Journal Article

In press

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.

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.

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.

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.

2009

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.

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

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.

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.

2008

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.

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

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.

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.

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.

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.

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)

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.

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.

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.

2006

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

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.

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.

2005

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.

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

2004

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 | )

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.

2003

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.

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)

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

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)

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

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.

2001

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

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.

1997

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

1994

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.

Book

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.

Section

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.

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

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.

2000

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.

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.

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.

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.

Contract Report

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.

1994

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

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.

Technical Memorandum

2008

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

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.

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.

2005

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.

1995

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)

Report

2001

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

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.

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