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Jennifer Lee Nielsen, Ph.D. Fisheries Supervisor Marine and Freshwater Ecology Branch |  |
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[Research
Interests] [Current Projects] [Education]
[Professional Experience] |
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Molecular genetics, stock identification, conservation and management of Pacific salmonids; evolution and biogeography in fishes; marine and freshwater fish behavior and habitat use; impacts of sport and recreational fishing on resource management.
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1994 Ph.D. University of California, BerkeleyEnvironmental Science, Policy and Management Dissertation: Molecular Genetics and Stock Identification in Pacific Salmon (Oncorhynchus spp.) Majors: Molecular Population Genetics
1990 M.S. University of California, BerkeleyDepartment of Wildlands Resource Sciences Thesis title: Environment and behavior affecting growth and development of juvenile coho salmon (Oncorhynchus kisutch). Majors: Fisheries Biology & Ethology
1987 B.S. The Evergreen State College, Olympia, WAEnvironmental Studies
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Grants Pending
Grants Awarded
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May 2004. July 2002. August 2001. June 2000. May 2-6, 2000. Editor of Proceedings: Symposium on Interactions Between Aquaculture and the Environment, Aquaculture 2000, Nice, France. February 7-11, 2000. Editor of Proceedings: Symposium on Tagging and Tracking Marine Fish with Electronic Devices. University of Hawaii, Honolulu. August 1999. Annual American Fisheries Society Meeting, Charlotte, N.C. Organizer: The role of hybridization in the distribution, conservation, and management of aquatic species. August 26, 1998. Annual American Fisheries Society Meeting, Hartford, Conn. Session Chair: Ecology, physiology, and genetics of salmon at the southern edge of their distribution: Implications for conservation. June 24-27, 1998. Ecology, Ethology, and Evolution of Fishes (EEEF). Seattle Washington. Symposium Chair: "The Intersection of Molecular and Behavioral Science." August 24-29, 1997. National American Fisheries Society Meeting, Monterey CA. Program Chair. February 16-20, 1997. Keystone Symposium on Evolution of Molecular Mechanisms. Session Chair - Repetitive DNA and the evolution of repeat units. December 4-14, 1995. USDA Ecological Stewardship Workshop, Tucson, AZ. Scientific Committee (Author) - Genetic and Species Diversity. July 16-19, 1995. |
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Journal/Book Articles Submitted for Publication 6)
Nielsen, J. L., I. Williams, G. K. Sage and C. E. Zimmerman. The importance of
genetic varification of identification of Atlantic salmon in Pacific waters.
CJAFS Rapid Com. 5)
Seitz,
A., D. Wilson, and J. L. Nielsen. Pop-up satellite tagging of Pacific halibut
(Hippoglossus stenolepis) in the Gulf of Alaska.
Fisheries Bulletin. 4)
Thrower,
F., C. Guthrie III, and J. L. Nielsen, and J. Joyce. 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. 3)
Nielsen,
J. L. and H. Regier. Sustaining salmonid populations: a caring understanding
of the naturalness of taxa. Sustainable
Fisheries in North America. D. MacDonald and E. Knudsen (eds.) 2)
Scribner,
K. Y., G. K. Sage, C. Soiseth, L. Thorsteinson, E. Knudsen and J. L. Nielsen.
Coho salmon colonization in recently deglaciated streams in Glacier Bay,
Alaska: Implications for Pacific salmon restoration. Proc. Natl. Acad. Sci. 1)
Camarena,
F., G. R. Campos, A. Daza, H. Espinoza, L. Findley, W. Forbes, F. Garcia de
Leon, A. van der Heiden, D. A. Hendrickson, B. Jensen, R. L. Mayden, J. L.
Nielsen, L. Ruiz, J. R. Tomelleri, A. Varela. Truchas Mexicanas: An
international partnership for the study of native trout of southern North
America. Reviews in Fish Biology and Fisheries. Journal/Book Articles Published (*
= Peer-reviewed professional journal or book chapter) 78)
Ruggerone,
G. T., E. Farley, J. L. Nielsen, S. Ignell and P. Hagen. 2002. Seasonal marine scale
growth of Bristol Bay sockeye salmon in relation to pink salmon abundance,
1955-2000. Fisheries and Oceanography. 77) Nielsen,
J. L. and G. K. Sage. 2002. Microsatellite sequence reveals significant
haplotypes diversity in Central Valley chinook stocks. Final Technical Report
Submitted to California Department of Fish and Game June 2002. 76) *Ruggerone,
G. T., M. Zimmermann, K. W. Meyers, J. L. Nielsen and D. E. Rogers. 2002.
Competition between Asian pink salmon and North American sockeye salmon in the
North Pacific Ocean. Fisheries and Oceanography. 75) Nielsen,
J. L. and G. K. Sage. 2002. Genetic analysis of temporal spawning populations
of Lahontan cutthroat trout (Oncorhynchus clarki henshawi) from Pyramid Lake.
Technical report submitted to Bailey Environmental, June 2002. 74) *Seitz,
A., D. 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. 73) *Porath,
M. T. and J. L. Nielsen. In Press. Evidence of sexually dimorphic
introgression in Pinaleno Mountain Apache trout. N. Am. J. Fish. Mgmt. 72) Ruggerone,
G., J. Nielsen, E. Farley, S. Ignell, P. Hagen, B. Agler, D. Rogers and J.
