Publications

2017

Ackerman, M. W., B. K. Hand, R. K. Waples, G. Luikart, R. S. Waples, C. A. Steele, B. A. Garner, J. McCane, and M. R. Campbell. 2017. Effective number of breeders from sibship reconstruction: empirical evaluations using hatchery steelhead. Evol Appl 10(2):146-160.   10.1111/eva.12433

Canales-Aguirre, C.B., L.W. Seeb, J.E. Seeb, M.I. Cadiz, S.S. Musleh, I. Arismendi,  G. Gajardo, R. Galleguillos, and D. Gomez-Uchida. 2017. Contrasting genetic metrics and patterns among naturalized rainbow trout (Oncorhynchus mykiss) in two Patagonian lakes differentially impacted by trout aquaculture. Ecology and Evolution.

Cunningham, C. J., T. A. Branch, T. H. Dann, M. Smith, J. E. Seeb, L. W. Seeb, and R. Hilborn. 2017. A general model for salmon run reconstruction that accounts for interception and differences in availability to harvest. Canadian Journal of Fisheries and Aquatic Sciences:    10.1139/cjfas-2016-0360

Larson, W. A., M. T. Limborg, G. J. McKinney, D. E. Schindler, J. E. Seeb, and L. W. Seeb. 2017. Genomic islands of divergence linked to ecotypic variation in sockeye salmon. Molecular Ecology 26(2):554-570. 10.1111/mec.13933

Larson, W. A., Y. Palti, G. Gao, K. I. Warheit, and J. E. Seeb. 2017. Rapid discovery of SNPs that differentiate hatchery steelhead trout from ESA-listed natural-origin steelhead trout using a 57K SNP array. Canadian Journal of Fisheries and Aquatic Sciences.  10.1139/cjfas-2017-0116

Limborg, M.T., W.A. Larson, L.W. Seeb, and J.E. Seeb. 2017. Screening of duplicated loci reveals hidden divergence patterns in a complex salmonid genome. Mol Ecol 26(17): 4509-4522. 10.1111/mec.14201/ful

Limborg, M.T., W.A. Larson, K. Shedd, L.W. Seeb, and J.E. Seeb. 2017. Novel RAD sequence data reveal a lack of genomic divergence between dietary ecotypes in a landlocked salmonid population. Conservation Genetics Resources. 10.1007/s12686-017-0791-4

McKinney, G.J., W.A. Larson, L.W. Seeb, and J.E. Seeb. 2017. RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al. (2016). Mol Ecol Resour 17(3): 356-361. 10.1111/1755-0998.12649

McKinney, G.J., J.E. Seeb, and L.W. Seeb. 2017. Managing mixed-stock fisheries: genotyping multi-SNP haplotypes increases power for genetic stock identification. Canadian Journal of Fisheries and Aquatic Sciences 74(4): 429-434. 10.1139/cjfas-2016-0443

McKinney, G.J., R.K. Waples, L.W. Seeb, and J.E. Seeb. 2017. Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping-by-sequencing data from natural populations. Molecular Ecology Resources 17(4): 656-669. 10.1111/1755-0998.12613

Seeb, L.W., W.D. Templin, C. Habicht, F.M. Utter, and J.E. Seeb. In press. Methods Used to Study the Ocean Ecology of Pacific Salmon and Trout: Salmon Genetic Stock Identification. In: The Ocean Ecology of Pacific Salmon and Trout. Edited by R. Beamish. American Fisheries Society.

Tarpey, C.M., J.E. Seeb, G.J. McKinney, W.D. Templin, A.V. Bugaev, S. Sato, and L.W. Seeb. 2017. SNP data describe contemporary population structure and diversity in allochronic lineages of pink salmon (Oncorhynchus gorbuscha). Canadian Journal of Fisheries and Aquatic Sciences. 10.1139/cjfas-2017-0023

Waples, R.K., J.E. Seeb, and L.W. Seeb. 2017. Congruent population structure across paralogous and nonparalogous loci in Salish Sea chum salmon (Oncorhynchus keta). Mol Ecol 26(16): 4131-4144. 10.1111/mec.14163

2016

Larson, W.A., P.J. Lisi, J.E. Seeb, L.W. Seeb, and D.E. Schindler. 2016. Major histocompatibility complex diversity is positively associated with stream water temperatures in proximate populations of sockeye salmon. J Evol Biol 29(9): 1846-1859. 10.1111/jeb.12926

Larson, W.A., G.J. McKinney, M.T. Limborg, M.V. Everett, L.W. Seeb, and J.E. Seeb. 2016. Identification of multiple QTL hotspots in sockeye salmon (Oncorhynchus nerka) using Genotyping-by-Sequencing and a dense linkage map. Journal of Heredity 107(2): 122-133. 10.1093/jhered/esv099

