ph.D. Thesis University of Washington, vii, 223 p.

1994

Ruckelshaus, M. H. 1994. Ecological and genetic factors affecting population structure in the marine angiosperm, Zostera marina L. Ph. D University of Washington, Seattle, WA, v, 207 p.

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