Bumgarner. 2002. Long-term trends in annual Bristol Bay sockeye salmon scale
growth at sea in relation to sockeye abundance and environmental trends,
1955-2000. Proceedings of the Joint Meeting on Causes of Marine Mortality of
Salmon in the North Pacific and North Atlantic Oceans and in the Baltic Sea.
North Pacific Fisheries Commission Annual Meeting, March 2002,
Vancouver, B.C. 71) Nielsen,
J. L. and G. K. Sage. 2002. Microsatellite analyses of San Mateo Creek trout,
2001. Technical Report submitted
to US Department of Defense, Camp Pendleton, CA. January 14, 2002. 70) *Nielsen,
J. L. and G. K. Sage. 2002. Population genetic structure in Lahontan cutthroat
trout. Transactions American Fisheries Society. 131: 376-388. 69) *Nielsen,
J. L., J. M. Scott and J. L. Aycrigg. 2002. Endangered species and peripheral
populations: Cause for conservation. Endangered
Species UPDATE 18:194-197. 68) Nielsen,
J. L. 2001. Report on mitochondrial DNA haplotypes and microsatellite loci for
San Mateo steelhead/rainbow trout. Final
technical report submitted 9/30/01 Department of Defense, Camp Pendelton, CA. 67) *Nielsen, J. L. and K. Sage 2001. Microsatellite analyses of the trout of Northwest Mexico. Genetica 111(No.1-3): 269-278. 66) Avelino, O. 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, pp. 76. 65) *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 (in press). 64) 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, September 19, 2000. 63) Nielsen, J. L. 2000. Population genetic structure in Lahontan cutthroat trout (Oncorhynchus clarki henshawi). USFWS Reno, NV Grant #142408H057 Final report. 62) Burnham-Curtis, M., S. Haig, T. King, G. Kurath, J. Nielsen, and G. Smith 2000. Genetics and molecular tools: Setting the standard for biological science in USGS. Summary of discussions and dialogue from the workshop: Integration and Collaboration on Emerging Biological Issues and Research Goals (ICEBIRG) I: Genetics and Molecular Tools. USGS – BRD Ruston, VA. 61) *Nielsen, J. L., E. L. Heine, C. A. Gan, and M. C. Fountain. 2000. Molecular analyses of population structure and recolonization of rainbow trout following a fish-kill event. California Fish and Game 86(1): 21-40. 60) Nielsen, J. L. 2000. Report on mitochondrial DNA haplotypes 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, California. 3 pp. 59) Nielsen, J. L. 2000. Microsatellite analyses of San Francisquito Creek rainbow trout. Report submitted to Center for Conservation, Stanford University, Stanford, CA. Jan. 12, 2000. 19pp. 58) *Nielsen, J. L., K. D. Crow, and M. C. Fountain. 1999. Microsatellite diversity and conservation of a relic trout population: the McCloud River redband trout. Molecular Ecology 8:129-142. * 57) Nielsen, J. L. and M. C. Fountain 1999. Microsatellite analyses of Alameda Creek rainbow/steelhead trout. Technical Report submitted October 7, 1999 to Applied Marine Sciences, Inc. Livermore, CA. 56) *Nielsen, J. L. & M. C. Fountain 1999. Microsatellite diversity in sympatric reproductive ecotypes of Pacific steelhead (Oncorhynchus mykiss) from the Middle Fork Eel River, California. Ecology of Freshwater Fish 8: 159-168.* 55) Nielsen, J. L., D. S. Wiltse and M. C. Fountain 1999. Testing for rainbow trout introgression in Arizona Apache trout populations using microsatellites. Technical report submitted Aug. 11, 1999 to Arizona Game and Fish. 54) Nielsen, J. L., O. L. Avelino and M. C. Fountain. 1999. Tests of genetic population structure in Stanislaus River trout using microsatellites. Technical report submitted Aug. 24, 1999 to SP Cramer and Associates. 53) Nielsen, J. L. 1999. Variation in mtDNA and nuclear microsatellite DNA markers in Pinole Creek trout. Technical Report submitted March 19, 1999 to East Bay Municipal Utilities District. 28 pp. 52) *Nielsen, J. L. 1999. The evolutionary history of steelhead (Oncorhynchus mykiss) along the US Pacific coast: Developing a conservation strategy using genetic diversity. ICES Journal of Marine Science 56:449-458.* 51) *Huston, M. C., G. McVicker and J. L. Nielsen. 1999. A functional approach to ecosystem management: Implications for species diversity. Pages 45-85 in The Ecological Stewardship Program: A common reference for Ecosystem Management (3 Volumes). Elsevier Science Limited, Oxford, England.* 50) *Dunham, J. B., M. M. Peacock, J. L. Nielsen, C. R. Tracy, and G. L. Vinyard. 1999. Extinction risk assessment: Integrating genetic information. Conservation Ecology [on line] 3(1):2 Available from the Internet URL: http://www.consecol.org/vol3/iss1/art2.* 49) Nielsen, J. L. 1998. Molecular genetics and the conservation of salmonids biodiversity: Oncorhynchus at the edge of their range. Pages 234 – 279 in Proceedings of the Symposium Restoring the Southern California Steelhead. MH. Capelli (ed.) University of California Extension, Santa Barbara, CA. 48) Dunham, J. B., G. L. Vinyard, and J. L. Nielsen. 1998. Evaluating the genetic identity of Pilot Peak cutthroat in relation to hatchery broodstock development at the Lahontan National Fish Hatchery and recovery of Lahontan cutthroat trout in the Truckee River subbasin. Final Technical Report to U. S. Fish and Wildlife Service Region 1, Reno, Nevada. 