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Publications

Total pubs: 76

Nielsen, J. L., G. T. Ruggerone, and C. E. Zimmerman. 2013. Adaptive strategies and life history characteristics in a warming climate: salmon in the Arctic? . Environmental Biology of Fishes 96(10-11):1187-1226. doi:10.1007/s10641-012-0082-6 [Details] [Full Publication]

Zimmerman, C. E., A. M. Ramey, S. M. Turner, F. J. Mueter, S. M. Murphy, and J. L. Nielsen. 2013. Genetics, recruitment, and migration patterns of Arctic Cisco (Coregonus autumnalis) in the Colville River, Alaska and Mackenzie River, Canada. Polar Biology 36(11):1543-1555. doi:10.1007/s00300-013-1372-y [Details] [Full Publication]

Nielsen, J. L., S. M. Turner, and C. E. Zimmerman. 2011. Electronic tags and genetics explore variation in migrating steelhead kelts, Ninilchik River, Alaska. Canadian Journal of Fisheries and Aquatic Sciences 68:1-16. doi:10.1139/F10-124 [Details] [Full Publication]

Nielsen, J. L., S. L. Graziano, and A. C. Seitz. 2010. Fine-scale population genetic structure in Alaskan Pacific halibut Hippoglossus stenolepis. Conservation Genetics 11(3):999-1012. doi:10.1007/s10592-009-9943-8 [Details] [Full Publication]

Nielsen, J. L., S. L. Graziano, and A. C. Seitz. 2009. Fine-scale population genetic structure in Alaskan Pacific halibut (Hippoglossus stenolepis). Conservation Genetics. [Details]

Ruggerone, G. T. and J. L. Nielsen. 2009. A review of growth and survival of salmon at sea in response to competition and climate change. American Fisheries Society Symposium 70. [Details]

Ruggerone, G. T., J. L. Nielsen, and B. A. Agler. 2009. Climate, growth and population dynamics of Yukon River Chinook salmon. North Pacific Anadromous Fish Commission Bulletin Technical Report 5. [Details]

Ruggerone, G. T., J. L. Nielsen, and B. A. Agler. 2009. Linking marine and freshwater growth in western Alaska Chinook salmon, Oncorhynchus tshawytscha. Journal of Fish Biology. [Details]

Nielsen, J. L., H. Arrizabalaga, N. Fragoso, A. Hobday, M. Lutcavage, and J. Sibert. 2009. Tagging and tracking of marine animals with electronic devices. Reviews: Methods and Technologies in Fish Biology and Fisheries 9. [Details]

Nielsen, J. L., A. Byrne, S. L. Graziano, and C. C. Kozfkay. 2009. Steelhead genetic diversity at multiple spatial scales in a managed basin: Snake River, Idaho. North American Journal of Fisheries Management 29:680-701. [Details]

Nielsen, J. L. and G. T. Ruggerone. 2008. Climate change and a dynamic ocean carrying capacity: Growth and survival of Pacific salmon at sea. American Fisheries Society Symposium 71. [Details]

Nielsen, J. L., C. E. Zimmerman, A. M. Ramey, S. L. Graziano, and V. R. Von Biela. 2008. Testing molecular and otolith tools to investigate population of origin and migration in Arctic cisco found in the Colville River, Alaska. Technical Report submitted to MMS OCS Program, 51 p. [Details]

Ramey, A. M., S. L. Graziano, and J. L. Nielsen. 2008. Isolation and characterization of microsatellite loci from the Arctic cisco Coregonus autumnalis. Molecular Ecology Resources 8(2):357-359. doi:10.1111/j.1471-8286.2007.01955.x [Details] [Full Publication]

Farley, E. V., J. M. Murphy, M. D. Adkison, L. B. Eisner, J. H. Helle, J. H. Moss, and J. L. Nielsen. 2007. Early marine growth in relation to marine-stage survival rates for Alaska sockeye salmon (Oncorhynchus nerka). Fishery Bulletin 105(1):121-130. [Details]

Verspoor, E., L. Stradmeyer, and J. L. Nielsen. 2007. Atlantic Salmon: Genetics, Conservation and Management. Blackwell Publishing, 500 p. , Oxford, UK. [Details]

