2019
Arostegui, M.C., T.P. Quinn, L.W. Seeb, J.E. Seeb, and G.J. McKinney. 2019. Retention of a chromosomal inversion from an anadromous ancestor provides the genetic basis for alternative freshwater ecotypes in rainbow trout. Mol Ecol 28(6): 1412-1427. https://doi.org/10.1111/mec.15037
Larson, W.A., T.H. Dann, M.T. Limborg, G.J. McKinney, J.E. Seeb, and L.W. Seeb. 2019. Parallel signatures of selection at genomic islands of divergence and the major histocompatibility complex in ecotypes of sockeye salmon across Alaska. Molecular Ecology 28(9): 2254-2271. https://doi.org/10.1111/mec.15082
McKinney, G.J., C.E. Pascal, W.D. Templin, S.E. Gilk-Baumer, T.H. Dann, L.W. Seeb, and J.E. Seeb. 2019. Dense SNP panels resolve closely related Chinook salmon populations. Canadian Journal of Fisheries and Aquatic Sciences Early online. https://doi.org/10.1139/cjfas-2019-0067
McKinney, G.J., J.E. Seeb, C.E. Pascal, D.E. Schindler, S.E. Gilk-Baumer, and L.W. Seeb. 2019. Y-chromosome haplotypes drive variation in size and age at maturity in male Chinook salmon. bioRxiv: 691063. https://doi.org/10.1101/691063
Phelps, M.P., L.W. Seeb, and J.E. Seeb. 2019. Transforming ecology and conservation biology through genome editing. Conserv Biol Early online. https://doi.org/10.1111/cobi.13292
2018
Canales-Aguirre, C.B., L.W. Seeb, J.E. Seeb, M.I. Cádiz, S.S. Musleh, I. Arismendi, . . . D. Gomez-Uchida. 2018. Contrasting genetic metrics and patterns among naturalized rainbow trout (Oncorhynchus mykiss) in two Patagonian lakes differentially impacted by trout aquaculture. Ecology and Evolution 8(1): 273-285. 10.1002/ece3.3574
Cunningham, C.J., T.A. Branch, T.H. Dann, M. Smith, J.E. Seeb, L.W. Seeb, and R. Hilborn. 2018. A general model for salmon run reconstruction that accounts for interception and differences in availability to harvest. Canadian Journal of Fisheries and Aquatic Sciences 75(3):439-451. 10.1139/cjfas-2016-0360
Gomez-Uchida, D., D. Cañas-Rojas, C. M. Riva-Rossi, J. E. Ciancio, M. A. Pascual, B. Ernst, E. Aedo, S. S. Musleh, F. Valenzuela-Aguayo, T. P. Quinn, J. E. Seeb, and L. W. Seeb. 2018. Genetic signals of artificial and natural dispersal linked to colonization of South America by non-native Chinook salmon (Oncorhynchus tshawytscha). Ecology and Evolution 8(12):6192-6209. 10.1002/ece3.4036
Larson, W. A., Y. Palti, G. Gao, K. I. Warheit, and J. E. Seeb. 2018. 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 75(7): 1160-1168 10.1139/cjfas-2017-0116
McKinney, G. J., R. K. Waples, C. E. Pascal, L. W. Seeb, and J. E. Seeb. 2018. Resolving allele dosage in duplicated loci using genotyping-by-sequencing data: A path forward for population genetic analysis. Mol Ecol Resour 18(3):570-579. 10.1111/1755-0998.12763
Schindler, D. E., L. W. Seeb, and J. E. Seeb. 2018. Diversity in Bristol Bay sockeye salmon and their habitat: implications for fisheries and wildlife. Pages 475-489 in C. A. Woody, editor. Bristol Bay Alaska: Natural Resources of the Aquatic and Terrestrial Ecosystems. J. Ross Publishing, Plantation, FL.
Seeb, L. W., W. D. Templin, C. Habicht, F. M. Utter, and J. E. Seeb. 2018. Methods Used to Study the Ocean Ecology of Pacific Salmon and Trout: Genetic Stock Identification of Pacific Salmon. Pages 1020-1042 in R. Beamish, editor. The Ocean Ecology of Pacific Salmon and Trout. American Fisheries Society.
Seeb, L.W., G.J. McKinney, and J.E. Seeb. 2018. “Chromosomes and genes, spawned these fateful scenes”: Rapid adaptation in an introduced fish. Molecular Ecology 27(20): 3965-3967. 10.1111/mec.14797
Spano, C. A., V. Häussermann, F. H. Acuña, C. Griffiths, L. W. Seeb, and D. Gomez-Uchida. 2018. Hierarchical biogeographical processes largely explain the genomic divergence pattern in a species complex of sea anemones (Metridioidea: Sagartiidae: Anthothoe). Molecular Phylogenetics and Evolution 127:217-228. 10.1016/j.ympev.2018.05.022
Tarpey, C. M., J. E. Seeb, G. J. McKinney, W. D. Templin, A. Bugaev, S. Sato, and L. W. Seeb. 2018. Single-nucleotide polymorphism data describe contemporary population structure and diversity in allochronic lineages of pink salmon (Oncorhynchus gorbuscha). Canadian Journal of Fisheries and Aquatic Sciences 75(6):987-997.DOI 10.1139/cjfas-2017-0023
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
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
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(2): 169-171. 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.
Seeb Lab 