17pp. 47) *Dodson, J., J. Nielsen, M. Gross, K. Friedland, R. Newberry, M. Power, C. Garcia de Leaniz, S. Roy, R. Cunjak, and J. Gibson 1998. Development and implementation of a conservation plan for Atlantic salmon. In M. Mather (ed.) Proceeding of Integrating Across Scales: Predicting Patterns of Change in Atlantic Salmon. Canadian Journal Fisheries Aquatic Science 55(Suppl. 1):000-000.* 46) *Nielsen, J. L. 1998. Population genetics and the conservation and management of Atlantic salmon (Salmo salar). In M. Mather (ed.) Proceeding of Integrating Across Scales: Predicting Patterns of Change in Atlantic Salmon. Canadian Journal Fisheries Aquatic Science 55(Suppl. 1): 145-152.* 45) *Nielsen, J. L. 1998. Scientific sampling effects: electrofishing California's endangered fish populations. Fisheries 23:6-12.* 44) Nielsen, J. L. 1998. Molecular genetic population structure in steelhead/rainbow trout (Oncorhynchus mykiss) from the Santa Ynez River, 1994-1997. Technical Report submitted to the Santa Ynez River Technical Advisory Committee 8/5/98. 31pp. 43) Nielsen, J. L. 1998. Genetic issues concerning southern coho restoration in California. Technical Report CDFG & Southern Coho Restoration Team submitted 11/13/97 9 pp. 42) *Nielsen, J. L. 1998. Threatened Fishes of the World: Oncorhynchus mykiss nelsoni Evermann 1908 (Salmonidae). Environmental Biology of Fishes 51:376.* 41) *Nielsen, J. L., M. C. Fountain, J. Campoy-Favela, K. Cobble, and B. Jensen. 1998. Oncorhynchus at the southern extent of their range: a study based on mtDNA control-region sequence with special reference to an undescribed subspecies of O. mykiss from Mexico. Environmental Biology of Fishes. 51:7-23.* 40) Nielsen, J. L. 1997. Molecular genetics and evolutionary status of the trout of the Sierra Madre. Proceedings of Wild Trout VI: Putting the Native Back in Wild Trout, Aug. 17-20, 1997, Montana State University, Bozeman MT. pp 103-109. 39) Nielsen, J. L. 1997. Mitochondrial DNA and ten nuclear microsatellite loci depict population structure in rainbow trout (Oncorhynchus mykiss) from southeast Alaska. Technical Report submitted 7/97 to NMSF Auke Bay Laboratory, Juneau AK. 32pp. 38) Nielsen, J. L. 1997. Molecular genetic diversity and stock structure in rainbow trout from the Clavey River. Technical Report submitted 6/5/97 to CA Department of Fish and Game, Wild Trout Committee Sacramento, CA and USDA FS Region 5, San Francisco, CA. 37) Nielsen, J. L., C. A. Gan, C. Carpanzano, and M. C. Fountain 1997. Mitochondrial DNA and nuclear microsatellite frequency differences in hatchery and wild Oncorhynchus mykiss from freshwater habitats in southern California. Transactions of the American Fisheries Society 126:397-417.* 36) *Nielsen, J. L., M. C. Fountain, and J. M. Wright 1997. Biogeographic analysis of Pacific trout (Oncorhynchus mykiss) in California and Mexico based on mtDNA and nuclear microsatellites. Pages 53-73 in Molecular Systematics of Fishes. T. Kocher and C. A. Stepien (eds.) Academic Press. * 35) Nielsen, J. L. 1997. Mitochondrial DNA and nuclear microsatellite polymorphisms in chinook salmon from the Sacramento-San Joaquin basin, 1991-1995. Technical report #FG6038IF submitted to CA Department of Fish and Game, Inland Fisheries Division, Sacramento CA. 34) Nielsen, J. L. 1996. About gender. Book review of D. Pauly. 1994. On the Sex of Fish and the Gender of Scientists: a collection of essays in fisheries science. Environmental Biology of Fishes 47:415-416. 33) *Nielsen, J. L. 1996. Molecular genetics and the conservation of salmonid biodiversity: Oncorhynchus at the edge of their range. Pages 383-398 in T. B. Smith and R. K. Wayne (eds.) Molecular Genetics Approaches in Conservation. Oxford University Press.* 32) *Castleberry, D., J. Cech, D. Erman, D. Hankin, M. Healey, M. Kondolf, M. Mengel, M. Mohr, P. Moyle, J. Nielsen, T. Speed, and J. Williams. 1996. Uncertainty and instream flow standards. Fisheries 21(8):20-21.* 31) Nielsen, J. L. 1996. Using mitochondrial and nuclear DNA to separate hatchery and wild stocks of rainbow trout in California and Mexico. Pages 139-147 in E. M. Donaldson and D. D. MacKinlay (eds.) Aquaculture Biotechnology Symposium Proceedings International Congress on the Biology of Fishes, July 14-18, 1996, San Francisco, CA. 30) *Quinn, T. P., Nielsen, J. L., C. A. Gan, M. J. Unwin, R. Wilmot, C. Guthrie, and F. M. Utter. 1996. Origin and genetic structure of chinook salmon (Oncorhynchus tshawytscha) transplanted from California to New Zealand: allozyme and mtDNA evidence. Fisheries Bulletin 94(3):506-521.* 29) Nielsen, J. L. 1996. Anadromous Fishes of the Monterey Bay National Marine Sanctuary. NOAA Monterey Bay National Marine Sanctuary internet web site http://color.mlml.calstate.edu/www/mbnms/docs92/fish.html 28) Nielsen, J. L. and M. C. Fountain. 1996. Kern River basin trout stock structure: evidence using mtDNA and nuclear microsatellites. USDA FS Region 5 internal report. 