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

Journal Article

In press

Andersen, L. W., E. W. Born, D. W. Doidge, I. Gjertz, O. Wiig, R. S. Waples. In press. Genetic signals of historic and recent migration between sub-populations of Atlantic walrus (Odobenus rosmarus rosmarus) west and east of Greenland. Endangered Species Research.

Laikre, L., R. S. Waples. In press. Neglect of genetic diversity in implementation of the Convention on Biological Diversity. Conservation Biology.

Waples, R. S. In press. Conserving the legacy of Arctic-Yukon-Kushokwim salmon. American Fisheries Society Symposium.

Waples, R. S., D. W. Jensen, M. M. McClure. In press. Empirical evidence for eco-evolutionary interactions and tradeoffs: Annual variation in productivity reduces effective population size in Chinook salmon. Ecology.

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.

2009

Chopelet, J., R.S. Waples, and S. Mariani. 2009. Sex change and the genetic structure of marine fish populations. Fish and Fisheries 10:329-343.

Waples, R. S., T. Beechie, and G. R. Pess. 2009. Evolutionary history, habitat disturbance regimes, and anthropogenic changes: What do these mean for resilience of Pacific salmon populations? Ecology and Society 14(1): 3 [online] URL: http://www.ecologyandsociety.org/vol14/iss1/art3/

Waples, R. S., and J. R. Faulkner. 2009. Modeling evolutionary processes in small populations: Not as ideal as you think. Molecular Ecology 18:1834-1847.

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.

Hauser, L., R.S. Waples, and G.R. Carvalho. 2008. Editorial: Introduction to the special issue. Fish and Fisheries 9:331-332.

Hom, T., T. K. Collier, M. M. Krahn, M. S. Strom, G. M. Ylitalo, W. B. Nilsson, R. N. Paranjpye, U. Varanasi. 2008. Assessing Seafood Safety in the Aftermath of Hurricane Katrina. American Fisheries Society Symposium, 64:73-93.

Waples, R. S., G. R. Pess, and T. Beechie. 2008. Evolutionary history of Pacific salmon in dynamic environments. Evolutionary Applications 1:189-206.

Waples, R. S., A. P. Hendry. 2008. Evolutionary perspectives on salmonid conservation and management. Evolutionary Applications, 1:183-188.

Waples, R. S., R. W. Zabel, M. D. Scheuerell, and B. L. Sanderson. 2008. Evolutionary responses by native species to major anthropogenic changes to their ecosystems: Pacific salmon in the Columbia River hydropower system. Molecular Ecology 17:84-96.

Waples, R. S., A. E. Punt, and J. Cope. 2008. Integrating genetic data into fisheries management: how can we do it better? Fish and Fisheries 9:423449.

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.

Waples, R. S., P. B. Adams, J. Bohnsack, and B. L. Taylor. 2008. Legal viability, societal values, and SPOIR: response to DElia et al. Conservation Biology 22:1075-1077.

Waples, R. S., W. W. Dickhoff, L. Hauser, and N. Ryman. 2008. Six decades of fishery genetics: taking stock. Fisheries 33(2):76-79.

Williams, J., R.W. Zabel, R.S. Waples. J.A. Hutchings, and W.P. Connor. 2008. Potential for anthropogenic disturbances to influence evolutionary change in the life history of a threatened salmonid. Evolutionary Applications 1:271-285.

2007

Araki H. A., R. S. Waples, and M S. Blouin. 2007. A potential bias in the temporal method for estimating Ne in admixed populations under natural selection. Molecular Ecology 16:2261-2271.

Araki H. A., R. S. Waples, W. R. Ardren, B. Cooper, and M S. Blouin. 2007. Effective population size of steelhead trout: influence of variance in reproductive success, hatchery programs, and genetic compensation between life-history forms. Molecular Ecology 16:953-966.

Dickhoff, W. W., T. K. Collier, U. Varanasi. 2007. The seafood "dilemma". Fisheries, 32(5):244-246.

Faubet, F., R. S. Waples, and O. E. Gaggiotti. 2007. Evaluating the performance of a multilocus Bayesian method for the estimation of migration rates. Molecular Ecology 16:11491166.

Gardner, S. C., G. M. Ylitalo, U. Varanasi. 2007. Comparative assessment of organochlorine concentrations in porpoise melon and blubber. Marine Mammal Science, 23(2):434-444.

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)

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.

Schwartz, M.K., G. Luikart, and R.S. Waples. 2007. Genetic monitoring: a promising tool for conservation and management. Trends. Ecol. Evol. 22:25-33.

Waples, R. S., P. B. Adams, J. Bohnsack, and B. L. Taylor. 2007. A biological framework for evaluating whether an ESA species is threatened or endangered in a significant portion of its range. Conservation Biology 21:964-974.

Waples, R. S., P. B. Adams, J. Bohnsack, and B. L. Taylor. 2007. Normativity redux. Conservation Biology 21:1649-1650.

Waples, R.S., M. Masuda, and J. Pella. 2007. SALMONNb: A program for computing cohort-specific effective population sizes (Nb) in Pacific salmon and other semelparous species using the temporal method. Mol. Ecol. Notes 7:21-24.

Waples, R.S., and M. Yokota. 2007. Temporal estimates of effective population size in species with overlapping generations. Genetics 175:219-233.

2006

Waples, R. S. 2006. A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conservation Genetics, 7(2):167-184.

Waples, R. S. 2006. Seed banks, salmon, and sleeping genes: Effective population size in semelparous, age-structured species with fluctuating abundance. American Naturalist, 167:118-135.

Waples, R. S., O. Gaggiotti. 2006. What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology, 15(6):1419-1439.

2005

Manel, S., O. Gaggiotti, R. S. Waples. 2005. Assignment methods: matching biological questions with appropriate techniques. Trends in Ecology and Evolution, 20:136-142.

Waples, R. S. 2005. Genetic estimates of contemporary effective population size: to what time periods do the estimates apply? Molecular Ecology, 14:3335-3352.

Ylitalo, G. M., J. E. Stein, T. Hom, L. L. Johnson, K. L. Tilbury, A. J. Hall, T. Rowles, D. Greig, L. J. Lowenstine, F. Gulland. 2005. The role of organochlorines in cancer-associated mortality in California sea lions (Zalophus californianus). Marine Pollution Bulletin, 50:30-39.

2004

Helser, T. E., A. E. Punt, R. D. Methot. 2004. A generalized linear mixed model analysis of a multi-vessel fishery resource survey. Fisheries Research, 70:251-264.

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.

Levings, C., J. E. Stein, C. M. Stehr, S. C. Samis. 2004. Introduction to the PICES practical workshop: objectives, overview of the study area, and projects conducted by the participants. Marine Environmental Research, 57(1-2):3-18.

Stehr, C. M., M. S. Myers, L. L. Johnson, S. Spencer, J. E. Stein. 2004. Toxicopathic liver lesions in English sole and chemical contaminant exposure in Vancouver Harbour, Canada. Marine Environmental Research, 57:55-74.

Tallmon, D. A., G. Luikart, R. S. Waples. 2004. The alluring simplicity and complex reality of genetic rescue. Trends in Ecology and Evolution, 19:489-496.

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)

2003

Gardner, S. C., U. Varanasi. 2003. Isovaleric acid accumulation in odontocete melon during development. Naturwissenschaften, 90:528-531.

Hey, J., R. S. Waples, M. L. Arnold, R. K. Butlin, R. G. Harrison. 2003. Understanding and confronting species uncertainty in biology and conservation. Trends in Ecology and Evolution, 18:597-603.

Krahn, M. M., G. M. Ylitalo, J. E. Stein, A. Aguilar, A. Borrell. 2003. Organochlorine contaminants in cetaceans: how to facilitate interpretation and avoid errors when comparing datasets. Journal of Cetacean Research and Management, 5:103-113.

Parrish, J. K., R. Bailey, A. Copping, J. E. Stein. 2003. The Pacific Northwest coastal ecosystems regional study. Estuaries, 26(4B):991-993.

2002

Johnson, L. L., T. K. Collier, J. E. Stein. 2002. An analysis in support of sediment quality thresholds for polycyclic aromatic hydrocarbons (PAHs) to protect estuarine fish. Aquatic Conservation: Marine and Freshwater Ecosystems, 12:517-538.

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

Meador, J. P., T. K. Collier, J. E. Stein. 2002. Determination of a tissue and sediment threshold for tributyltin to protect prey species for juvenile salmonids listed by the U. S. Endangered Species Act. Aquatic Conservation: Marine and Freshwater Ecosystems, 12:539-551.

Meador, J. P., T. K. Collier, J. E. Stein. 2002. Use of tissue and sediment-based threshold concentrations of polychlorinated biphenyls (PCBs) to protect juvenile salmonids listed under the U.S. Endangered Species Act. Aquatic Conservation: Marine and Freshwater Ecosystems, 12:493-516.

Millar, R. B., R. D. Methot. 2002. Age-Structured Meta-Analysis of Us West Coast Rockfish (Scorpaenidae) Populations and Hierarchical Modeling of Trawl Survey Catchabilities. Canadian Journal of Fisheries and Aquatic Sciences, 59:383-392.

Tilbury, K. L., J. E. Stein, C. A. Krone, R. L. Brownell Jr., S. A. Blokhin, J. L. Bolton, D. W. Ernest. 2002. Chemical contaminants in juvenile gray whales (Eschrichtius robustus) from a subsistence harvest in Arctic feeding grounds. Chemosphere, 47:555-564.