Nielsen, J. L. 2007. Atlantic salmon genetics: Past, present, and what's in the future?. Pages 470-481 in E. Vespoor, L. Stradmeyer, and J. L. Nielsen, (eds.), Atlantic Salmon: Genetics, Conservation and Management. Blackwell Science, Ltd., Oxford, UK. [Details]

Williams, I.Williams, J., G. H. Reeves, S. L. Graziano, J. L. Nielsen. 2007. Genetic investigation of natural hybridization between rainbow and coastal cutthroat trout in the Copper River Delta, Alaska. Transactions of the American Fisheries Society 136:926-942. [Details]

Pavey, S. A., T. R. Hamon, and J. L. Nielsen. 2007. Revisiting evolutionary dead ends in sockeye salmon (Oncorhynchus nerka) life history. Canadian Journal of Fisheries and Aquatic Sciences 64:1199-1208. [Details]

Boughton, D. A., P. B. Adams, E. Anderson, C. Fusaro, E. Keller, E. Kelley, L. Lentsch, J. L. Nielsen, K. Perry, H. Regan, J. Smith, C. Swift, L. Thompson, and F. Watson. 2007. Viability criteria for steelhead of the south-central and southern California coast. NOAA Technical Memorandum NMFS-SWFSC-407, 28 p. [Details]

Ruggerone, G. T., J. L. Nielsen, and B. A. Agler. 2007. Retrospective analysis of AYK Chinook salmon growth. 2007 Arctic Yukon Kuskokwim Sustainable salmon initiative project product. Sea Grant Publication [Details]

Nielsen, J. L., C. E. Zimmerman, S. L. Graziano, and A. M. Ramey. 2007. Testing molecular and otolith tools to investigate population of origin and migration in Arctic cisco found in the Colville River, Alaska. Technical Report submitted to MMS OCS Program, U.S. Geological Survey, Alaska Science Center, AK, 39 p. [Details]

Seitz, A. C., B. L. Norcross, D. Wilson, and J. L. Nielsen. 2006. Evaluating light-based geolocation for demersal fishes in northern latitudes. Fishery Bulletin. [Details]

Hendrickson, D. A., J. L. Nielsen, R. L. Mayden, and S. M. Norris. 2006. Family Salmonidae Truchas; Trouts and salmons. Pages 176-178 in R. R. Miller, W. L. Minkley, and S. M. Norris, (eds.). Freshwater Fishes of Mexico. University of Chicago Press, 652 p. , Chicago, IL, USA. [Details]

Boughton, D. A., P. B. Adams, E. Anderson, C. Fusaro, E. Keller, E. Kelley, L. Lentsch, J. L. Nielsen, K. Perry, H. Regan, J. Smith, C. Swift, L. Thompson, and F. Watson. 2006. Steelhead of the south-central/southern California coast: Population characterization for recovery planning. NOAA Technical Memorandum 394. [Details]

Farley, E. V., J. M. Murphy, J. Adkison, L. B. Eisner, J. H. Helle, J. H. Moss, and J. L. Nielsen. 2005. Critical-size, critical-period hypothesis: An example of the relationship between early marine growth of juvenile Bristol Bay sockeye salmon, subsequent marine survival, and ocean condition. North Pacific Anadromous Fish Commission Bulletin Technical Report 7. [Details]

Burkett, V. R., D. A. Wilcox, R. Stottlemyer, W. Barrow, D. B. Fagre, J. Baron, J. L. Nielsen, C. D. Allen, D. L. Peterson, G. T. Ruggerone, and T. Doyle. 2005. Non-linearity dynamics in ecosystem response to climate change: Case studies and policy implications. Ecological Complexity 2:357-394. [Details]

Hamon, T. R., S. A. Pavey, J. L. Miller, and J. L. Nielsen. 2005. Aniakchak sockeye salmon investigations. Alaska Park Science 3:35-39. [Details]

Seitz, A. C., B. L. Norcross, D. R. Wilson, and J. L. Nielsen. 2005. Identifying spawning behavior in Pacific halibut (Hippoglossus stenolepis) using electronic tags. Environmental Biology of Fishes 73:445-451. [Details]

Graziano, S. L., K. H. Brown, and J. L. Nielsen. 2005. Nomenclature of mitochondrial DNA haplotypes for Oncorhynchus mykiss. Transactions of the American Fisheries Society 134:1271-1273. [Details]