21pp. 27) Nielsen, J. L., M. C. Fountain, and K. Crow. 1996. Molecular systematics of a relic trout population: the McCloud River redband trout. CDFG Report FG5004-IF, California Department of Fish and Game, Inland Fisheries Division, Sacramento, CA. 61pp. 26) Nielsen, J. L. 1995. Variation in individual life history strategies in coho salmon from northern California. Pages 40-41 in Janis Duncan-Vaughn (ed.) Proceedings of the Thirteenth Annual Salmonid Restoration Federation Conference, Feb. 23-26, 1995, Santa Rosa and Rohnert Park CA. 25) Nielsen, J. L. 1995. Mitochondrial DNA frequency distributions in chinook salmon from the Sacramento-San Joaquin Basin and Guadalupe Creek, 1992-1994. CDFG Report No. IFGAD95-22 , CA Dept. Fish and Game, Inland Fisheries Division, Redding, CA. 17pp. 24) Nielsen, J. L. 1995. Upper Sacramento River Rainbow trout: molecular genetics and stock identification. CDFG Report No. IFG95-03, CA Dept. Fish and Game, Inland Fisheries Division, Redding, CA. 37pp. 23) Nielsen, J. L. (ed.) 1995. Evolution and the Aquatic Ecosystem: Defining Unique Units in Population Conservation. American Fisheries Society Monograph Series No. 17. 435 pp. 22) Nielsen, J. L., C. A. Gan, and Kelly Cuffe. 1994. Effects of habitat and population manipulation on unique genotypes of chinook and steelhead in urbanized watersheds in California. Pages 77-83 in M. L. Keefe (ed.) Salmon Ecosystem Restoration: Myth and Reality. Proceedings of the 1994 Northeast Pacific Chinook and Coho Workshop, Eugene OR, Nov. 7-10, 1994. 21) Monroe, J. and J. L. Nielsen. 1994. Evolution and the aquatic ecosystem: Defining unique units in population conservation: Executive Summary. The American Fisheries Society, Bethesda, MD. 19pp. 20) *Nielsen, J. L., C. A. Gan, J. M. Wright, D. B. Morris, and W. K. Thomas 1994. Biogeographic distributions of mitochondrial and nuclear markers for southern steelhead. Molecular Marine Biology and Biotechnology 3(5):281-293.* 19) Nielsen, J. L., C. Gan, J. M. Wright, and W. K. Thomas. 1994. Phylogeographic patterns in California steelhead using mtDNA and microsatellites. Proceedings of the 1993 CALCOFI Conference: Genetics of Organisms of the California Current. Lake Arrowhead Conference Center 2-4 Nov. 1993. CALCOFI Report Vol. 35:90-92. 18) *Nielsen, J. L., D. Tupper, and W. K. Thomas. 1994. Mitochondrial DNA polymorphisms in unique runs of chinook salmon (Oncorhynchus tshawytscha) from the Sacramento-San Joaquin River basin. Conservation Biology 8(3):882-884.* 17) Cuffe, C. K., P. Goodwin, and J. L. Nielsen. 1994. Physical and biological effects of inlet closure and breaching - Russian River estuary, California. Proceeding of the Western Division American Fisheries Society and Western Association of Fish and Wildlife Associations, July 26-30, 1993. Sacramento, CA. 16) *Nielsen, J. L., C. A. Gan and W. K. Thomas. 1994. Differences in genetic diversity for mtDNA between hatchery and wild populations of Oncorhynchus. Proceedings of the International Symposium on Genetics of Subarctic Fish and Shellfish, Juneau, Alaska, May 19, 1993. Canadian Journal of Fish and Aquatic Sciences. (Supl.1) 51:290-297.* 15) Nielsen, J. L., W. K. Thomas, C. A. Gan, and D. Tupper. 1994. Intrapopulation differences found in California steelhead trout using direct sequence of mtDNA. Pages 63-65 in Proceedings of Application of DNA Technology to the Management of Pacific Salmon. NOAA NMFS workshop, March 22-23, 1993. National Marine Fisheries Service, 2725 Montlake Blvd., Seattle, WA 98112. p63-65. 14) *Nielsen, J. L. 1994. Invasive cohorts: Impacts of hatchery-reared coho salmon on the trophic, developmental, and genetic ecology of wild stocks. In: D. J. Stouder, K. L. Fresh, and R. J. Feller (eds.) Theory and Application in Fish Feeding Ecology. Belle W. Baruch Library in Marine Sciences Number 18:361-385.* 13) *Nielsen, J. L. 1994. Molecular genetics and stock identification in Pacific salmon (Oncorhynchus spp.). Ph. D. Dissertation, University of CA, Berkeley. 12) *Nielsen, J. L., T. E. Lisle and V. Ozaki. 1994. Formation of thermally stratified "cold pools" and utilization by steelhead trout, northern California. Transactions of the American Fisheries Society 123:613-626.* 11) Nielsen, J. L., P. Goodwin, C. K. Cuffe and T. Light. 1994. Russian River Estuary Study, 1992-1993: Hydrologic, Limnological, and Biological Aspects of an Estuary Management Plan. Technical report published by the Planning Department of Sonoma County, Santa Rosa, CA. 186 pp. plus IX appendices. 10) *Goodwin, P., J. L. Nielsen and C. K. Cuffe. 1993. The tidal Inlet characteristics of a small California Estuary. Hydraulic Engineering 93:562-567.* 9) Nielsen, J. L. 1992. The role of cold-pool refugia in the freshwater fish assemblage in northern California rivers. Pages 79-88 in: Proceedings of a symposium on biodiversity in northwestern California, Santa Rosa, CA, Oct. 28-30, 1991. Published by the Wildland Resources Center Division of Agriculture and Natural Resources, University of California, Berkeley, CA. Report 29, December, 1992. 8) *Nielsen, J. L. 1992. Microhabitat specific forage behavior, diet and growth rates in juvenile coho salmon. Transactions of the American Fisheries Society. 