Select Publications

2007  Habicht, C., L.W. Seeb, and J.E. Seeb. Genetic and ecological divergence defines population structure of sockeye salmon populations returning to Bristol Bay, Alaska, and provides a tool for admixture analysis.  Trans. Amer. Fish. Soc. 136:82-94. 

2007  Ramstad, K.M., C.A.Woody,  C. Habicht, G.K. Sage, J.E. Seeb, and F.W. Allendorf. Concordance of nuclear and mitochondrial DNA markers in detecting a founder event in Lake Clark sockeye salmon. Amer. Fish. Soc. Symp. 54:31-50. 

2006  Elfstrom, C.M., C.T. Smith, and J.E. Seeb. Thirty-two single nucleotide polymorphism markers for high-throughput genotyping of sockeye salmon. Mol. Ecol. Notes 6: 1255-1259.

2005  Smith, C.T., C.M. Elfstrom, L.W. Seeb, and J.E. Seeb. Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon.  Mol. Ecol. 205(14):4193-4203.

2005  Elfstrom, C.M, P.M. Gaffney, C.T. Smith, and J.E. Seeb. Characterization of 12 single nucleotide polymorphisms in weathervane scallop. Mol. Ecol. Notes 5:406-409.

2005  Smith, C.T, J.E. Seeb, P. Schwenke, and L.W. Seeb. Use of the 5’nuclease reaction for single nucleotide polymorphism genotyping in Chinook salmon. Trans. Amer. Fish. Soc. 134:207-217.

2005  Smith, C.T, W.D. Templin, J.E. Seeb, and L.W. Seeb. Single nucleotide polymorphisms provide rapid and accurate estimates of the proportions of U.S. and Canadian Chinook salmon caught in Yukon River fisheries. N. Amer. J. Fish. Man. 25:944–953, 2005.

2005  Smith, C.T., J. Baker, L. Park, L.W. Seeb, C. Elfstrom, S. Abe, J.E. Seeb. Characterization of 13 single nucleotide polymorphism markers for chum salmon. Mol. Ecol. Notes 5:259-262.

2004  Seeb, L.W., P.A. Crane, K.M. Kondzela, R.L. Wilmot, S. Urawa, N. Varnavskaya, and J.E. Seeb. Migration of Pacific Rim chum salmon on the high seas: insights from genetic data. Env. Biol. Fish. 69:21-36.

2004  Olsen, J.B., C. Habicht, and J.E. Seeb. Moderately and highly polymorphic microsatellites provide discordant estimates of population divergence in sockeye salmon, Oncorhynchus nerka. Env. Biol. Fish. 69:261-273.

2004  Habicht, C., J.B. Olsen, L. Fair, and J.E. Seeb. Smaller effective population sizes evidenced by loss of microsatellite alleles in tributary-spawning populations of sockeye salmon from the Kvichak River drainage. Env. Biol. Fish. 69:51-62.

Current students may contact this person about availability as a faculty advisor.

My research focuses upon identifying gene markers that distinguish populations, demes, or individual Pacific salmon. I currently have projects or am collaborating on projects to use these markers to study migration of adults in the Bering Sea or migration of juveniles in complex lake systems. The gene marker that provides the most information for this work is the single nucleotide polymorphism (SNP).

We discover SNPs using various DNA chemistry approaches including highly parallel DNA sequencing. In a new effort during summer 2008, 454 Life Sciences provided us with 250,000,000 bp each from two chum salmon from Alaska; sequence from these two individuals provides an important backbone for SNP discovery in salmon throughout the species range. Much of this effort is enabled by a grant from the Gordon and Betty Moore Foundation.

The Moore Foundation funded the International Program for Salmon Ecological Genetics here in the University of Washington School of Aquatic and Fisheries Sciences (SAFS). Lisa Seeb and I cooperatively run the program which provides an important intersection between the Alaska Salmon Program and the SAFS Molecular Ecology Research Laboratory. With this grant we are building a high throughput genotyping laboratory, conducting research to discover single nucleotide polymorphisms that may be used in studies of stock identification or ecological genetics, and conducting an array of projects examining the distribution and migration of salmon.

Two important missions of IPSEG are to (1) host scientists from Asia to establish cooperative studies of mutual interest and (2) generate and develop and online database of SNP frequencies for Pacific salmon. We plan to engage scientists from the Russian Federal Institute of Fisheries (VNIRO), Pacific Scientific Research Fisheries Centre (TINRO), Hokkaido University, Fisheries Agency of Japan, or others who might share interest in these missions.

As of summer 2008, IPSEG is composed of 2 faculty, 2 research scientists, and 4 graduate students. We are currently seeking 2 post-docs and plan to accept 1-3 students next year.