Ruggerone, G. T., E. V. Farley, J. L. Nielsen, S. Ignell, and P. Hagen. 2005. Seasonal marine scale growth of Bristol Bay sockeye salmon in relation to pink salmon abundance, 1955-2000. Fishery Bulletin 103:355-370. [Details]

Nielsen, J. L., T. C. Wiacek, and S. L. Graziano. 2005. Population genetic structure of rainbow trout in the upper Ventura River watershed based on microsatellite and mtDNA analyses. Final Technical Report to USGS Western Fisheries Research Center, Seattle, WA, Dr. Reginald Reisenbichler, August 19, 2005. [Details]

Nielsen, J. L., S. A. Pavey, T. C. Wiacek, and I. Williams. 2005. Genetics of Central Valley O. mykiss populations: Drainage and watershed analyses. San Francisco Estuary and Watershed Science 3(2). [Details] [Full Publication]

Crusius, J. and J. L. Nielsen. 2005. Coastal iron fluxes to surface waters of the NE Pacific: A driver of the marine ecosystem and carbon cycle. USGS White Paper. [Details]

Nielsen, J. L., S. L. Graziano, I. Williams, and A. Byrne. 2005. Genetic population structure of Snake River Basin steelhead in Idaho. Technical Report submitted to Idaho Department of Fish and Game. [Details]

Seitz, A. C., T. Loher, and J. L. Nielsen. 2005. Seasonal movements and environmental conditions experienced by Pacific halibut in the Bering Sea, examined by pop-up tags. Technical Report submitted to International Pacific Halibut Commission, March 2005. [Details]

Nielsen, J. L. and G. T. Ruggerone. 2005. Linkages between climate, growth, competition at sea and production of sockeye salmon populations in Bristol Bay, 1955-2000. Pages 198 in Proceedings: Study of Environmental Arctic Change 370 p. Seattle, WA, USA. [Details]

Zimmerman, C. E. and J. L. Nielsen. 2004. Introduction: Special Issue Interactions of Hatchery and Wild Fishes in Marine and Estuarine Environments. Reviews in Fish Biology and Fisheries 14(3):301-303. [Details]

Ruggerone, G. T. and J. L. Nielsen. 2004. Evidence for competitive dominance of pink salmon (Oncorhynchus gorbuscha) over other salmonids in the North Pacific Ocean. Reviews in Fish Biology and Fisheries 14:371-390. [Details]

Nielsen, J. L. 2004. Exploitation dynamics of small fish stocks. Proceedings of a workshop on the variability of Arctic cisco (Qaaktaq) in the Colville River. MBC Applied Environmental Sciences, Costa Mesa, CA. MMS OCS Study 2004-033 [Details]

Nielsen, J. L., P. J. Richards, D. R. Wilson, C. E. Zimmerman, and T. Tingey. 2004. Testing electronic archival tags in Pacific salmon. Exxon Valdez Oil Spill Restoration Project Final Report, (Restoration Project 02404), U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska. [Details]

Nielsen, J. L. 2004. History and effects of hatchery salmon in the Pacific. Pages 153-168 in P. Gallaugher and L. Wood, (eds.). Proceedings: World Summit on Salmon, Simon Fraser University, June 10-13, 2003 [Details] [Full Publication]

Nielsen, J. L., R. Valenzuela, T. C. Wiacek, and S. L. Graziano. 2004. Genetic population structure of Snake River steelhead in Idaho. Technical Report submitted to Idaho Department of Fish and Game, 11 January, 2004. [Details]

Nielsen, J. L. and H. Regier. 2004. Sustaining salmonid populations: A caring understanding of the naturalness of taxa. Pages 203-211 in E. E. Knudsen, C. R. Steward, D. D. MacDonald, J. E. Williams, and D. W. Reiser, (eds.). Sustainable Fisheries Management: Pacific Salmon. Lewis Publisher, Boca Raton, FL, USA. [Details]

Graziano, S. L. and J. L. Nielsen. 2004. Genetic population structure of rainbow trout from the White Salmon River sub-drainage: Including inference on hybridization with coastal cutthroat trout. US Forest Service Technical Report, USFS Gifford Pinchot National Forest, 27 June 2004, Wind River, WA. [Details]

Nielsen, J. L. 2004. Investigations of the linkages between climate, growth, and production of sockeye salmon populations in Bristol Bay, Alaska. Final Technical Report to USGS Global Challenges Initiative, 10 June 2004. [Details]