121(4): 617:634.* 7) Nielsen, J. L., M. Maahs & G. Baldwin. 1991. Anadromous Salmonid Resources of Mendocino Coastal and Inland Rivers, 1989-1991: An Evaluation of Rehabilitation Efforts Based on Carcass Recovery and Spawning Activity. Work Report No. FG9364 California Department of Fish and Game, Inland Fisheries Div., Sacramento CA. 95814. 98 p. 6) *Nielsen, J. L. 1990. Environment and behavior affecting growth and development of juvenile coho salmon (Oncorhynchus kisutch). Masters Thesis University of California, Berkeley. 148 p. 5) *Bisson, P. A., J. L. Nielsen, J. W. Ward. 1988. Summer production of coho salmon stocked in Mount St. Helens streams 3-6 years after the 1980 eruption. Transactions of the American Fisheries Society 117:322-335.* 4) *Bisson, P. A., K. Sullivan & J. L. Nielsen. 1988. Channel hydraulics, habitat use, and body form of juvenile coho salmon, steelhead, and cutthroat trout in streams. Transactions of the American Fisheries Society 117:262-273.* 3) *Bisson, P. A., J. L. Nielsen, M. W. Chilcote, B. A. Crawford & S. A. Leider. 1986. Occurrence of anadromous brown trout in two lower Columbia River tributaries. North American Journal of Fisheries Management 6:290-292.* 2) Bisson, P. A., J. L. Nielsen & J. W. Ward. 1985. Experimental release of coho salmon (Oncorhynchus kisutch) into a stream impacted by Mount Saint Helens volcano. Pages 422-435, in Proceedings of the Annual Meeting of the Western Division, American Fisheries Society and the Western Association of Fish and Wildlife Agencies, held July 16-19, Victoria, British Columbia. 1) Bisson, P. A., J. L. Nielsen, R. A. Palmason, L. E. Grove. 1982. A system of naming habitat types in small streams with examples of habitat utilization by salmonids during low stream flow. Pages 62-73, in N.B. Armantrout, editor, Acquisition and utilization of aquatic habitat inventory information. Proceedings of a symposium held 28-30 October, 1981, Portland, Ore. Western Division, American Fisheries Society.
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American Association for the
Advancement of Science American Fisheries Society American Society of Ichthyologists
and Herpetologists American Society of Naturalists Desert Fishes Council Ecological & Evolutionary
Ethology of Fishes Society for Conservation Biology Society for the Study of Evolution
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Invited papers before professional societies: August 20, 2002 (pending). AFS Annual Meeting 2002, Baltimore, MD. “Development and application of microsatellites for Pacific halibut.” J. L. Nielsen*, G. K. Sage, B. Pierson, I. Williams, T. Waicek, S. Talbot, D. Wilson, and A. Seitz.August 17, 2002 (pending). EEEF 2002, Quebec City, CA. “Satellite pop-up tags and molecular genetics describe unique behavior for Pacific halibut in Alaska.” J. L. Nielsen*, G. K. Sage, D. Wilson, and A. Seitz. July, 6, 2002. ASIH annual meeting, Kansas City, MI. “Microsatellite analyses of the trout of northwest Mexico” J. L. Nielsen* and G. K. Sage. April 30, 2002. Toward ecosystem-based management, American Fisheries Society Western Division, Spokane, WA. “Hatchery and wild steelhead genetics in Idaho” J. L. Nielsen*, A. Byrne, S. Pavey and G. K. Sage. January 23, 2002. Exxon Valdes Trustee Committee Annual Meeting. “Using new Technologies in Ecosystem Science” J. L Nielsen (invited). August 24, 2001. American Fisheries Society, Phoenix, AZ. “Molecular genetics of the trout of northern Mexico” J. L. Nielsen and G. K. Sage (invited). March 30, 2001. American Fisheries Society Cal-Neva Chapter Meeting, Santa Rosa, CA. “Colonization by coho salmon (Oncorhynchus kisutch) in recently deglaciated streams in Glacier Bay, Alaska: Inference for restoration of Pacific salmon” J. L. Nielsen*, G. K. Sage, K. T. Scribner, E. Knudsen, and C. Soilseth (invited). February 22, 2001. American Fisheries Society Idaho Chapter Meeting, Boise, ID. Plenary Presentation: “Genetics vs. ecomorphology in fish management: Does it matter if reproductive isolation precedes or follows divergence between lineages?” J. L. Nielsen (invited). June 15, 2000. American Association of Ichthyology and Herpetology, La Paz, Mexico. "Molecular systematics and evolutionary status of the trout of the Sierra Madre, Mexico" J. L. Nielsen (invited). October 30, 1999. Pacific Fisheries Biologists, Astoria, Oregon. "Genetic analysis and management – Is near-real-time information on the Horizon" J. L. Nielsen (invited). October 30, 1999. Pacific Fisheries Biologists, Astoria , Oregon. "Advances in genetic techniques for stock discrimination: Finding the markers" J. L. Nielsen (invited). June 28, 1999. Joint Meeting ASIH, AES, HL, and SSAR. Pennsylvania State University. "Within basin life history divergence based on alternate reproductive strategies in steelhead: genetic and environmental considerations." J. L. Nielsen (invited). August 26, 1998. American Fisheries Society Annual Meeting, Hartford, Connecticut. "Molecular genetics and conservation of salmonids at the southern