Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)
Article first published online: 2 JAN 2014
© 2013 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Volume 7, Issue 3, pages 355–369, March 2014
How to Cite
Larson, W. A., Seeb, L. W., Everett, M. V., Waples, R. K., Templin, W. D. and Seeb, J. E. (2014), Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha). Evolutionary Applications, 7: 355–369. doi: 10.1111/eva.12128
- Issue published online: 17 MAR 2014
- Article first published online: 2 JAN 2014
- Manuscript Accepted: 2 OCT 2013
- Manuscript Received: 19 JUN 2013
- NOAA. Grant Number: # 44515
- Gordon and Betty Moore Foundation
- H. Mason Keeler Endowment for Excellence
- National Science Foundation. Grant Number: # DGE-0718124
- 2011. Single-nucleotide polymorphisms (SNPs) under diversifying selection provide increased accuracy and precision in mixed-stock analyses of sockeye salmon from the Copper River, Alaska. Transactions of the American Fisheries Society 140:865–881. , , and
- ADF&G. 2013. Chinook salmon stock assessment and research plan [online]. Alaska Department of Fish and Game, Special Publication No. 13-01. Available from http://www.adfg.alaska.gov/static/home/news/hottopics/pdfs/chinook_research_plan.pdf (accessed on 7 March 2013).
- 1984. Polyploidy and the evolution of salmonid fishes. In B. J. Turner, eds. The Evolutionary Genetics of Fishes, pp. 1–53. Plenum Press, New York. , and
- 2010. Genomics and the future of conservation genetics. Nature Reviews Genetics 11:697–709. , , and
- 1990. Basic local alignment search tool. Journal of Molecular Biology 215:403–410. , , , , and
- 2010. Assessing the power of informative subsets of loci for population assignment: standard methods are upwardly biased. Molecular Ecology Resources 10:701–710.
- 2012. Genomic toolboxes for conservation biologists. Evolutionary Applications 5:130–143. , , , and
- 2010. Perspective: conservation genetics enters the genomics era. Conservation Genetics 11:665–669.
- 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3:e3376. , , , , , , et al.
- 2007. 2005 Annual management report for Norton Sound, Port Clarence, and Kotzebue [online]. Alaska Department of Fish and Game, Fishery Management Report No. 07-32. http://www.adfg.alaska.gov/FedAidPDFs/fmr07-32.pdf (accessed on 30 January 2013). , , , and
- 2011. Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PLoS ONE 6:e19315. , , , , , , and
- 2013. SNP-array reveals genome-wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar). Molecular Ecology 22:532–551. , , , , , , et al.
- 2013. Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish. Evolutionary Applications 6:450–461. , , , , , , et al.
- 2013. The impact of transposable elements in environmental adaptation. Molecular Ecology 22:1503–1517. , and
- 2010. A second generation genetic linkage map of Japanese flounder (Paralichthys olivaceus). BMC Genomics 11:554. , , , , , , et al.
- 2011. Stacks: building and genotyping loci de novo from short-read sequences. G3 Genes Genomes Genetics 1:171–182. , , , and
- 2013. Exploiting genetic diversity to balance conservation and harvest of migratory salmon. Canadian Journal of Fisheries and Aquatic Sciences 70:785–793. , , , and
- 2014. NeEstimator v2.0: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources 41:209–214. , , , , , and
- 2010. A gene-based SNP linkage map for Pacific white shrimp, Litopenaeus vannamei. Animal Genetics 41:286–294. , , , , , , and
- 2011. Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS ONE 6:e18561. , , , , and
- 2011. Short reads and nonmodel species: exploring the complexities of next-generation sequence assembly and SNP discovery in the absence of a reference genome. Molecular Ecology Resources 11:93–108. , , and
- 2012. Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing. BMC Genomics 13:521. , , and
- 2014. Detection and mapping of QTL for temperature tolerance and body size in Chinook salmon (Oncorhynchus tshawytscha) using genotyping by sequencing. Evolutionary Applications DOI: 10.1111/eva.12147. , and
- 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10:564–567. , and
- 2009. Detecting loci under selection in a hierarchically structured population. Heredity 103:285–298. , , and
- 2005. Distribution, migration pathways, and size of western Alaska juvenile salmon along the eastern Bering Sea Shelf. Alaska Fishery Research Bulletin 11:15–26. , , , , and
- 2005. Genetics and extinction. Biological Conservation 126:131–140.
- 2012. Harnessing genomics for delineating conservation units. Trends in Ecology & Evolution 27:489–496. , , , and
- 2013. Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis). Molecular Ecology 22:3036–3048. , , , and
- 2013. Recent physical connections may explain weak genetic structure in western Alaskan chum salmon (Oncorhynchus keta) populations. Ecology and Evolution 3:2362–2377. , , , , , , et al.