Nielsen, J. L. and T. C. Wiacek. 2004. Population genetic structure of rainbow trout above the Matilija Dam based on microsatellite and mtDNA analyses. Final Technical Report to USGS Western Fisheries Research Center, Seattle, WA. [Details]

Nielsen, J. L. 2004. San Mateo Trout mtDNA Analyses 2004. Report submitted to Department of Defense, USGS Alaska Science Center, Anchorage, Alaska. [Details]

Hendrickson, D. A., H. Espanoza-Perez, L. T. Findley, W. Forbes, J. R. Tomelleri, R. L. Mayden, J. L. Nielsen, B. Jensen, G. R. Campos, A. V. Romero, A. Van der Heiden, F. Camarena, and F. J. Garcia de Leon. 2003. Mexican native trouts: a review of their history and current systematic and conservation status. Reviews in Fish Biology and Fisheries. [Details]

Ruggerone, G. T., M. Zimmerman, K. W. Myers, J. L. Nielsen, and D. E. Rogers. 2003. Competition between Asian pink salmon (Oncorhynchus gorbuscha) and Alaskan sockeye salmon (O. nerka) in the North Pacific Ocean. Cambridge University Press 12:209-219. [Details]

Seitz, A. C., D. R. Wilson, B. L. Norcross, and J. L. Nielsen. 2003. Pop-up archival transmitting (PAT) tags: a method to investigate the migration and behavior of Pacific halibut (Hippoglossus stenolepis) in the Gulf of Alaska. Alaska Fishery Research Bulletin. [Details] [Full Publication]

Thrower, F., J. Joyce, C. Guthrie, III, and J. L. Nielsen. 2003. Comparison of genetic variation between an anadromous steelhead (Oncorhynchus mykiss) population and seven derived populations sequestered in freshwater for 70 years. Environmental Biology of Fishes. [Details]

Ruggerone, G. T., J. L. Nielsen, E. V. Farley, S. Ignell, P. Hagen, B. A. Agler, D. E. Rogers, and J. Bumgarner. 2003. Long-term trends in annual Bristol Bay sockeye salmon growth at sea in relation to sockeye abundance and environmental trends, 1955-2000. North Pacific Anadromous Fish Commission Bulletin Technical Report 4:56-58. [Details]

Porath, M. T. and J. L. Nielsen. 2003. Evidence of sexually dimorphic introgression in Pinaleno Mountain Apache trout. North American Journal of Fisheries Management 23:172-180. [Details]

Nielsen, J. L., J. B. Olsen, T. C. Wiacek, E. Kretschmer, G. Greenwald, and J. K. Wenburg. 2003. Population genetic structure of Santa Ynez rainbow trout - 2001 based on microsatellite and mtDNA analyses. Technical Report submitted to U.S. Fish and Wildlife Service Region 1, 1 April 2003. [Details]

Nielsen, J. L., G. K. Sage, S. A. Pavey, R. Valenzuela, and T. C. Wiacek. 2003. Hatchery and wild steelhead genetics in Idaho: Report #1: Dworshak Hatchery stocks in the Clearwater drainage. Technical Report submitted to Idaho Department of Fish and Game, April 2003. [Details]

Nielsen, J. L., I. Williams, G. K. Sage, and C. E. Zimmerman. 2003. The importance of genetic verification for determination of Atlantic salmon in north Pacific waters. Journal of Fish Biology 62(4):871-878. doi:10.1046/j.1095-8649.2003.00072.x [Details] [Full Publication]

Nielsen, J. L. and T. Waicek. 2003. Population genetic structure of Alameda Creek rainbow/steelhead trout 2002. Technical Report submitted to Hagar Environmental Science, 3 January 2003. [Details]

Scribner, K. T., G. K. Sage, C. Soiseth, L. K. Thorsteinson, E. E. Knudsen, and J. L. Nielsen. 2003. Genetic analysis of coho salmon colonization in recently deglaciated streams in Glacier Bay, Alaska. Report submitted to National Park Service, USGS Alaska Science Center, Anchorage, Alaska. [Details] [Full Publication]

Seitz, A. C., D. R. Wilson, and J. L. Nielsen. 2002. Testing pop-up satellite tags as a tool for identifying critical habitat for Pacific halibut (Hippoglossus stenolepis) in the Gulf of Alaska. Exxon Valdez Oil Spill Restoration Project Final Report, (Restoration Project 01478), U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska. [Details]