extent of their range in California and Mexico." J. L. Nielsen (invited). July 24, 1998. VII International Congress of Ecology, Florence, Italy. Special Symposium: Gene conservation: Identification and Management of Genetic Diversity. "Incorporating molecular evolutionary hybrids into ESU criteria" J. L. Nielsen (invited). Sept. 25, 1997. International Congress on the Exploration of the Sea (ICES) 1997 Annual Science Conference, Baltimore, MD. "Extinction risk and genetic variation in anadromous salmonids at the southern extent of their range." J. L. Nielsen (invited). June 29, 1997. American Association of Ichthyology and Herpetology, Seattle, WA - Special Symposium: Nuclear DNA and the Evolutionary Genetics of Fishes, Amphibians and Reptiles. "Molecular genetics and evolutionary status of the trout of the Sonora and Chihuahua desert region of Mexico." J. L. Nielsen*, M. C. Fountain, K. Cobble, J. Campoy Favela, and B. L. Jensen (invited). Nov. 7, 1996. Desert Fishes Council Annual Meeting. La Paz, Mexico. "Molecular genetics and evolutionary status of the trout of the Rio Yaqui drainage, Oncorhynchus mykiss spp., and San Pedro Matir rainbow trout Oncorhynchus mykiss nelsoni. J. L. Nielsen (invited). Presentations at technical conferences, seminars, and workshops: June 19, 2002. Alaska’s oceans and watersheds: sustainability in the context of change, EVOS Trustee Council, Anchorage, AK. “Electronic tagging and tracking of marine fishes?” J. L. Nielsen (invited).March 15, 2002. NPAFC/NASCO Conference, Vancouver, B.C. “Long-term trends in annual Bristol Bay sockeye salmon scale growth at sea in relation to sockeye abundance and environmental trends, 1955-2000.” (Poster) G. T. Ruggeroni, J. Nielsen, E. Farley, S. Ignell, P. Hagen, B. Agler, D. Rogers, and J. Bumgarner. January 16, 2002. 4th Annual Salmon Ocean Ecology Meeting, Santa Cruz, CA. “Testing Electronic Archival Tags in Coho Salmon in Alaska” J. L. Nielsen (invited). November 30, 2001. Departmental Seminar University of Alaska, Juneau, AK. “Electronic tagging and tracking of marine organisms in Alaska waters.” J. L. Nielsen (invited). November 14, 2001. The Status of Anadromous Fish in Bay Area Streams, Oakland, CA. “DNA sleuthing in urban streams: using molecular genetics to identify native California steelhead.” J. L. Nielsen (invited). November 13, 2001. AFS AK Chapter meeting, Sitka, AK. “ Testing satellite pop-up tags as a tool for identifying critical habitat.” J. L. Nielsen and D. Wilson*. November 6, 2001. Pacific Rim Wild Salmon and Steelhead Conference, Portland Oregon. “Steelhead distribution throughout Alaska.” (Poster) J. L. Nielsen* and D. Wilson. November 5, 2001. Pacific Rim Wild Salmon and Steelhead Conference, Portland Oregon. “Testing new electronic archival tags in Pacific salmon.” (Poster) J. L. Nielsen* and D. Wilson. October 26, 2001. Salmonid Coastwide genetics Meeting, Bodega Bay, CA. “Standardization of microsatellite alleles in Oncorhynchus mykiss.” J. L. Nielsen (invited). September 12, 2001. Special seminar University of Amsterdam, The Netherlands. “Scientific publication and resource conservation in the new century.” J. L. Nielsen (invited). July 9, 2001. Special seminar Idaho Department of Fish and Game. “Conservation units in resource management: Integrating genetics and ecology.” J. L. Nielsen (invited). May 3, 2001. Bering Sea Salmon Science Symposium, Dillingham, AK. “Global climate change and freshwater growth in sockeye salmon in drainages of the Bering Sea.” J. L. Nielsen (invited). January 24, 2001. SW Alaska National Parks science and research symposium, Anchorage, AK. “Effects of catch-and-release fishing and hooking injury on the physiology and behavior of Alagnak River rainbow trout.” D. Wilson, J. Meka, J. L. Nielsen, and E. Knudsen. January 24, 2001. SW Alaska National Parks science and research symposium, Anchorage, AK. “ Genetic population structure of rainbow trout (Oncorhynchus mykiss) within the Alagnak River drainage.” G. K. Sage*, J. Meka, J. L. Nielsen, D. Wilson, I. Williams, and E. Knudsen. January 24, 2001. SW Alaska National Parks science and research symposium, Anchorage, AK. “ Interesting salmon biology in the wake of cataclysmic geology.” T. Hamon* and J. L. Nielsen. Dec. 9, 2000.Census of Marine Life (CoML) Workshop on Pacific salmon, Vancouver, B. C. "Identifying research hypotheses for the study of wild salmon in the ocean" J. L. Nielsen (invited). Nov. 16, 2000. Distinguished Marine Scientists Seminar Series Hastings Marine Science Center, Newport, OR. "How do human impacts and genetic lineages limit our efforts to conserve salmonids" J. L. Nielsen (invited). Nov. 7, 2000. Workshop for standardization of microsatellite alleles in chinook and sockeye, Vancouver B. C. "Using the internet for standardization of microsatellite alleles" J. L. Nielsen (invited). Nov. 3, 2000. Russian-U. S. Fisheries Working Group, Leavenworth, WA. "Salmonid research in Alaska" J. L. Nielsen (invited). May 31, 2000.Symposium on the detection, status and management of introgressed populations of cutthroat trout, Boise ID. "Using