Larson, W.A., G.J. McKinney, J.E. Seeb, and L.W. Seeb. 2016. Identification and Characterization of Sex-Associated Loci in Sockeye Salmon Using Genotyping-by-Sequencing and Comparison with a Sex-Determining Assay Based on the sdY Gene. Journal of Heredity 107(6): 559-566. 10.1093/jhered/esw043

Limborg, M. T., McKinney, G. J., Seeb, L. W. and Seeb, J. E. (2016), Recombination patterns reveal information about centromere location on linkage maps. Molecular Ecology Resources 16: 655–661. 10.1111/1755-0998.12484

Limborg, M. T., Seeb, L. W. and Seeb, J. E. (2016), Sorting duplicated loci disentangles complexities of polyploid genomes masked by genotyping by sequencing. Molecular Ecology 25(10):2117-2129. 10.1111/mec.13601

McKinney, G. J., Seeb, L. W., Larson, W. A., Gomez-Uchida, D., Limborg, M. T., Brieuc, M. S. O., Everett, M. V., Naish, K. A., Waples, R. K. and Seeb, J. E. (2016), An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha). Molecular Ecology Resources 16: 769–783. 10.1111/1755-0998.12479

Waples, R.K., W.A. Larson, and R.S. Waples. 2016. Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci. Heredity (Edinb) 117(4): 233-240. 10.1038/hdy.2016.60

Waples, R. K., L. W. Seeb, and J. E. Seeb. 2016. Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta). Molecular Ecology Resources 16(1):17-28. 10.1111/1755-0998.12394

2015

Allendorf, F. W., S. Bassham, W. A. Cresko, M. T. Limborg, L. W. Seeb, and J. E. Seeb. 2015a. Effects of crossovers between homeologs on inheritance and population genomics in polyploid-derived salmonid fishes. Journal of Heredity 106(3):217-27. 10.1093/jhered/esv015

Allendorf, F. W., S. Bassham, W. A. Cresko, M. T. Limborg, L. W. Seeb, and J. E. Seeb. 2015b. Response to May and Delany: We Never Said Wright was Wrong. Journal of Heredity. 10.1093/jhered/esv072

Bekkevold, D., S. J. Helyar, M. T. Limborg, E. E. Nielsen, J. Hemmer-Hansen, L. A. W. Clausen, and G. R. Carvalho. 2015. Gene-associated markers can assign origin in a weakly structured fish, Atlantic herring. ICES Journal of Marine Science: Journal du Conseil. 10.1093/icesjms/fsu247

Benavente, J. N., L. W. Seeb, J. E. Seeb, I. Arismendi, C. E. Hernandez, G. Gajardo, R. Galleguillos, M. I. Cadiz, S. S. Musleh, and D. Gomez-Uchida. 2015. Temporal genetic variance and propagule-driven genetic structure characterize naturalized rainbow trout (Oncorhynchus mykiss) from a Patagonian lake impacted by trout farming. PLoS ONE e0142040. 10.1371/journal.pone.0142040

Candy, J. R., N. R. Campbell, M. H. Grinnell, T. D. Beacham, W. A. Larson, and S. R. Narum. 2015. Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt. Molecular Ecology Resources 15(6):1421-1434. 10.1111/1755-0998.12400

Jones, M. H., J. E. Seeb, K. I. Warheit, T. R. Seamons, T. P. Quinn, and L. W. Seeb. 2015. Consequences of emergence timing for the growth and relative survival of steelhead fry from naturally spawning wild and hatchery parents. Transactions of the American Fisheries Society 144(5):977-989. 10.1080/00028487.2015.1057346

Limborg, M. T., R. K. Waples, F. W. Allendorf, and J. E. Seeb. 2015. Linkage mapping reveals strong chiasma interference in sockeye salmon: implications for interpreting genomic data. G3: Genes|Genomes|Genetics 5(11):2463-2473. 10.1534/g3.115.020222

McKinney, G. J., M. C. Hale, G. Goetz, M. Gribskov, F. P. Thrower, and K. M. Nichols. 2015. Ontogenetic changes in embryonic and brain gene expression in progeny produced from migratory and resident Oncorhynchus mykiss. Molecular Ecology 24(8):1792-1809. 10.1111/mec.13143

Small, M. P., S. D. Rogers Olive, L. W. Seeb, J. E. Seeb, C. E. Pascal, K. I. Warheit, and W. Templin. 2015. Chum salmon genetic diversity in the Northeastern Pacific Ocean assessed with single nucleotide polymorphisms (SNPs): Applications to fishery management. North American Journal of Fisheries Management 35(5):974-987. 10.1080/02755947.2015.1055014