Nielsen, J. L. and G. K. Sage. 2002. Microsatellite sequence reveals significant haplotype diversity in Central Valley chinook stocks. California Dept. of Fish and Game, June 2002. [Details]

Nielsen, J. L. and G. K. Sage. 2002. Genetic analysis of temporal spawning populations of Lahontan cutthroat (Oncorhynchus clarki henshawi) from Pyramid Lake. Bailey Environmental Consulting, 11 p. [Details]

Nielsen, J. L. and G. K. Sage. 2002. Population genetic structure in Lahontan cutthroat trout. Transactions of the American Fisheries Society 131:376-388. [Details]

Nielsen, J. L. and G. K. Sage. 2002. Microsatellite analyses of San Mateo Creek trout, 2001. Technical Report submitted to U.S. Department of Defense, Camp Pendleton, CA. [Details]

Nielsen, J. L. 2001. Report on mitochondrial DNA haplotypes and microsatellite loci for San Mateo steelhead/rainbow trout. Final Technical Report to the Department of Defense, Camp Pendelton, CA. [Details]

Nielsen, J. L. and G. K. Sage. 2001. Microsatellite analyses of the trout of Northwest Mexico. Genetica 111(No.1-3):269-278. [Details] [Full Publication]

Burnham-Curtis, M., S. M. Haig, T. King, G. Kurath, J. L. Nielsen, G. Smith, G. Smith. 2000. Genetics and molecular tools: Setting the standard for biological science in USGS. USGS BRD Genetics and Molecular Tools. [Details]

Avelino, O. L. and J. L. Nielsen. 2000. Genetic analysis of hatchery and wild fall-run Chinook salmon (Oncorhynchus tshawystcha) in the Central Valley, California. (Grant# FG 8002 IF). Technical Report submitted to California Department of Fish and Game, Inland Fisheries Division, Sacramento, CA, 76 p. [Details]

Epifanio, J. and J. L. Nielsen. 2000. Symposium Review: The role of hybridization in the distribution, conservation, and management of aquatic species. Reviews in Fish Biology and Fisheries 10:245-251. [Details]

Nielsen, J. L. 2000. Variation in mtDNA and nuclear microsatellite DNA markers from San Gabriel Creek rainbow trout. Report submitted to Federation of Fly Fishers, Southwest Council, 19 September 2000. [Details]

Nielsen, J. L. 2000. Population genetic structure in Lahontan cutthroat trout (Oncorhynchus clarki henshawi). Final Report to the U.S. Fish and Wildlife Service, USGS Alaska Science Center, Anchorage, Alaska. [Details]

Nielsen, J. L., E. L. Heine, C. A. Gan, and M. C. Fountain. 2000. Molecular analyses of population genetic structure and recolonization of rainbow trout following a fish-kill event. California Fish and Game 86(1):21-40. [Details]

Nielsen, J. L. 2000. Report on mitochrondrial DNA halotypes for San Mateo steelhead. Appendix B in Steelhead Rainbow Trout in San Mateo Creek, San Diego County, California. Report for the National Marine Fisheries Service by the California Department of Fish and Game, Native Anadromous Fish and Watershed Branch, South Coast Region, February 2000. Sacramento, CA. California Fish and Game, 3 p. [Details]

Nielsen, J. L. 2000. Microsatellite analyses of San Franciscuito Creek rainbow trout. Report submitted to Center for Conservation, Stanford University, Stanford, CA, 12 January 2000, 19 p. [Details]

Nielsen, J. L. and M. C. Fountain. 1999. Microsatellite analyses of Alameda Creek rainbow/steelhead trout. Technical Report submitted to Applied Marine Sciences, Inc. Livermore, CA, 7 October 1999, 17 p. [Details]

Nielsen, J. L., K. D. Crow, and M. C. Fountain. 1999. Microsatellite diversity and conservation of a relic trout population: the McCloud River redbad trout. Molecular Ecology 8:129-142. [Details]

Nielsen, J. L. 1999. The evolutionary history of steelhead (Oncorhynchus mykiss) along the US Pacific coast: Developing a conservatin strategy using genetic diversity. ICES Journal of Marine Science 56:449-458. [Details]

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