mitochondrial DNA and microsatellite analyses to determine rainbow trout introgression in lahontan cutthroat trout" J. L Nielsen (invited). December 8, 1999, ICEBIRG: Genetics and Molecular Tools, Leetown Science Center, Kearneysville, WV. " Capstome Presentation: Genetics and molecular tools in USGS and successful partnerships." J. L. Nielsen (invited) Nov. 10, 1999, Alaska AFS Section Meeting, Kodiak, AK. "Differences in genetic diversity: Marine and landlocked steelhead from southeast Alaska." J. L. Nielsen. Sept. 2, 1999. National AFS Meeting, Charlotte, N. C. "Molecular systematics and conservation of a relic trout population: McCloud River redband trout." D. S. Wiltse (speaker), O. L. Avelino, M. C. Fountain, and J. L. Nielsen. Sept. 2, 1999. National AFS Meeting, Charlotte, N. C. "Comparative collection methods from carcass tissue of chinook salmon." O. L. Avelino (speaker) and J. L. Nielsen. Aug. 31, 1999. National AFS Meeting, Charlotte, N. C. "The role of hybridization in the distribution, conservation, and management of aquatic species." J. L. Nielsen. June 16, 1999. Department of Interior Coaster Brook Trout Meeting. "Biogeography of salmonid populations." J. L. Nielsen (invited). June 4, 1999. Coastwide Salmonid Genetics Workshop, Missoula, Montana. "Evaluating genetic diversity of Lahontan Cutthroat trout in Nevada, California and Oregon." J. L. Nielsen (invited). March 2, 1999. Lahontan Cutthroat Trout Genetic Management Workshop, Reno, NV. Use of DNA microsatellite markers, 1997 – present. J. L. Nielsen (invited). September 27, 1998. Northern California Chapter Federation of Fly Fishers, North Lake Tahoe. "Molecular genetics and conservation of Mexican golden trout." J. L. Nielsen (invited) June 2, 1998. University of California, Santa Barbara. "Molecular genetics of southern steelhead." J. L. Nielsen (invited). May 19, 1998. University of Nevada Reno. "Microsatellite analyses of Lahontan cutthroat trout." J. L. Nielsen (invited). April 15, 1998. Ecology of Stream Fish: State of the Art and Future Prospects, Luarca, Oviedo, Spain. "Genetic diversity in sympatric reproductive ecotypes of Pacific steelhead (Oncorhynchus mykiss) from the Middle Fork Eel River, California." J. L. Nielsen (invited). April 9, 1998. University of California, Berkeley, Department of Integrative Biology Seminar Series. "Molecular genetics and the conservation of wild salmonids in western North America." J. L. Nielsen (invited). March 27, 1998. Restoring the Southern California Steelhead: Issues and Implications. University of California, Santa Barbara. "The life history and genetics of southern California steelhead. " J. L. Nielsen (invited). Jan. 12-14, 1998. Stream Temperature Monitoring and Assessment Workshop, Sacramento, CA. "Stream temperature considerations in determining Evolutionarily Significant Units for recent listings of salmonids under the Federal Endangered Species Act." J. L. Nielsen (invited). Oct. 14, 1997. Friends of Hopkins Lecture, Hopkins Marine Station, Department of Biology, Stanford University. "Molecular genetics and the conservation of southern steelhead in California." J. L. Nielsen (invited). Sept. 17, 1997. National Marine Fisheries Service, Tiburon Laboratory. "The importance of genetic diversity for salmonids at the edge of their range." J. L. Nielsen (invited). Aug. 19, 1997. Wild Trout VI, Montana State University, Bozeman, MT. "Molecular genetics and evolutionary status of the trout of the Sierra Madre." J. L. Nielsen. Aug. 12, 1997. Department of Biology, San Francisco State University. "Molecular genetics and evolutionary status of the trout of the Sierra Madre." J. L. Nielsen (invited). July 9, 1997. Monterey Bay Aquarium. "Molecular genetics and conservation of southern steelhead." J. L. Nielsen (invited). June 2, 1997. University of California, Santa Barbara, Seminar Series in Endangered Species Management, Department of Environmental Studies. "Conservation Genetics of Southern Steelhead." J. L. Nielsen, (Invited). March 27, 1997. NOAA NMFS Northwest Science Center, Seattle WA. Salmonid Genetics Symposium. " Mitochondrial DNA and nuclear microsatellite diversity in hatchery and wild Oncorhynchus mykiss from freshwater habitats in southern California." J. L. Nielsen (invited). March 18, 1997. Integrating Across Scales: Predicting Patterns of Change in Atlantic Salmon. Focus Talk #9: Population Genetics. Aberdeen Scotland. J. L. Nielsen (invited). March 3, 1997. Washington State University, Department of Biology Seminar Series, Pullman, WA. "Molecular genetics and the conservation of southern steelhead in California." J. L. Nielsen (invited) Feb. 27, 1997. Eighth Conference of the U.S./Mexico Border States on Recreation, Parks and Wildlife, Hermosillo, Mexico. "Molecular genetics and evolutionary status of the trout of the Rio Yaqui drainage." J. L. Nielsen (invited) Feb. 19, 1997. Keystone Symposium - Molecular Mechanisms of Evolution, Santa Fe NM. "Form follows function: replication-competent salmonid mitochondrial control region lacking direct repeat with heavy-strand promoter." J. L. Nielsen (invited).
