Select Publications

2012 Roberts, SB, L Hauser, LW Seeb, JE Seeb. Development of genomic resources for Pacific herring through targeted transcriptome pyrosequencing. PLOS One 7(2):e30908.  doi:10.1371/journal.pone.0030908.

2012 Gomez-Uchida, D, JE Seeb, C Habicht, LW Seeb. Allele frequency stability in large, wild exploited populations over multiple generations: insights from Alaska sockeye salmon (Oncorhynchus nerka). Can. J. Fish. Aquat. Sci. 69:916-929. doi:10.1139/F2012-029.

2011 Seeb, L. W., J. E. Seeb, C. Habicht, E. V. Farley, and F. M. Utter. Single-nucleotide polymorphic genotypes reveal patterns of early juvenile migration of sockeye salmon in the Eastern Bering Sea. Transactions of the American Fisheries Society 140(3):734-748, doi:10.1080/00028487.2011.584493.

2011 Seeb, JE, G Carvalho, L Hauser, K Naish, S Roberts, and LW Seeb.  Single-nucleotide polymorphism (SNP) discovery and  applications of SNP genotyping in non-model organisms.  Molecular Ecology Resources 11: in press.

2011  Everett MV, ED Grau, and JE Seeb.  Short reads and non-model species:  Exploring the complexities of next generation sequence assembly and SNP discovery in the absence of a reference genome. Molecular Ecology Resources 11: in press.

2011  Seeb, JE, CE Pascal, ED Grau, LW Seeb, WD Templin, SB Roberts, and T Harkins. Transcriptome sequencing and high-resolution melt analysis advance SNP discovery in duplicated salmonids. Molecular Ecology Resources online early doi: 10.1111/j.1755-0998.2010.02936.x.

2010  Gaffney, PM, CM Elfstrom, CT Smith, J Barnhart, WS Grant and JE Seeb.  Genetic Homogeneity of Weathervane Scallops in the Northeastern Pacific.  Canadian Journal of Fisheries and Aquatic Sciences 67:1827–1839.

2010  Habicht, C, LW Seeb, KW Myers, EV Farley, and JE Seeb.  Summer-fall distribution of stocks of immature sockeye salmon in the Bering Sea as revealed by single nucleotide polymorphisms (SNPs). Transactions of the American Fisheries Society 139:1171-1191.

2010  Utter, FM, and JE Seeb. A perspective on positive relationships between genetic diversity and abundance in fishes.  Molecular Ecology 9:4831-4833.

2009  Seeb JE, CE Pascal, R Ramakrishnan, and LW Seeb.  SNP genotyping by the 5'-nuclease reaction: advances in high throughput genotyping with non-model organisms. In: Methods in Molecular Biology, Single Nucleotide Polymorphisms, 2d Edition (ed. A Komar), pp. 277-292. Humana Press, New York.

2007  Habicht, C, LW Seeb, and JE 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. 

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 and map SNPs using various approaches including highly parallel DNA sequencing.  As of early 2011 we had sequenced the transcriptomes of several individuals from each of four Oncorhynchus species using a combination of 454 and SOLiD platforms.  Our current focus is to use RAD sequencing on an Illumina platform to genotype individuals from paired haploid and diploid families.  This approach will accelerate discovery, elimination of paralogous sequence variants, and mapping.  Much of this effort is enabled by a grant from the Gordon and Betty Moore Foundation.

The Moore Foundation provided seed funding for 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 to conduct both basic and applied research.  A newly developing goal is to seek to better understand the genetic mechanisms underlying  response to environmental change by placing our newly acquired and abundant sequence information into an ecological genomics context. 

Two additional and 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 2011, IPSEG is composed of 2 faculty, 1 research scientist, 2 post docs, and 4 graduate students. We plan to accept 1-2 students next year.