Waples, R. S. 2002. Effective size of fluctuating salmon populations. Genetics, 161:783-791.

Waples, R. S. 2002. Evaluating the effect of stage-specific survivorship on the N- e/N ratio. Molecular Ecology, 11:1029-1037.

2001

Arkoosh, M. R., E. Casillas, E. R. Clemons, P. A. Huffman, A. N. Kagley, T. K. Collier, J. E. Stein. 2001. Increased susceptibility of juvenile chinook salmon (Oncorhynchus tshawytscha) to vibriosis after exposure to chlorinated and aromatic compounds found in contaminated urban estuaries. Journal of Aquatic Animal Health, 13:257-268.

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

Krahn, M. M., G. M. Ylitalo, D. G. Burrows, J. Calambokidis, S. E. Moore, M. Gosho, P. Gearin, P. D. Plesha, R. L. Brownell Jr., S. A. Blokhin, K. L. Tilbury, T. Rowles, J. E. Stein. 2001. Organochlorine contaminant concentrations and lipid profiles in eastern North Pacific gray whales (Eschrichtius robustus). Journal of Cetacean Research and Management, 3(1):19-29.

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.

Ylitalo, G. M., C. O. Matkin, J. Buzitis, M. M. Krahn, L. L. Jones, T. Rowles, J. E. Stein. 2001. Influence of life-history parameters on organochlorine concentrations in free-ranging killer whales (Orcinus orca) from Prince William Sound, AK. Science of the Total Environment, 281:183-203.

1999

Jonsson, B., R. S. Waples, K. D. Friedland. 1999. Extinction considerations for diadromous fishes. ICES Journal of Marine Science, 56:405-409.

Krahn, M. M., D. G. Burrows, J. E. Stein, P. R. Becker, M. M. Schantz, D. C. Muir, T. M. O'Hara. 1999. White whales (Delphinapterus leucas) from three Alaskan stocks: concentrations and patterns of persistent organochlorine contaminants in blubber. Journal of Cetacean Research and Management, 1:239-249.

Krishnakumar, P. K., E. Casillas, R. G. Snider, A. N. Kagley, U. Varanasi. 1999. Environmental contaminants and the prevalence of hemic neoplasia (leukemia) in the common mussel (Mytilus edulis complex) from Puget sound, Washington, USA. Journal of Invertebrate Pathology, 73:135-146.

Krone, C. A., P. A. Robisch, K. L. Tilbury, J. E. Stein, E. A. Mackey, P. R. Becker, T. M. O'Hara, L. M. Philo. 1999. Elements in liver tissues of bowhead (Balaena mysticetus) whales. Marine Mammal Science, 15:123-142.

Krone, C. A., J. E. Stein. 1999. Species dependent biotransformation and tissue distribution of tributyltin in two marine teleosts. Aquatic Toxicology, 45:209-222.

Meador, J. P., D. W. Ernest, A. A. Hohn, K. L. Tilbury, J. Gorzelany, G. Worthy, J. E. Stein. 1999. Comparison of elements in bottlenose dolphins stranded on the beaches of Texas and Florida in the Gulf of Mexico over a one-year period. Archives of Environmental Contamination and Toxicology, 36:87-98.

Reichert, W. L., B. L. French, J. E. Stein. 1999. Biological effects of contaminants: Measurement of DNA adducts in fish by 32P -postlabelling. International Council for the Exploration of the Sea Techniques in Marine Environmental Sciences, 25(1-45).

Reichert, W. L., B. L. French, J. E. Stein. 1999. Exposure of Marine Mammals to Genotoxic Environmental Contaminants: Application of the 32p-Postlabeling Assay for Measuring DNA-Xenobiotic Adducts. Environmental Monitoring and Assessment, 56:223-239.

Tilbury, K. L., N. G. Adams, C. A. Krone, J. P. Meador, G. Early, U. Varanasi. 1999. Organochlorines in stranded pilot whales (Globicephala melaena) from the Coast of Massachusetts. Archives of Environmental Contamination and Toxicology, 37:125-134.

Waples, R. S. 1999. Dispelling some myths about hatcheries. Fisheries, 24(2):12-21.

1998

Arkoosh, M. R., E. Casillas, E. R. Clemons, A. N. Kagley, R. Olson, P. Reno, J. E. Stein. 1998. Effect of pollution on fish diseases: Potential impacts on salmonid populations. Journal of Aquatic Animal Health, 10:182-190.

Arkoosh, M. R., E. R. Clemons, A. N. Kagley, R. Olson, P. Reno, E. Casillas, J. E. Stein. 1998. Effects of pollution of fish diseases: Potential impacts on salmonid populations. Journal of Aquatic Animal Health, 10:182-190.

Arkoosh, M. R., E. Casillas, P. A. Huffman, E. R. Clemons, J. Evered, J. E. Stein, U. Varanasi. 1998. Increased susceptibility of juvenile chinook salmon from a contaminated estuary to Vibrio anguillarum. Transactions of the American Fisheries Society, 127:360-374.

Collier, T. K., L. L. Johnson, C. M. Stehr, M. S. Myers, J. E. Stein. 1998. A comprehensive assessment of the impacts of contaminants on fish from an urban waterway. Marine Environmental Research, 46:243-247.

Johnson, L. L., J. T. Landahl, L. A. Kubin, B. H. Horness, M. S. Myers, T. K. Collier, J. E. Stein. 1998. Assessing the effects of anthropogenic stressors on Puget Sound flatfish populations. Journal of Sea Research, 39:125-137.

Krahn, M. M., J. E. Stein. 1998. Assessing exposure of marine biota and habitats to petroleum compounds. Analytical Chemistry, 70:186A-192A.

Myers, M. S., B. L. French, W. L. Reichert, M. L. Willis, B. F. Anulacion, T. K. Collier, J. E. Stein. 1998. Reductions in CYP1A expression and hydrophobic DNA adducts in liver neoplasms of English sole (Pleuronectes vetulus): Further support for the "resistant hepatocyte" model of hepatocarcinogenesis. Marine Environmental Research, 46:197-202.

Myers, M. S., L. L. Johnson, T. Hom, T. K. Collier, J. E. Stein, U. Varanasi. 1998. Toxicopathic hepatic lesions in subadult English sole (Pleuronectes vetulus) from Puget Sound, Washington, USA: Relationships with other biomarkers of contaminant exposure. Marine Environmental Research, 45:47-67.

Peck-Miller, K. A., M. S. Myers, T. K. Collier, J. E. Stein. 1998. Complete cDNA sequence of the Ki-ras proto-oncogene in liver of wild English sole (Pleuronectes vetulus) and mutation analysis of hepatic neoplasms and other toxicopathic liver lesions. Molecular Carcinogenesis, 23:207-216.

Reichert, W. L., M. S. Myers, K. A. Peck-Miller, B. L. French, B. F. Anulacion, T. K. Collier, J. E. Stein, U. Varanasi. 1998. Molecular epizootiology of genotoxic events in marine fish: linking contaminant exposure, DNA damage, and tissue-level alterations. Mutatation Research, 411:215-225.

Wainwright, T. C., R. S. Waples. 1998. Prioritizing Pacific salmon stocks for conservation: Response to Allendorf et al. Conservation Biology, 12:1144-1147.

Waples, R. S. 1998. Evolutionarily significant units, distinct population segments, and the endangered species act: Reply to Pennock and Dimmick. Conservation Biology, 12:718-721.

Waples, R. S. 1998. Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. Journal of Heredity, 89:438-450.

1997

Eufemia, N. A., T. K. Collier, J. E. Stein, D. E. Watson, R. T. DiGiulio. 1997. Biochemical responses to sediment-associated contaminants in brown bullhead (Ameriurus nebulosus) from the Niagara River ecosystem. Ecotoxicology, 6:13-34.

Krahn, M. M., J. E. Stein. 1997. Analytical approaches for assessing exposure of marine biota and habitats to petroleum-related aromatic compounds. Analytical Chemistry, 70:186A-192A.

Krahn, M. M., P. R. Becker, K. L. Tilbury, J. E. Stein. 1997. Organochlorine contaminants in blubber of four seal species: Integrating biomonitoring and specimen banking. Chemosphere, 34:2109-2121.

Krishnakumar, P. K., E. Casillas, U. Varanasi. 1997. Cytochemical responses in the digestive tissue of Mytilus edulis complex exposed to microencapsulated PAHs or PCBs. Comparative Biochemistry and Physiology, Part C: Toxicology and Pharmocology, 118:11-18.

Landahl, J. T., L. L. Johnson, T. K. Collier, J. E. Stein, U. Varanasi. 1997. Marine pollution and fish population parameters: English sole (Pleuronectes vetulus) in Puget Sound, Washington. Transactions of the American Fisheries Society, 126:519-535.

Meador, J. P., C. A. Krone, D. W. Dyer, U. Varanasi. 1997. Toxicity of sediment-associated tributyltin to infaunal invertebrates: species comparison and the role of organic carbon. Marine Environmental Research, 43:219-241.

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.

Stehr, C. M., M. S. Myers, D. G. Burrows, M. M. Krahn, J. P. Meador, B. B. McCain, U. Varanasi. 1997. Chemical contamination and associated liver diseases in two species of fish from San Francisco Bay and Bodega Bay, CA. Ecotoxicology, 6(1):35-65.