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Avelino, Olivia 2000 – present, M. Sc. Sacramento State University. Employed in lab 1998 - 1999. Carpanzano, Cindy 1996, M. Sc. University of California, Santa Barbara. Habitat relationships in southern steelhead. JLN served on Thesis Committee and funded research. Cheney, Lisa C. 1995, M. Sc. San Jose State University, Moss Landing Marine Lab. Thesis topic: conservation genetic of the Pacific sea otter. Employed in lab 1995-1996. Crewdson, Yarrow 2000, Undergraduate Whitman College, Washington. Employed in lab 2000-2002. Crow, Karen 1995, M. Sc. San Francisco State University, Moss Landing Marine Lab. Thesis topic: conservation genetics of kelp greenling. Employed in lab 1995-1996. Currently a Ph.D. student at UC Santa Cruz. Fountain, Monique C. 1997, M. Sc. San Francisco State University. Thesis topic: Conservation genetics and the European green crab introduction into San Francisco Bay. Employed in lab 1995 - present. Gan, Christina A. 1997, M. Sc. Humboldt State University. Thesis topic: Golden trout genetics of the Kern Plateau. JLN served on Graduate Committee and funded research. Heine, Erica 1997, B. Sc. California Polytechnic University. Student technician in Nielsen laboratory 1997- 1998. Currently M. Sc. Student California Polytechnic University. Lowery. Alex 1997, Mountain View H. S. Senior Project - MHC polymorphisms in steelhead from Alaska to California. Molecular science work done in Nielsen lab. Currently undergraduate at Stanford University. McClean, Scott 1999-2002. M. Sc. University of Alaska Fairbanks. Research sponsor and supervisor. Effects of upwelling on survival and production of chum salmon in redds on the Yukon River. JLN funded thesis research. Malone, Catherine L. 1994, B. A. University of California Santa Cruz. Americorp volunteer in lab 1994-1995. Currently Ph. D. student Texas A & M Univ. Employed in lab 1996. Meka, Julie 2000 – 2003. M. Sc. University of Alaska Fairbanks. Thesis topic: stress physiology and injury in rainbow trout subject to catch-and-release fishing. JLN serves on Thesis Committee and funds research. Neville, Helen M. 1998 – present, Ph. D. student University of Nevada, Reno. Thesis topic: Metapopulations structure and genetics of Lahontan Cutthroat trout. JLN serves on Graduate Committee. Pavey, Scott 2001-2004, M. Sc. University of Alaska – Anchorage. Thesis topic: Rapid microevolution in sockeye salmon on the Aniakchak River, Alaska. JLN serves on Thesis Committee and funds research. Pelot, Sage, 2000. Undergraduate University of California Davis. Student appointment 2000. Rasgon. Jason 1996, Senior San Jose State University. Employed in lab 1996. Currently M. Sc. Student California Polytechnic University. Rathhouz. Margaret M. 1996, Ph. D. University of California, San Diego. Employed in lab 1996-1997. Reamey, Jacklyn 2001-04, DOI SCEP Native America student appointment. Sheldon Jackson College, Sitka, AK. Study topic is Alaska blackfish genetics. Seitz, Andy 2002. Ph. D. University of Alaska, Fairbanks. Population substructure derived from satellite pop-up tags in Pacific halibut. JLN serves on Thesis Committee and funds research. Sundermeyer, Ruth, 1999, M. Sc., San Jose State University. Thesis topic: Molecular genetics of steelhead in the Pajaro River basin. Employed in lab 1996 - 1999. Waicek, Talia C. 2000, Senior University of Alaska Anchorage, Employed in lab 2000-2002. Williams, Ian 2001-2004, M. Sc. University of Alaska Anchorage. Thesis topic: Genetic introgression between coastal cutthroat trout and steelhead on the Copper River, Alaska. JLN serves on Thesis Committee and funds research. Wiltse, Darren S. 1998, M. Sc. San Jose State University. Employed in lab 1998 - 1999. Wise, Lawrence M. 1996, M. Sc., San Francisco State University. Thesis: Consistency of Focal Position by Juvenile Rainbow Trout and Brown Trout in a Central Sierra Nevada Stream. JLN served on Thesis Committee and advised funding agency (EPRI).
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Last Reviewed: 09/11/2002