Stockwell, B. L., W. A. Larson, R. K. Waples, R. A. Abesamis, L. W. Seeb, and K. E. Carpenter. 2015. The application of genomics to inform conservation of a functionally important reef fish (Scarus niger) in the Philippines. Conservation Genetics:1-11. 10.1007/s10592-015-0776-3

2014

Andrews, K. R., P. A. Hohenlohe, M. R. Miller, B. K. Hand, J. E. Seeb, and G. Luikart. 2014. Trade-offs and utility of alternative RADseq methods: Reply to Puritz et al. Molecular Ecology 23(24):5943-5946. 10.1111/mec.12964

Bond, M. H., P. A. Crane, W. A. Larson, and T. P. Quinn. 2014. Is isolation by adaptation driving genetic divergence among proximate Dolly Varden char populations? Ecology and Evolution 4(12):2515-2532.DOI 10.1002/ece3.1113

Brieuc, M. S., C. D. Waters, J. E. Seeb, and K. A. Naish. 2014. A dense linkage map for Chinook salmon (Oncorhynchus tshawytscha) reveals variable chromosomal divergence after an ancestral whole genome duplication event. G3: Genes|Genomes|Genetics 4(3):447-60. 10.1534/g3.113.009316

Gomez-Uchida, D., L. W. Seeb, K. I. Warheit, G. J. McKinney, and J. E. Seeb. 2014. Deep sequencing of the transcriptome and mining of single nucleotide polymorphisms (SNPs) provide genomic resources for applied studies in Chinook salmon (Oncorhynchus tshawytscha). Conservation Genetics Resources 6(4):807-811. 10.1007/s12686-014-0235-3

Gruenthal, K. M., D. A. Witting, T. Ford, M. J. Neuman, J. P. Williams, D. J. Pondella, A. Bird, N. Caruso, J. R. Hyde, L. W. Seeb, and W. A. Larson. 2014. Development and application of genomic tools to the restoration of green abalone in southern California. Conservation Genetics 15(1):109-121. 10.1007/s10592-013-0524-5

Khrustaleva, A. M., N. V. Klovach, O. F. Gritsenko, and J. E. Seeb. 2014. Intra- and interpopulation variability of southwestern Kamchatka sockeye salmon Oncorhynchus nerka inferred from the data on single nucleotide polymorphism. Russian Journal of Genetics 50(7):736-748. 10.1134/s1022795414070096

Larson, W. A., J. E. Seeb, T. H. Dann, D. E. Schindler, and L. W. Seeb. 2014. Signals of heterogeneous selection at an MHC locus in geographically proximate ecotypes of sockeye salmon. Molecular Ecology 23(22):5448-5461. 10.1111/mec.12949

Larson, W. A., L. W. Seeb, M. V. Everett, R. K. Waples, W. D. Templin, and J. E. Seeb. 2014. Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha). Evol Appl 7(3):355-69. 10.1111/eva.12128

Limborg, M. T., R. K. Waples, J. E. Seeb, and L. W. Seeb. 2014. Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation. Journal of Heredity 105(6):741-751. 10.1093/jhered/esu063

Petrou, E. L., J. E. Seeb, L. Hauser, M. J. Witteveen, W. D. Templin, and L. W. Seeb. 2014. Fine-scale sampling reveals distinct isolation by distance patterns in chum salmon (Oncorhynchus keta) populations occupying a glacially dynamic environment. Conservation Genetics 15(1):229-243. 10.1007/s10592-013-0534-3

Sato, S., W. D. Templin, L. W. Seeb, J. E. Seeb, and S. Urawa. 2014. Genetic structure and diversity of Japanese chum salmon populations inferred from single-nucleotide polymorphism markers. Transactions of the American Fisheries Society 143(5):1231-1246. 10.1080/00028487.2014.901251

Seeb, L. W., R. K. Waples, M. T. Limborg, K. I. Warheit, C. E. Pascal, and J. E. Seeb. 2014. Parallel signatures of selection in temporally isolated lineages of pink salmon. Molecular Ecology 23(10):2473-2485. 10.1111/mec.12769

Willette, D. A., F. W. Allendorf, P. H. Barber, K. E. Carpenter, C. E. D., W. A. Cresko, I. Fernandez-Silva, M. V. Matz, E. Meyer, M. D. Santos, L. W. Seeb, and J. E. Seeb. 2014. So, you want to use next-generation sequencing in marine systems? Insight from the Pan-Pacific Advanced Studies Institute. Bulletin of Marine Science 90(1):79-122. 10.5343/bms.2013.1008

2013

Dann, T. H., C. Habicht, T. T. Baker, and J. E. Seeb. 2013. Exploiting genetic diversity to balance conservation and harvest of migratory salmon. Canadian Journal of Fisheries and Aquatic Sciences 70(5):785-793. 10.1139/cjfas-2012-0449