Tilbury, K. L., J. E. Stein, J. P. Meador, C. A. Krone, S. Chan. 1997. Chemical contaminants in harbor porpoise (Phocoena phocoena) from the north Atlantic coast: Tissue concentrations and intra- and inter-organ distribution. Chemosphere, 34(9/10):2159-2181.

1996

Arkoosh, M. R., E. R. Clemons, P. A. Huffman, H. R. Sanborn, E. Casillas, J. E. Stein. 1996. Evaluation of the leukoproliferative response of English sole (Pleuronectes vetulus) as a biomarker for immune dysfunction. Marine Environmental Research, 42:181-186.

Arkoosh, M. R., E. R. Clemons, P. A. Huffman, H. R. Sanborn, E. Casillas, J. E. Stein. 1996. Leukoproliferative response of splenic leukocytes from English sole (Pleuronectes vetulus) exposed to chemical contaminants. Environmental Toxicology and Chemistry, 15(7):1154-1162.

Collier, T. K., C. A. Krone, M. M. Krahn, J. E. Stein, S. Chan, U. Varanasi. 1996. Petroleum exposure and associated biochemical effects in subtidal fish after the Exxon Valdez oil spill. Transactions of the American Fisheries Society, 18:671-683.

French, B. L., W. L. Reichert, T. Hom, M. Nishimoto, H. R. Sanborn, J. E. Stein. 1996. Accumulation and dose-response of hepatic DNA adducts in English sole (Pleuronectes vetulus) exposed to a gradient of contaminated sediments. Aquatic Toxicology, 36:1-16.

Krone, C. A., J. E. Stein, U. Varanasi. 1996. Butyltin contamination of sediments and benthic fish from the East, Gulf and Pacific coasts of the United States. Environmental Monitoring and Assessment, 40:75-89.

McCain, B. B., D. W. Brown, T. Hom, M. S. Myers, S. M. Pierce, T. K. Collier, J. E. Stein, S. Chan, U. Varanasi. 1996. Chemical contaminant exposure and effects in four fish species from Tampa Bay, Florida. Estuaries, 19:86-104.

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

Collier, T. K., B. F. Anulacion, J. E. Stein, A. Goksoyr, U. Varanasi. 1995. A field evaluation of cytochrome P4501A as a biomarker of contaminant exposure in three species of flatfish. Environmental Toxicology and Chemistry, 14:143-152.

Johnson, L. L., J. E. Stein, T. Hom, T. K. Collier, S. Y. Sol, U. Varanasi. 1995. Effects of exposure to Prudhoe Bay crude oil on reproductive function in gravid female flatfish. Environmental Science, 3(2):67-81.

Krishnakumar, P. K., E. Casillas, U. Varanasi. 1995. Effects of chemical contaminants on the health of Mytilus edulis from Puget Sound, Washington .2. Cytochemical detection of subcellular changes in digestive cells. Marine Biology, 124:251-259.

Meador, J. P., J. E. Stein, W. L. Reichert, U. Varanasi. 1995. Bioaccumulation of polycyclic aromatic hydrocarbons by marine organisms. Reviews of Environmental Contamination and Toxicology, 143:79-165.

Meador, J. P., E. Casillas, C. A. Sloan, U. Varanasi. 1995. Comparative bioaccumulation of polycyclic aromatic hydrocarbons from sediment by two infaunal invertebrates. Marine Ecology Progress Series, 123:107-124.

Nishimoto, M., B. L. Eberhart, H. R. Sanborn, C. A. Krone, U. Varanasi, J. E. Stein. 1995. Effects of a complex mixture of chemical contaminants of hepatic glutathione, L-cysteine and gamma -glutamylcysteine synthetase in English sole (Pleuronectes vetulus). Environmental Toxicology and Chemistry, 14:461-469.

Stein, J. E., T. Hom, T. K. Collier, D. W. Brown, U. Varanasi. 1995. Contaminant exposure and biochemical effects in outmigrant juvenile chinook salmon from urban and non-urban estuaries of Puget Sound, WA. Environmental Toxicology and Chemistry, 14:1019-1029.

Stein, J. E., W. L. Reichert, B. L. French, B. F. Anulacion, U. Varanasi. 1995. Toxicokinetics of xenobiotic-DNA adducts in English sole (Pleuronectes vetulus): studies with laboratory and environmentally exposed sole. Marine Environmental Research, 39:373.

Waples, R. S. 1995. Evolutionarily significant units and the conservation of biological diversity under the Endangered Species Act. American Fisheries Society Symposium, 17:8-27.

1994

Johnson, L. L., J. E. Stein, T. K. Collier, E. Casillas, U. Varanasi. 1994. Indicators of reproductive development in prespawning female winter flounder (Pleuronectes americanus) from urban and non-urban estuaries in the northeast United States. Science of the Total Environment, 141:241-260.

Krahn, M. M., G. M. Ylitalo, J. Buzitis, C. A. Sloan, D. T. Boyd, S. Chan, U. Varanasi. 1994. Screening for planar chlorobiphenyl congeners in tissues of marine biota by high-performance liquid chromatography with photodiode array detection. Chemosphere, 29(1):117-139.

Krishnakumar, P. K., E. Casillas, U. Varanasi. 1994. Effect on the health of Mytilus edulis from Puget Sound Washington, Washington, USA. Cytochemical measures of lysosomal responses in the digestive cells using automatic image analysis. Marine Ecology Progress Series, 106:249-261.

Meador, J. P., U. Varanasi, P. A. Robisch, S. Chan. 1994. Toxic metals in pilot whales (Globicephala melaena) from strandings in 1986 and 1990 on Cape Cod, Massachusetts. Canadian Journal of Fisheries and Aquatic Sciences, 50:2698-2706.

Myers, M. S., C. M. Stehr, O. P. Olson, L. L. Johnson, B. B. McCain, S. Chan, U. Varanasi. 1994. Relationships between toxicopathic hepatic lesions and exposure to chemical contaminants in English sole (P. vetulus), starry flounder (P. stellatus), and white croaker (G. lineatus) from selected marine sites on the Pacific Coast, USA. Environmental Health Perspectives, 102:200-215.

Stein, J. E., W. L. Reichert, U. Varanasi. 1994. Molecular epizootiology: Assessment of exposure to genotoxic compounds in teleosts. Environmental Health Perspectives, 102(Suppl. 12):19-23.

Varanasi, U., J. E. Stein, K. L. Tilbury, J. P. Meador, C. A. Sloan, R. C. Clark Jr., S. Chan. 1994. Chemical contaminants in gray whales (Eschrichtius robustus) stranded along the west coast of North America. Science of the Total Environment, 145:29-53.

Waples, R. S. 1994. Genetic considerations in recovery efforts for Pacific salmon. Conservation Biology, 8:884-886.

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.

Wirgin, J. I., C. Grunwald, S. Courtenay, G. Kreamer, W. L. Reichert, J. E. Stein. 1994. A biomarker approach to assessing xenobiotic exposure in Atlantic tomcod from the North American Atlantic Coast. Environmental Health Perspectives, 102:764-770.

1993

Casillas, E., L. L. Johnson, D. Misitano, T. K. Collier, J. E. Stein, B. B. McCain, U. Varanasi. 1993. Inducibility of spawning, reproductive success, and egg production of flatfish species form urban and non-urban areas of Puget Sound, Washington. Marine Environmental Research, 35:227.

Collier, T. K., J. E. Stein, H. R. Sanborn, T. Hom, M. S. Myers, U. Varanasi. 1993. A field study of the relationship between bioindicators of maternal contaminant exposure and egg and larval viability of English sole (Parophrys vetulus). Marine Environmental Research, 35:171-175.

Collier, T. K., J. E. Stein, A. Goksoyr, M. S. Myers, J. W. Gooch, R. J. Huggett, U. Varanasi. 1993. Biomarkers of PAH exposure in oyster toadfish (Opsanis tau) from the Elizabeth River, Virginia. Environmental Science, 2:161-177.

Johnson, L. L., C. M. Stehr, O. P. Olson, M. S. Myers, S. M. Pierce, C. A. Wigren, B. B. McCain, U. Varanasi. 1993. Chemical contaminants and hepatic lesions in winter flounder (Pleuronectes americanus) from the Northeast Coast of the United States. Environmental Science & Technology, 27:2579-2771.

Johnson, L. L., E. Casillas, T. K. Collier, J. E. Stein, U. Varanasi. 1993. Contaminant effects on reproductive success in selected benthic fish. Marine Environmental Research, 35:165-170.

Krahn, M. M., G. M. Ylitalo, J. Buzitis, J. L. Bolton, C. A. Wigren, S. Chan, U. Varanasi. 1993. Analyses for petroleum-related contaminants in marine fish and sediments following the ROPME Sea oil spill. Marine Pollution Bulletin, 27:285-292.

Krahn, M. M., G. M. Ylitalo, J. Buzitis, S. Chan, U. Varanasi, T. L. Wade, T. J. Jackson, J. M. Brooks, D. A. Wolfe, C. Manen. 1993. Comparison of high-performance liquid chromatography/fluorescence screening and gas chromatography/mass spectrometry analysis for aromatic compounds in sediments sampled after the Exxon Valdez oil spill. Environmental Science & Technology, 27(4):699-708.

Krahn, M. M., G. M. Ylitalo, J. Buzitis, S. Chan, U. Varanasi. 1993. Rapid high-performance liquid chromatographic methods that screen for aromatic compounds in environmental samples. J. Chromat, 642:15-32.

Meador, J. P., U. Varanasi, C. A. Krone. 1993. Differential sensitivity of marine infaunal amphipods to tributyltin. Marine Biology, 116:231-239.

Stein, J. E., W. L. Reichert, B. L. French, U. Varanasi. 1993. 32P-postlabeling analysis of DNA adduct formation and persistence in English sole (Pleuronectes vetulus) exposed to benzo[a]pyrene and 7H-dibenzo[c,g]carbazole. Chemico-Biological Interactions, 88:55-69.

Stein, J. E., T. K. Collier, W. L. Reichert, E. Casillas, T. Hom, U. Varanasi. 1993. Bioindicators of Contaminant Exposure and Sublethal Effects in Benthic Fish from Puget Sound, WA. Marine Environmental Research, 35:95-100.

1992

Collier, T. K., J. E. Stein, H. R. Sanborn, T. Hom, M. S. Myers, U. Varanasi. 1992. Field Studies of Reproductive Success and Bioindicators in English Sole (Parophrys vetulus): Correlations with Bioindicators of Maternal Contaminant Exposure. Sci. Tot. Environ, 116:169-185.

Collier, T. K., J. E. Stein, H. R. Sanborn, T. Hom, M. S. Myers, U. Varanasi. 1992. Field studies of reproductive success in English sole (Parophrys vetulus): Correlations with bioindicators of maternal contaminant exposure. Science of the Total Environment, 116:169-185.

Hedgecock, D., V. Chow, R. S. Waples. 1992. Effective population numbers of shellfish broodstocks estimated from temporal variance in allele frequencies. Aquaculture, (108)215-232.

Johnson, L. L., E. Casillas, J. E. Stein, T. K. Collier, U. Varanasi. 1992. Contaminant effects on reproductive effects on reproductive success in selected benthic fish species. Marine Environmental Research, 35:165-170.

Krahn, M. M., G. M. Ylitalo, J. Buzitis, S. Chan, U. Varanasi. 1992. Comparison of HPLC/Fluorescence Screening and GC/MS Analysis for Aromatic Compounds in Sediments Sampled after the Exxon Valdez Oil Spill. Environmental Science & Technology, 27:699-708.

Krahn, M. M., D. G. Burrows, G. M. Ylitalo, D. W. Brown, C. A. Wigren, T. K. Collier, S. Chan, U. Varanasi. 1992. Mass spectrometric analysis for aromatic compounds in bile of fish sampled after the EXXON Valdez oil spill. Environmental Science & Technology, 26:116-126.

Krone, C. A., J. E. Stein, U. Varanasi. 1992. Estimation of levels of metabolites of aromatic hydrocarbons in fish tissues by HPLC/fluorescence analysis. Chemosphere, 27:699-708.

McCain, B. B., S. Chan, M. M. Krahn, D. W. Brown, M. S. Myers, J. T. Landahl, S. M. Pierce, R. C. Clark Jr., U. Varanasi. 1992. Chemical contamination and associated fish diseases in San Diego Bay. Environmental Science & Technology, 26:725-733.

Myers, M. S., P. Olson, L. L. Johnson, C. S. Stehr, T. Hom, U. Varanasi. 1992. Hepatic Lesions Other than Neoplasms in Subadult Flatfish from Puget Sound, WA; Relationships with Indices of Contaminant Exposure. Marine Environmental Research, 34:45-51.

Nishimoto, M., G. K. Yanagida, J. E. Stein, W. M. Baird, U. Varanasi. 1992. Metabolism of benzo(a)pyrene by English sole (Parophrys vetulus): comparison between isolated hepatocytes in vitro and liver in vivo. Xenobiotica, 22:949-961.

Reichert, W. L., J. E. Stein, B. L. French, P. Goodwin, U. Varanasi. 1992. Storage phosphor imaging technique for detection and quantitation of DNA adducts measured by the 32P-postlabeling assay. Carcinogenesis, 13:1475-1479.

Stein, J. E., T. K. Collier, W. L. Reichert, E. Casillas, U. Varanasi. 1992. Bioindicators of contaminant exposure and sublethal effects: Studies with benthic fish in Puget Sound, WA. Environmental Toxicology and Chemistry, 11:701-714.

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.

1991

Arkoosh, M. R., E. Casillas, E. R. Clemons, B. B. McCain, U. Varanasi. 1991. Suppression of immunological memory in juvenile chinook salmon (Oncorhynchus tshawytscha) from an urban estuary. Fish and Shellfish Immunology, 1:261-277.

Casillas, E., D. Misitano, L. L. Johnson, L. D. Rhodes, T. K. Collier, J. E. Stein, B. B. McCain, U. Varanasi. 1991. Inducibility of spawning and reproductive success of female English sole (Parophrys vetulus) from urban and nonurban areas of Puget Sound, Washington. Marine Environmental Research, 31:99-122.

Gronlund, W. D., S. Chan, B. B. McCain, R. C. Clark Jr., M. S. Myers, P. D. Plesha, J. E. Stein, D. W. Brown, J. T. Landahl, M. M. Krahn, W. L. Reichert, U. Varanasi. 1991. Multidisciplinary assessment of pollution in Long Island Sound. Estuaries, 14:299-305.

Krone, C. A., J. E. Stein, U. Varanasi. 1991. Estimation of the levels of aromatic xenobiotic metabolites in tissues of fish by HPLC fluorescence analysis. Chemosphere, 24:497-510.

Nishimoto, M., W. T. Roubal, J. E. Stein, U. Varanasi. 1991. Oxidative DNA damage in tissues of English Sole (Parophrys vetulus) exposed to nitrofurantoin. Chemico-Biological Interactions, 80:317-326.

Stein, J. E., T. Hom, H. R. Sanborn, U. Varanasi. 1991. Effects of exposure to contaminated-sediment extract on the metabolism and disposition of 17β-estradiol in English sole (Parophrys vetulus). Comparative Biochemistry and Physiology, 99C:231-240.

Varanasi, U., J. E. Stein. 1991. Disposition of xenobiotic chemicals and metabolites in marine organisms. Environmental Health Perspectives, 90:93-100.

Waples, R. S. 1991. Genetic interactions between wild and hatchery salmonids: lessons from the Pacific Northwest. Canadian Journal of Fisheries and Aquatic Sciences, (48 (Supplement 1))124-133.

Waples, R. S. 1991. Heterozygosity and life-history variation in bony fishes. Evolution, (45)1275-1280.

Waples, R. S. 1991. Pacific salmon, Oncorhynchus spp., and the definition of "species" under the Endangered Species Act. Marine Fisheries Review, (53(3))11-22.

1990

Graves, J. E., M. J. Curtis, P. A. Oeth, R. S. Waples. 1990. Biochemical genetics of southern California basses of the genus Paralabrax and a method for the specific identification of fresh and ethanol-preserved individual eggs and early larvae. Fishery Bulletin, (88)59-66.

Smouse, P. E., R. S. Waples, J. A. Tworek. 1990. A mixed fishery model for use with incomplete source population data. Canadian Journal of Fisheries and Aquatic Sciences, (47)620-634.

Stein, J. E., W. L. Reichert, M. Nishimoto, U. Varanasi. 1990. Overview of studies on liver carcinogenesis in English sole from Puget Sound, evidence for a xenobiotic chemical etiology II. Biochemical studies. Science of the Total Environment, 94:51-69.

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. 1990. Conservation genetics of Pacific salmon. II. Effective population size and the rate of loss of genetic variability. Journal of Heredity, (81)267-276.

Waples, R. S. 1990. Conservation genetics of Pacific salmon. III. Estimating effective population size. Journal of Heredity, (81)277-289.

Waples, R. S., P. E. Smouse. 1990. Gametic disequilibrium analysis as a means of identifying mixtures of salmon populations. American Fisheries Society Symposium, (7)439-458.

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. 1990. Temporal changes of allele frequency in Pacific salmon populations: implications for mixed-stock fishery analysis. Canadian Journal of Fisheries and Aquatic Sciences, (47)968-976.

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

Varanasi, U., W. L. Reichert, J. E. Stein. 1989. 32P-Postlabeling analysis of DNA adducts in liver of wild English sole (Parophrys vetulus) and winter flounder (Pseudopleuronectes americanus). Cancer Research, 49:1171-1177.

Varanasi, U., W. L. Reichert, B. L. Eberhart, J. E. Stein. 1989. Formation and persistence of benzo(a)pyrene-diolepoxide DNA adducts in liver of English sole (Parophrys vetulus). Chemico-Biological Interactions, 69:203-216.

Waples, R. S. 1989. A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics, (121)379-391.

Waples, R. S. 1989. Further problems with mosquitofish genetics. Copeia, (3)793-795.

Waples, R. S. 1989. Temporal stability of allele frequencies: testing the right hypothesis. Evolution, (43)1236-1251.

1988

Plesha, P. D., J. E. Stein, M. H. Schiewe, B. B. McCain, U. Varanasi. 1988. Toxicity of marine sediments supplemented with mixtures of chlorinated and aromatic hydrocarbons to the infaunal amphipod Rhepoxynius abronius. Marine Environmental Research, 25:85-97.

Stein, J. E., T. Hom, H. R. Sanborn, U. Varanasi. 1988. The metabolism and disposition of 17β-estradiol in English sole exposed to a contaminated sediment extract. Mar. Environmental Research, 24:252-253.

Waples, R. S., J. E. Randall. 1988. A revision of the Hawaiian lizardfishes of the genus Synodus, with descriptions of four new species. Pacific Science, (42)178-213.