Griffiths, J. R., D. E. Schindler, and L. W. Seeb. 2013. How stock of origin affects performance of individuals across a meta-ecosystem: an example from sockeye salmon. PLoS ONE 8(3):e58584. 10.1371/journal.pone.0058584

Jones, M. 2013. AFS Genetics Section Members Attend Meeting on “Next Generation” DNA Sequencing for Fisheries Research in Southeast Asia. Fisheries 38(May 2013):228-229. 10.1080/03632415.2013.800352

Jones, M. 2013. Environmental DNA: Genetics steps forward when traditional ecological surveys fall short. Fisheries 38(July 2013):332-333. 10.1080/03632415.2013.810984

Larson, W. A., F. M. Utter, K. W. Myers, W. D. Templin, J. E. Seeb, G. I. C. M., A. V. Bugaev, and L. W. Seeb. 2013. Single-nucleotide polymorphisms reveal distribution and migration of Chinook salmon (Oncorhynchus tshawytscha) in the Bering Sea and North Pacific Ocean. Canadian Journal of Fisheries and Aquatic Sciences 70(1):128-141. 10.1139/cjfas-2012-0233

Moran, P., D. J. Teel, M. A. Banks, T. D. Beacham, M. R. Bellinger, S. M. Blankenship, J. R. Candy, J. C. Garza, J. E. Hess, S. R. Narum, L. W. Seeb, W. D. Templin, C. G. Wallace, C. T. Smith, and E. Taylor. 2013. Divergent life-history races do not represent Chinook salmon coast-wide: the importance of scale in Quaternary biogeography. Canadian Journal of Fisheries and Aquatic Sciences 70(3):415-435. 10.1139/cjfas-2012-0135

Warheit, K. I., L. Seeb, W. D. Templin, and J. Seeb. 2013. Moving GSI into the Next Decade: SNP coordination for Pacific Salmon Treaty Fisheries, Washington Department of Fish and Wildlife Report FPT-13-09, Olympia. Available at: http://wdfw.wa.gov/publications/01629/.

2012

Everett, M. V., M. R. Miller, and J. E. Seeb. 2012. Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing. BMC Genomics 13(1):521. 10.1186/1471-2164-13-521

Gomez-Uchida, D., James E. Seeb, C. Habicht, and Lisa W. Seeb. 2012. Allele frequency stability in large, wild exploited populations over multiple generations: insights from Alaska sockeye salmon (Oncorhynchus nerka). Canadian Journal of Fisheries and Aquatic Sciences 69(5):916-929. 10.1139/f2012-029

Limborg, M. T., S. J. Helyar, M. de Bruyn, M. I. Taylor, E. E. Nielsen, R. Ogden, G. R. Carvalho, D. Bekkevold, and F. P. T. Consortium. 2012. Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus). Molecular Ecology 21(15):3686-3703. 10.1111/j.1365-294X.2012.05639.x

Limborg, M. T., S. M. Blankenship, S. F. Young, F. M. Utter, L. W. Seeb, M. H. H. Hansen, and J. E. Seeb. 2012. Signatures of natural selection among lineages and habitats in Oncorhynchus mykiss. Ecology and Evolution 2(1):1-18. 10.1002/ece3.59

Petrou, E. L., L. Hauser, R. S. Waples, J. E. Seeb, W. D. Templin, D. Gomez-Uchida, and L. W. Seeb. 2013. Secondary contact and changes in coastal habitat availability influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta). Molecular Ecology 22(23):5848-60. 10.1111/mec.12543

Roberts, S. B., L. Hauser, L. W. Seeb, and J. E. Seeb. 2012. Development of genomic resources for Pacific herring through targeted transcriptome pyrosequencing. PLoS ONE 7(2):e30908. 10.1371/journal.pone.0030908

Simmons, R., T. Quinn, L. Seeb, D. Schindler, and R. Hilborn. 2013. Role of estuarine rearing for sockeye salmon in Alaska (USA). Marine Ecology Progress Series 481:211-223. 10.3354/meps10190

Simmons, R. K., T. P. Quinn, L. W. Seeb, D. E. Schindler, and R. Hilborn. 2013. Summer emigration and resource acquisition within a shared nursery lake by sockeye salmon (Oncorhynchus nerka) from historically discrete rearing environments. Canadian Journal of Fisheries and Aquatic Sciences 70(1):57-63. 10.1139/cjfas-2012-0159

Storer, C. G., C. E. Pascal, S. B. Roberts, W. D. Templin, L. W. Seeb, and J. E. Seeb. 2012. Rank and Order: Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism. PLoS ONE 7(11):e49018. 10.1371/journal.pone.0049018

For a list of publications prior to 2012, please click HERE.

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