Waples, R. S. 1988. Estimation of allele frequencies at isoloci. Genetics, (118)371-384.

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

Malins, D. C., B. B. McCain, D. W. Brown, U. Varanasi, M. M. Krahn, M. S. Myers, S. Chan. 1987. Sediment-associated contaminants and liver diseases in bottom-dwelling fish. Hydrobiologia, 149:67-74.

Stein, J. E., T. Hom, E. Casillas, A. Freidman, U. Varanasi. 1987. Simultaneous exposure of English sole (Parophrys vetulus) to sediment-associated xenobiotics: Part 2 - Chronic exposure to an urban estuarine sediment with added 3H-benzo(a)pyrene and 14C-polychlorinated biphenyls. Marine Environmental Research, 22:123-149.

Varanasi, U., J. E. Stein, M. Nishimoto, W. L. Reichert, T. K. Collier. 1987. Chemical Carcinogenesis in feral fish--uptake, activation and detoxication of organic xenobiotics. Environmental Health Perspectives, 71:155-170.

Waples, R. S. 1987. Sperm storage, multiple insemination, and genetic variability in mosquitofish: a reassessment. Copeia, 1068-1071.

1986

Collier, T. K., J. E. Stein, R. J. Wallace, U. Varanasi. 1986. Xenobiotic metabolizing enzymes in spawning English sole (Parophrys vetulus) exposed to organic-solvent extracts of marine sediments from contaminated and reference areas. Comparative Biochemistry and Physiology, 84C:291-298.

Varanasi, U., M. Nishimoto, W. L. Reichert, B. L. Eberhart. 1986. Comparative Metabolism of Benzo(a)pyrene and Covalent Binding to Hepatic DNA in English Sole, Starry Flounder, and Rat. Cancer Research, 46:3817-3824.

1985

DOGRA, S. C., K. L. Khanduja, R. R. Sharma, T. Hom, U. Varanasi. 1985. Effect of Vitamin A Deficiency on Pulmonary and Hepatic In Vitro Metabolism of Benzo(a)pyrene in Rat. Biochem. International, 11:869-884.

Reichert, W. L., B. L. Eberhart, U. Varanasi. 1985. Exposure of two species of deposit-feeding amphipods to sediment-associated [3H]benzo[a]pyrene: uptake, metabolism and covalent binding to tissue macromolecules. Aquatic Toxicology, 6:45-56.

Stein, J. E., T. Hom, E. Casillas, A. Freidman, U. Varanasi. 1985. Simultaneous Exposure of English sole (Parophrys vetulus) to Sediment-Associated Xenobiotics: Part 2 - Chronic Exposure to a Urban Estuarine Sediment Having Added 3H-Benzo(a)pyrene and 14C-Polychlorinated Biphenyls. Marine Environmental Research, 22:123-149.

Varanasi, U., W. L. Reichert, J. E. Stein, D. W. Brown, H. R. Sanborn. 1985. Bioavailability and biotransformation of aromatic hydrocarbons in benthic organisms exposed to sediment from an urban estuary. Environmental Science & Technology, 19(9):836-841.

1984

Stein, J. E., T. Hom, U. Varanasi. 1984. Simultaneous Exposure of English sole (Parophrys vetulus) to Sediment-Associated Xenobiotics: Part 1 - Uptake and Disposition of 14C-Polychlorinated Biphenyls 3H-Benzo(a)pyrene. Marine Environmental Research, 13:97-119.

Stein, J. E., T. Hom, U. Varanasi. 1984. Uptake and metabolism of sediment-associated xenobiotics by English sole (Parophrys vetulus). Pharmacologist, 26:172.

Varanasi, U., J. E. Stein, M. Nishimoto, T. Hom. 1984. Isolation and characterization of benzo(a)pyrene metabolites formed in vivo by juvenile and adult English sole. Marine Environmental Research, 14:439-441.

1982

Varanasi, U., M. Nishimoto, W. L. Reichert, J. E. Stein. 1982. Metabolism and subsequent covalent binding of benzo(a)pyrene to macromolecules in gonads and liver of ripe English sole (Parophrys vetulus). Xenobiotica, 12:417-425.

1981

Varanasi, U., J. E. Stein, T. Hom. 1981. Covalent binding of benzo(a)pyrene to DNA in fish liver. Biochemical and Biophysical Research Communications, 103:780-787.

1980

Varanasi, U. 1980. Hydrocarbon metabolism in flatfish. Coastal Oceanography and Climatology News, 2(2):17-18.

Varanasi, U., D. J. Gmur. 1980. Metabolic activation and covalent binding of benzo(a)pyrene to deoxyribonucleic acid catalyzed by liver enzymes of marine fish. Biochem. Pharm, 29:753-761.

1978

Varanasi, U., P. Treseler, D. J. Gmur. 1978. Naphthalene metabolism in Pleuronectidae and characterization of individual metabolites in the bile. Fed. Proc, 37(6):1473.

1975

Varanasi, U., H. Feldman, D. C. Malins. 1975. Molecular basis for the formation of a lipid sound lens in echolocating cetaceans. Nature, 255:340-243.

1974

Varanasi, U., D. C. Malins. 1974. The structure of phospholipids and triacylglycerols containing long-chain iso acids in the porpoise (Tursiops gilli). Biochemica et Biophysica Acta, 348:55-62.

Book

2007

Waples, R. S. 2007. Captive breeding and the evolutionarily significant unit. Encyclopedia of Biodiversity Online (http://www.sciencedirect.com/science/referenceworks/9780122268656).

1999

Field, L. J., J. A. Fall, T. S. Nighswander, N. Peacock, U. Varanasi. (Eds.) 1999. Evaluating and communicating subsistence seafood safety in a cross-cultural context: lessons learned from the Exxon Valdez oil spill. Society of Environmental Toxicology and Chemistry (SETAC), Pensacola, FL, 338 p.

Reichert, W. L., B. L. French, J. E. Stein. 1999. Protocols for assaying levels of large hydrophobic DNA adducts in fish by 32P-postlabeling. Techniques in Marine Environmental Sciences no. 25. International Council for the Exploration of the Sea, Copenhagen, Denmark, 45 p.

1989

Varanasi, U. (Ed.) 1989. Metabolism of Polycyclic Aromatic Hydrocarbons in the Aquatic Environment. CRC Press, Inc., Boca Raton, FL, 341 p.

Section

2009

Waples, R. S. and K. A. Naish. 2009. Genetic and evolutionary considerations in fishery management: Research needs for the future. Pp. 427-451 In: The future of fisheries science in North America. R. J. Beamish and B. J. Rothschild, editors. Springer, Dordrechtscience in North America. R. Beamish and B. Rothschild, editors. Springer.

2007

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

Dawson, M., R. S. Waples, and G. Bernardi. 2006. Phylogeography. pp. 26-54 in The Ecology of Marine Fishes: California and Adjacent Waters. L. G. Allen, D. J. Pondella II, and M. H. Horn, eds. Univ. Calif. Press, Berkeley.

Geffen, E., G. Luikart, and R. S. Waples. 2006. Impacts of modern molecular genetic techniques on conservation biology. pp. 46-63 in Key Topics in Conservation Biology. D. W. Macdonald and K. Service, eds. Blackwell, London.

Naeem, S., R. S. Waples, and C. Moritz. 2006. Preserving nature. Pp. 70-79 In: J. M. Scott, D. D. Goble, and F. W. Davis, editors. The Endangered Species Act at Thirty: Conserving Biodiversity in Human-Dominated Landscapes. Island Press, Washington, D.C.

Waples, R. S. 2006. Distinct Population Segments. Pp. 127-149 In: J. M. Scott, D. D. Goble, and F. W. Davis, editors. The Endangered Species Act at Thirty: Conserving Biodiversity in Human-Dominated Landscapes. Island Press, Washington, D.C.

2005

Methot, R. D., I. J. Stewart. 2005. Status of the U.S. canary rockfish resource in 2005. In Status of the Pacific Coast Groundfish Fishery through 2005, Stock Assessment and Fishery Evaluation.

2004

Helser, T. E., R. D. Methot, G. W. Fleischer. 2004. Stock Assessment of Pacific Hake (Whiting) in U.S. and Canadian Waters in 2003. In Pacific Fishery Management Council, Appendix: Status of the Pacific Coast Groundfish Fishery Through 2004 and Stock Assessment and Fishery Evaluation. Pacific Fishery Management Council, 2130 SW Fifth Avenue, Suite 224, Portland, OR 97201.

Waples, R. S., J. Drake. 2004. Risk-benefit considerations for marine stock enhancement: a Pacific salmon perspective. Pages 260-306 in Stock Enhancement and Sea Ranching: Developments, Pitfalls and Opportunities. Blackwell, Oxford.

Waples, R. S. 2004. Salmonid insights into effective population size. Pages 295-314 in Hendry, A. P., S. C. Stearns. (Eds.) Evolution Illuminated. Salmon and their relatives. Oxford University Press.

2003

Stein, J. E., K. L. Tilbury, J. P. Meador, J. Gorzelany, G. Worthy, M. M. Krahn. 2003. Ecotoxicological Investigations of Bottlenose Dolphin (Tursiops truncatus) Strandings: Accumulation of Persistent Organic Chemicals and Metals. Pages 458-488 in Vos, J. G., e. al. (Eds.) Toxicology of marine mammals. Taylor & Francis, New York.

2002

Waples, R. S. 2002. Definition and estimation of effective population size in the conservation of endangered species. Pages 147-168 in Beissinger, S. R., D. R. McCullough. (Eds.) Population Viability Analysis. University of Chicago Press, Chicago, IL.

2001

Johnson, L. L., M. R. Arkoosh, T. K. Collier, M. M. Krahn, J. P. Meador, M. S. Myers, W. L. Reichert, J. E. Stein. 2001. The effects of Polycyclic aromatic hydrocarbons in fish from Puget Sound Washington. In Di Giulio, R. T., D. Hinton. (Eds.) The Toxicology of Fishes. Taylor & Francis, New York, London.

Schirripa, M. J., R. D. Methot. 2001. Status of the sablefish resource off the U. S. Pacific coast in 2001. In Pacific Fishery Management Council 2001. Appendix: Status of the Pacific coast groundfish fishery through 2001 and recommended acceptable biological catches for 2002: Stock assessment and fishery evaluation. Pacific Fishery Management Council, Portland, Oregon.

2000

Grant, W. S., R. S. Waples. 2000. Spatial and temporal scales of genetic variability in marine and anadromous species: Implications for fisheries oceanography. Pages 61-93 in Parsons, T., P. Harrison. (Eds.) Fisheries Oceanography: a science for the new millennium. Blackwell Science, Oxford, UK.

Methot, R. D., J. R. Wallace, C. W. West. 2000. Introducing a new trawl survey for West Coast slope groundfish. In Western Groundfish Conference, Sitka, Alaska. ICES C. M. 2000/W:11 15 pp.

Piner, R. K., K. M. Schirripa, T. L. Builder, R. D. Methot. 2000. Bank rockfish stock assessment for the Eureka and Monterey INPFC areas. PFMC, 2000. Status of the Pacific Coast groundfish fishery through 1999 and recommended biological catches for 2001: Stock assessment and fishery evaluation. In Status of the Pacific Coast groundfish fishery through 1999 and recommended biological catches for 2001: Stock assessment and fishery evaluation. Pacific Fishery Management Council.

Rogers, J. B., R. D. Methot, T. L. Builder, K. Piner, M. Wilkins. 2000. Status of the Darkblotched Rockfish (Sebastes crameri) Resource in 2000. In Status of the Pacific Coast Groundfish Fishery Through 1999 and Recommended Biological Catches for 2001: Stock Assessment and Fishery Evaluation. Pacific Fishery Management Council 2130 SW Fifth Avenue, Suite 224, Portland, Oregon 97201.

Rogers, J. B., R. D. Methot, T. L. Builder, M. Wilkins. 2000. Status of the Pacific Coast groundfish fishery through 1999 and recommended biological catches for 2001: Stock assessment and fishery evaluation. In Pacific Fishery Management Council 2130 SW Fifth Avenue, Suite 224, Portland, OR 97201.

1999

Brown, D. W., D. G. Burrows, C. A. Sloan, R. W. Pearce, S. M. Pierce, J. L. Bolton, K. L. Tilbury, K. L. Dana, M. M. Krahn, S. Chan, U. Varanasi. 1999. Exposure of Alaskan subsistence shellfish to oil spilled from the Exxon Valdez. Pages 135-167 in Field, L. J. (Ed.) Evaluating and communicating subsistence seafood safety in a cross-cultural context: lessons learned from the Exxon Valdez oil spill. SETAC Press, Pensacola, FL.

Fall, J. A., L. J. Field, T. S. Nighswander, J. E. Stein, M. Bolger. 1999. Overview of lessons learned from the Exxon Valdez oil spill: a 10-year retrospective. Pages 237-269 in Field, L. J., e. al. (Eds.) Evaluating and communicating subsistence seafood safety in a cross-cultural context: lessons learned from the Exxon Valdez oil spill. SETAC Press, Pensacola, FL.

Hom, T., D. W. Brown, J. E. Stein, U. Varanasi. 1999. Measuring the exposure of subsistence fish and marine mammal species to aromatic compounds following the Exxon Valdez oil spill. Pages 169-194 in Field, L. J. (Ed.) Evaluating and communicating subsistence seafood safety in a cross-cultural context: lessons learned from the Exxon Valdez oil spill. SETAC Press, Pensacola, FL.

1998

Livingston, P. A., R. D. Methot. 1998. Incorporation of predation and cannibalism into assessment model. Pages 663-678 in Fishery Stock Assessment Models, Lowell Wakefield Fisheries Symposium 15. American Fisheries Society.

Rogers, J. B., T. L. Builder, P. R. Crone, J. K. Brodziak, R. D. Methot, R. J. Conser. 1998. Status of the shortspine thornyhead (Sebastolobus alascanus) resource in 1998. In Pacific Fishery Management Council. Appendix: Status of the Pacific coast groundfish fishery through 1998 and Recommended Acceptable Biological Catches for 1999. PFMC, 2130 SW Fifth Avenue, Suite 224, Portland, Oregon 97201.

1997

Casillas, E., B. B. McCain, M. R. Arkoosh, J. E. Stein, U. Varanasi. 1997. Estuarine pollution and juvenile salmon health: Potential impact on survival. Pages 169-178 in Estuarine and Ocean Survival of Northeastern Pacific Salmon: Proceedings of the workshop, Newport, OR. , U. S. A. Emmett, R. L. , M. H. Schiewe. (Eds. ) 1997. Estuarine and ocean survival of Northeastern Pacific salmon: Proceedings of the workshop. NOAA Technical Memorandum NMFS-NWFSC-29.

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.

Stein, J. E., L. L. Johnson, J. T. Landahl, T. K. Collier, E. Casillas, U. Varanasi. 1997. Approaches for determining effects of pollution on fish populations in Puget Sound. Pages 121-126 in Stephan, C. D., K. Beidler. (Eds.) Philadelphia, PA, Management of Atlantic Coastal Marine Fish Habitat: Proceedings of a Workshop for Habitat Managers.

1996

Allendorf, F. W., R. S. Waples. 1996. Conservation and genetics of salmonid fishes. Pages 238-280 in Avise, J. C., J. L. Hamrick. (Eds.) Conservation genetics: Case histories from nature. Chapman and Hall, New York.

Brown, D. W., D. G. Burrows, C. A. Sloan, R. W. Pearce, S. M. Pierce, J. L. Bolton, K. L. Tilbury, K. L. Dana, S. Chan, U. Varanasi. 1996. Survey of Alaskan Subsistence Invertebrate Seafoods Collected in 1989-1991 to Determine Exposure to Oil Spilled from the Exxon Valdez. Pages 844-855 in Rice, S. D., R. B. Spies, D. A. Wolfe, B. A. Wright. (Eds.) Proceedings of the Exxon Valdez Oil Spill Symposium. American Fisheries Society Symposium.

Hom, T., U. Varanasi, J. E. Stein, C. A. Sloan, K. L. Tilbury, S. Chan. 1996. Assessment of the exposure of subsistence fish to aromatic compounds following the Exxon Valdez Oil Spill. Pages 856-866 in Rice, S. D., R. B. Spies, D. A. Wolfe, B. A. Wright. (Eds.) Proceedings of the Exxon Valdez Oil Spill Symposium. American Fisheries Society Symposium.

1995

Balch, G. C., C. D. Metcalfe, W. L. Reichert, J. E. Stein. 1995. Biomarkers of exposure of brown bullheads to contaminants in Hamilton Harbour, Ontario. Pages 249-273 in Butterworth, F. M. (Ed.) Biomonitors and biomarkers as indicators of environmental change. Plenum Press, NY, NY.

Casillas, E., M. R. Arkoosh, E. R. Clemons, T. Hom, D. Misitano, T. K. Collier, J. E. Stein, U. Varanasi. 1995. Chemical contaminant exposure and physiological effects in outmigrant juvenile Chinook salmon from urban estuaries of Puget Sound, Washington. Pages 86-102 in Keefe, M. (Ed.) Proceedings from the 1994 Northwest Pacific Chinook and Coho Workshop: Salmon Ecosystem Restoration: Myth and Reality.

Casillas, E., M. R. Arkoosh, E. R. Clemons, T. Hom, D. Misitano, T. K. Collier, J. E. Stein, U. Varanasi. 1995. Chemical contaminant exposure and physiological effects in outmigrant juvenile chinook salmon from urban estuaries of Puget Sound, Washington. Pages 657-665 in Proceedings Puget Sound Research '95.

Sol, S. Y., L. L. Johnson, T. K. Collier, M. M. Krahn, U. Varanasi. 1995. Contaminant effects on reproduction in North Pacific flatfish. Pages 547-560 in Proceedings of the International Pacific Flatfish Conference, Anchorage, AK 1994.

Sol, S. Y., L. L. Johnson, T. K. Collier, M. M. Krahn, U. Varanasi. 1995. Contaminant effects on reproductive output in North Pacific flatfish. Pages 547-560 in Proc. International Symposium on North Pacific Flatfish. Alaska Sea Grant College Program Report 95-04, Alaska Fairbanks.

Waples, R. S. 1995. Genetic effects of stock transfers of fish. Pages 51-69 in Philipp, D., e. al. (Eds.) Protection of aquatic biodiversity. Proceedings of the World Fisheries Congress, Theme 3. Oxford and IBH Publishing Co. Pvt. Ltd, New Delhi.

1994

Arkoosh, M. R., J. E. Stein, E. Casillas. 1994. Immunotoxicology of an anadromous fish: Field and laboratory studies of B-cell mediated immunity. Pages 33-48 in Stolen, J. S., T. C. Fletcher. (Eds.) Modulators of fish immune responses. Models for Environmental Toxicology/Biomarkers. Immunostimulators. Vol. 1. SOS Publications, Fair Haven, NY.

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.

Reichert, W. L., J. E. Stein, U. Varanasi. 1994. DNA adducts in fish as molecular dosimeters of exposure to genotoxic compounds. Pages 107-112 in Application of DNA technology to the management of Pacific salmon. NOAA Tech. Memo. NMFS-NWFSC-17.

1993

Casillas, E., J. E. Stein, M. R. Arkoosh, D. W. Brown, D. Misitano, S. Chan, U. Varanasi. 1993. Effects of estuarine habitat quality on juvenile salmon: I. Chemical contaminant exposure, and II. Altered growth and immune function. Pages 548-562 in Coastal Zone-93 Proceedings, The Eight Symposium on Coastal and Ocean Management, New Orleans, LA.

Krahn, M. M., G. M. Ylitalo, J. Buzitis, C. A. Krone, J. E. Stein, S. Chan, U. Varanasi. 1993. Screening methods for assessing damage to natural resources following the Exxon Valdez oil spill. Pages 872-3 in Proceedings 1993 International Oil Spill Conference.

Krahn, M. M., G. M. Ylitalo, J. Buzitis, J. L. Bolton, C. A. Wigren, S. Chan, U. Varanasi. 1993. Survey of oil contamination in marine fish and sediments following the ROPME Sea oil spill. In Proceedings of the Scientific Workshop on Results of the R/V Mt. Mitchell Cruise, Fisheries/Plankton Ecology Session, Kuwait City, Kuwait.

Nishimoto, M., B. L. Eberhart, H. R. Sanborn, J. E. Stein, U. Varanasi. 1993. Hepatic glutathione in English sole (Pleuronectes vetulus): Response to complex mixtures of xenobiotics. In Proceedings of the 7th PRIMO, Goteborg, Sweden.

Stein, J. E., T. Hom, C. A. Wigren, K. L. Tilbury, S. Chan, U. Varanasi. 1993. Assessment of exposure of subsistence fish species to aromatic compounds following the Exxon Valdez oil spill. Pages 206-209 in Proceedings of the Exxon Valdez Oil Spill Symposium.

Varanasi, U., J. E. Stein, K. L. Tilbury, D. W. Brown, J. P. Meador, M. M. Krahn, S. Chan. 1993. Contaminant monitoring for NMFS Marine Mammal Health and Stranding Response Program. Pages 2517-2530 in Coastal Zone 93 Proceedings of the Eighth Symposium on Coastal and Ocean Management, New Orleans, LA. Vol. 3.

Varanasi, U., B. B. McCain, J. E. Stein, S. Chan. 1993. Effects of coastal pollution on living marine resources. Pages 271-286 in Transactions of the 58th North American Wildlife and Natural Resources Conference, Washington, DC.

1992

Eberhart, B. L., M. Nishimoto, H. R. Sanborn, J. E. Stein. 1992. Hepatic glutathione levels in flatfish exposed to chemical contaminants. In Proceedings of the 1st annual meeting of the Pacific Northwest Chapter of the Society of Environmental Toxicology and Chemistry, Bellingham, Washington.

Shugart, L., J. Bickham, G. Jackim, W. Ridley, J. E. Stein, S. Steinert, R. J. Huggett, R. A. Kimerle, P. M. Mehrle Jr. 1992. DNA Alterations. Pages 125 - 153 in Huggett, R. J., R. A. Kimerle, P. M. Mehrle Jr., H. L. Bergman. (Eds.) Biomarkers. Biochemical, Physiological, and Histological Markers of Anthropogenic Stress. Lewis Publishers, Chelsea, MI.

Varanasi, U. 1992. Chemical Contaminants and Their Effects on Living Marine Resources. Proceedings of A Symposium on Conservation of Coastal Fish Habitat. Pages 59-71 in Stroud, R. H. (Ed.) Stemming the Tide of Coastal Fish Habitat Loss. National Coalition for Marine Conservation, Inc., Savannah, GA.

Varanasi, U., J. E. Stein, W. L. Reichert, K. L. Tilbury, S. Chan. 1992. Chlorinated and Aromatic Hydrocarbons in Bottom Sediments, Fish and Marine Mammals in US Coastal Waters: Laboratory and Field Studies of Metabolism and Accumulation. Pages 83-115 in Walker, C. H., D. R. Livingstone. (Eds.) Persistent Pollutants in the Marine Environment. Pergamon Press, New York, NY.

Varanasi, U., J. E. Stein, L. L. Johnson, T. K. Collier, E. Casillas, M. S. Myers. 1992. Evaluation of bioindicators of contaminant exposure and effects in coastal ecosystems. Pages 461 - 498 in McKenzie, D. H., D. E. Hyatt, V. J. McDonald. (Eds.) Proceedings International Symposium Ecological Indicators. Elseveir Applied Science, Barking, England.

1991

Brown, D. W., M. M. Krahn, D. G. Burrows, T. K. Collier, C. A. Wigren, G. M. Ylitalo, S. Chan, U. Varanasi. 1991. Metabolites of Aromatic Compounds in Bile of Fish Exposed to Weathered Crude Oil. In Proceedings of the 39th ASMS Conference on Mass Spectrometry and Allied Topics.

Eberhart, B. L., M. Nishimoto, H. R. Sanborn, J. E. Stein, U. Varanasi. 1991. Metabolism of xenobiotics by three species of crustacea. In Proceedings of the 12th annual meeting of the Society of Environmental Toxicology and Chemistry, Nov. 3-7.

Waples, R. S. 1991. Genetic methods for estimating the effective size of cetacean populations. Pages 279-300 in Report of the International Whaling Commission.

1990

Waples, R. S. 1990. Stock structure and gene conservation in Columbia River spring chinook salmon. Pages 14-21 in Status and Future of Spring Chinook Salmon in the Columbia River Basin--Conservation and Enhancement. NOAA Technical Memorandum NMFS F/NWC-187.

1989

Collier, T. K., B. L. Eberhart, J. E. Stein, U. Varanasi. 1989. Aryl hydrocarbon hydroxylase-A. Pages 608-610 in Proceed. Oceans '89.

Johnson, L. L., E. Casillas, D. Misitano, T. K. Collier, J. E. Stein, B. B. McCain, U. Varanasi. 1989. Bioindicators of reproductive impairment in female English sole (Parophrys vetulus) exposed to environmental contaminants. Pages 391-396 in Proceed. Oceans '89.

Stein, J. E., W. L. Reichert, B. L. Eberhart, U. Varanasi. 1989. 32P-Postlabeling of DNA: A sensitive method for assessing environmentally induced genotoxicity. Pages 385-390 in Proceed. Oceans '89.

Varanasi, U., J. E. Stein, M. Nishimoto. 1989. Biotransformation and disposition of polycyclic aromatic hydrocarbons in fish. Pages 93-149 in Varanasi, U. (Ed.) Metabolism of Polycyclic Aromatic Hydrocarbons in the Aquatic Environment. CRC Press, Boca Raton, FL.

1988

Schiewe, M. H., J. T. Landahl, M. S. Myers, P. D. Plesha, F. J. Jacques, J. E. Stein, B. B. McCain, D. D. Weber, S. Chan, U. Varanasi. 1988. Relating field and laboratory studies: Cause-and-effect research. Pages 577-584 in Proceedings of the Ist Annual Meeting on Puget Sound Research. Puget Sound Water Quality Authority, 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.

1983

Stein, J. E., T. Hom, U. Varanasi. 1983. Tissue disposition of 3H-BaP and 14C-Aroclor 1254 in English sole. Pages 190-191 in Proc. 185th Natl. Meet. Am. Chem. Soc. Div. Environ. Chem.

Varanasi, U., M. Nishimoto, J. Stover. 1983. Analysis of biliary conjugates and hepatic DNA binding in benzo(a)pyrene-exposed English sole. Pages 1315-1328 in Cooke, M. C., A. J. Dennis. (Eds.) Polynuclear Aromatic Hydrocarbons: Mechanisms,Methods and Metabolism. Battelle Press, OH.

Varanasi, U., J. E. Stein, M. Nishimoto, T. Hom. 1983. Benzo(a)pyrene Metabolites in Liver, Muscle, Gonads and Bile of Adult English sole (Parophrys vetulus). Pages 1221-1234 in Cook, M. W., A. J. Dennis. (Eds.) Proceedings of Seventh International Symposium on Formation, Metabolism, and Measurement of Polynuclear Aromatic Hydrocarbons. Battelle Press, Columbus, Ohio.

1981

Varanasi, U., D. J. Gmur, J. E. Stein. 1981. Hepatic metabolism and interaction of benzo(a)pyrene with cellular macromolecules in pleuronectid fish. Pages 21:212-213 in Proc. 182nd Natl. Meet. Am. Chem. Soc. Div. Environ. Chem.

1977

Varanasi, U., D. C. Malins. 1977. Metabolism of petroleum hydrocarbons: Accumulation and biotransformations in marine organisms. Pages 175-270 in Effects of Petroleum on Arctic and Subarctic Marine Environments and Organisms. Academic Press, New York.

Contract Report

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.

1993

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.

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.

Technical Memorandum

2007

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.

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

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.

2004

DeMaster, D. P., R. P. Angliss, J. Cochrane, P. M. Mace, R. Merrick, M. Miller, S. Rumsey, B. L. Taylor, G. G. Thompson, R. S. Waples. 2004. Recommendations to NOAA Fisheries: ESA Listing Criteria by the Quantitative Working Group, 10 June 2004. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-F/SPO-67, 85 p.

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.

Waples, R. S. (Ed.) 2004. Report of the working group on killer whales as a case study. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-SWFSC-363, 94 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.

2001

Meador, J. P., T. K. Collier, J. E. Stein. 2001. Determination of a tissue and sediment threshold for tributyltin (TBT) to protect prey species of juvenile salmonids listed under the Endangered Species Act. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-52, 21 p.

Meador, J. P., T. K. Collier, J. E. Stein. 2001. Use of tissue and sediment-based threshold concentrations of polychlorinated biphenyls (PCBs) to protect juvenile salmonids listed under the U.S. Endangered Species Act. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-48, 40 p.

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.

Turk, T. A., T. L. Builder, C. W. West, D. J. Kamikawa, J. R. Wallace, R. D. Methot, A. R. Bailey, K. L. Bosley, A. J. Cook, E. L. Fruh, B. H. Horness, K. Piner, H. R. Sanborn, W. W. Wakefield. 2001. The 1998 Northwest Fisheries Science Center Pacific West Coast Upper Continental Slope Trawl Survey of Groundfish Resources off Washington, Oregon, and California: Estimates of Distribution, Abundance, and Length Composition. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-50, 122 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.

McCain, B. B., D. W. Brown, S. Chan, J. T. Landahl, W. D. MacLeod Jr., M. M. Krahn, C. A. Sloan, K. L. Tilbury, S. M. Pierce, D. G. Burrows, U. Varanasi. 2000. National benthic surveillance project: Pacific Coast. Organic chemical contaminants, cycles I to VII (1984-90). U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-40, 121 p. (PDF | HTML)

Methot, R. D. 2000. Technical description of the stock synthesis assessment program. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-43, 46 p. (PDF | HTML)

1998

Collier, T. K., L. L. Johnson, M. S. Myers, C. M. Stehr, M. M. Krahn, J. E. Stein. 1998. Fish Injury in the Hylebos Waterway of Commencement Bay, Washington. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-36, 576 p.

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

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

Busby, P. J., T. C. Wainwright, R. S. Waples. 1994. Status review for Klamath Mountains Province steelhead. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-19, 130 p.

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.

Meador, J. P., R. C. Clark Jr., P. A. Robisch, D. W. Ernest, J. T. Landahl, U. Varanasi, S. Chan, B. B. McCain. 1994. National Benthic Surveillance Project: Pacific Coast. Analysis of elements in sediment and tissue Cycles I to V (1984-88). U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-16, 206 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.

Myers, M. S., C. M. Stehr, O. P. Olson, L. L. Johnson, B. B. McCain, S. Chan, U. Varanasi. 1993. National Status and Trends Program, National Benthic Surveillance Project: Pacific Coast, Fish histopathology and relationships between toxicopathic lesions and exposure to chemical contaminants for cycles I to V (1984-88). U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-6, 160 p.

Varanasi, U., J. E. Stein, K. L. Tilbury, J. P. Meador, C. A. Sloan, D. W. Brown, J. Calambokidis, S. Chan. 1993. Chemical contaminants in gray whales (Eschrichtius robustus) stranded in Alaska, Washington, and California, U.S.A. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-11, 115 p.

Varanasi, U., E. Casillas, M. R. Arkoosh, T. Hom, D. Misitano, D. W. Brown, S. Chan, T. K. Collier, B. B. McCain, J. E. Stein. 1993. Contaminant exposure and associated biological effects in juvenile Chinook salmon (Oncorhynchus tshawytscha) from urban and nonurban estuaries of Puget Sound, WA. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-8, 112 p.

Varanasi, U., D. W. Brown, T. Hom, D. G. Burrows, C. A. Sloan, L. J. Field, J. E. Stein, K. L. Tilbury, B. B. McCain, S. Chan. 1993. Vol. I. Survey of Alaskan Subsistence fish, marine mammal, and invertebrate samples collected 1989-91 for exposure to oil spilled from the Exxon Valdez. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-12, 110 p.

Varanasi, U., D. W. Brown, T. Hom, D. G. Burrows, C. A. Sloan, L. J. Field, J. E. Stein, K. L. Tilbury, B. B. McCain, S. Chan. 1993. Vol. II. Supplemental information concerning a survey of Alaskan subsistence fish, marine mammal, and invertebrate samples collected 1989-91 for exposure to oil spilled from the Exxon Valdez. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-13, 173 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.

Johnson, L. L., J. E. Stein, T. K. Collier, E. Casillas, B. B. McCain, U. Varanasi. 1992. Bioindicators of contaminant exposure, liver pathology and reproductive development in prespawning female winter flounder (Pleuronectes americanus) from urban and nonurban estuaries on the Northeast Atlantic coast. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-01, 76 p.

Johnson, L. L., C. M. Stehr, O. P. Olson, M. S. Myers, S. M. Pierce, B. B. McCain, U. Varanasi. 1992. Fish Histopathology and Relationships Between Lesions and Chemical Contaminants (1987-89). U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-4.

Stein, J. E., K. L. Tilbury, D. W. Brown, C. A. Wigren, J. P. Meador, P. A. Robisch, S. Chan, U. Varanasi. 1992. Intra-organ Distribution of Chemical Contaminants in Tissues of Harbor Porpoise (Phocoena phocoena) from the Northwest Atlantic. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-3, 76 p.

1991

Matthews, G. M., R. S. Waples. 1991. Status Review for Snake River Spring and Summer Chinook Salmon. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-F/NWC-200.

Waples, R. S. 1991. Definition of "Species" Under the Endangered Species Act: Application to Pacific Salmon. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-F/NWC-194.

Waples, R. S., R. P. Jones Jr., B. R. Beckman, G. A. Swan. 1991. Status Review for Snake River Fall Chinook Salmon. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-F/NWC-201.

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

Varanasi, U., S. Chan, W. D. MacLeod Jr., J. E. Stein, D. W. Brown, D. G. Burrows, K. L. Tilbury, J. T. Landahl, C. A. Wigren, T. Hom, S. M. Pierce. 1990. Survey of Subsistence Fish and Shellfish for Exposure to Oil Spilled from the Exxon Valdez First Year: 1989. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-F/NWC-191, 151 p.

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.

Waples, R.S., and A. R. Hoelzel. 2009. Under Development: Guidelines For The Analysis Of Population Genetic Data Used In An IWC Management Context. Paper SC/61/SD1 presented to the IWC Scientific Committee, June 2009, Madeira. 7pp.

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.

2004

Methot, R. D., C. Poset, G. J. Kobylinski. 2004. California pilot of EFCL Electronic Fish Ticketing: a case study and preliminary systems analysis. Northwest Fisheries Science Center, Seattle, WA, 49 p.

2002

Waples, R. S. 2002. Life history diversity, marine survival, and viability of Pacific salmon. N. Pac. Anadr. Fish Comm. Tech. Rept , 39-41 p.

1998

Krahn, M. M., J. Buzitis, G. M. Ylitalo, C. A. Sloan, D. W. Brown, D. G. Burrows, J. L. Bolton, T. K. Collier, J. E. Stein. 1998. Analyses for PCBs and PCTs in Sediment from the Duwamish River, Seattle, WA. Report to National Oceanic & Atmospheric Administration's Northwest Damage Assessment Center

Krahn, M. M., J. Buzitis, G. M. Ylitalo, C. A. Sloan, D. W. Brown, D. T. Boyd, J. L. Bolton, J. E. Stein. 1998. Comparison of PCB Concentrations in Split Samples of Sediment from the Duwamish River, Seattle, WA. Report to National Oceanic & Atmospheric Administration's Northwest Damage Assessment Center

1997

Casillas, E., B. L. Eberhart, F. Sommers, T. K. Collier, M. M. Krahn, J. E. Stein. 1997. Effects of Chemical Contaminants from the Hylebos Waterway on Growth of Juvenile Chinook Salmon: Hylebos Interpretive Report.

Collier, T. K., L. L. Johnson, T. Hom, M. M. Krahn, J. E. Stein. 1997. Exposure of winter flounder (Pleuronectes americanus) following the North Cape oil spill, and estimation of potential for biological injury. Summary Report submitted to Salt Pond Technical Working Group.

1995

Varanasi, U., T. K. Collier, C. A. Krone, M. M. Krahn, L. L. Johnson, M. S. Myers, S. Chan. 1995. Assessment of oil spill impacts on fisheries resources: Measurement of hydrocarbons and their metabolites, and their effects, in important species, Exxon Valdez Oil Spill State/Federal Natural Resource Damage Assessment Final Report (Subtidal 7). NMFS, NOAA, Seattle, Washington.

1994

Myers, M. S., L. L. Johnson, O. P. Olson, C. M. Stehr, D. P. Lomax, B. H. Horness, B. F. Anulacion, M. L. Willis, T. K. Collier, B. B. McCain, J. E. Stein, U. Varanasi. 1994. Toxicopathic hepatic lesions and other biomarkers of exposure to chemical contaminants in marine bottom fish species from the northeast and Pacific Coast. Report to U.S.A. Baltic Marine Biologists Publication No. 15, 81-98 p.

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