- 1987. Genetic-relationships among populations of Alaskan Chinook salmon (Oncorhynchus tshawytscha). Canadian Journal of Fisheries and Aquatic Sciences 44:765–774. , , and
- 2011. Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array. Bioinformatics 27:303–310. , , , and
- 2009. Salmon bycatch management in the Bering Sea walleye pollock fishery: threats and opportunities for western Alaska. American Fisheries Society Symposium 70:799–816.
- 2014. Development and application of genomic tools to the restoration of green abalone in southern California. Conservation Genetics 15:109–121. , , , , , , et al.
- 2011. Understanding and estimating effective population size for practical application in marine species management. Conservation Biology 25:438–449. , , , , , , et al.
- 2013. Genome-wide association reveals genetic basis for the propensity to migrate in wild populations of rainbow and steelhead trout. Molecular Ecology 22:3061–3076. , , , and
- 2013. A genomic island linked to ecotype divergence in Atlantic cod. Molecular Ecology 22:2653–2667. , , , , , , et al.
- 2013. Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species. Molecular Ecology 22:2898–2916. , , , , and
- 2003. Biocomplexity and fisheries sustainability. Proceedings of the National Academy of Sciences of the United States of America 100:6564–6568. , , , and
- 1981. Estimation of effective population-size from data on linkage disequilibrium. Genetical Research 38:209–216.
- 2010. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genetics 6 :e1000862. , , , , , and
- 2013. Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing. Molecular Ecology 22:3002–3013. , , , , , , et al.
- 2009. Yukon River Chinook salmon stock status and action plan 2010; a report to the Alaska Board of Fisheries. Alaska Department of Fish and Game, Special Publication No. 09-26. Available from http://www.sf.adfg.state.ak.us/FedAidpdfs/Sp09-26.pdf (accessed on 6 May 2012). , , and
- 2010. Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua). BMC Genomics 11:191. , , , and
- 2008. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403–1405.
- 2006. ML-RELATE: a computer program for maximum likelihood estimation of relatedness and relationship. Molecular Ecology Notes 6:576–579. , , and
- 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 70:128–141. , , , , , , et al.
- 1996. Norton Sound and Kotzebue Sound management area salmon catch and escapement report, 1995 [online]. Alaska Department of Fish and Game, Regional Information Report No. 3A96-23. Available from http://www.adfg.alaska.gov/FedAidpdfs/RIR.3A.1996.23.pdf (accessed on 30 January 2013). .
- 2011. 2010 Chinook salmon sonar enumeration on the Big Salmon River [online]. Prepared for the Yukon River Panel Restoration and Enhancement Fund, CRE-41-10. http://yukonriverpanel.com/salmon/wp-content/uploads/2011/04/cre-41-10-big-salmon-sonar-final-report.pdf (accessed on 30 January 2012). , and
- 2012. A conserved haplotype controls parallel adaptation in geographically distant salmonid populations. Molecular Ecology 21:237–249. , , , , , , et al.
- 2011. Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems. Genome Biology 12 :R112. , , and
- 2009. Stock-structured distribution of western Alaska and Yukon juvenile Chinook salmon (Oncorhynchus tshawytscha) from United States BASIS surveys, 2002–2007. North Pacific Anadromous Fish Commission Bulletin 5:51–59. , , , and
- 2013. Genotyping-by-sequencing in ecological and conservation genomics. Molecular Ecology 22:2841–2847. , , , , and
- 2001. A new approach to prioritizing marine fish and shellfish populations for conservation. Fish and Fisheries (Oxford) 2:328–343. , and
- 2009. Population genomics of marine fishes: identifying adaptive variation in space and time. Molecular Ecology 18:3128–3150. , , , and
- 2009. Divergent selection and heterogeneous genomic divergence. Molecular Ecology 18:375–402. , , and
- 2010. The influence of hydrology and waterway distance on population structure of Chinook salmon Oncorhynchus tshawytscha in a large river. Journal of Fish Biology 76:1128–1148. , , , , , , and
- 2011. Comparative landscape genetic analysis of three Pacific salmon species from subarctic North America. Conservation Genetics 12:223–241. , , , , , and
- 2008. Genetic estimates of contemporary effective population size: what can they tell us about the importance of genetic stochasticity for wild population persistence? Molecular Ecology 17:3428–3447. , and
- 2011. Demographic and genetic factors shaping contemporary metapopulation effective size and its empirical estimation in salmonid fish. Heredity 107:444–455. , and
- 2011. Effective population size of current human population. Genetics Research 93:105–114.
- 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537–2539. , and
- 2013. Accounting for missing data in the estimation of contemporary genetic effective population size (Ne). Molecular Ecology Resources 13:243–253. , , , , and
- 2004. GENECLASS2: A software for genetic assignment and first-generation migrant detection. Journal of Heredity 95:536–539. , , , , , and
- 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics 81:559–575. , , , , , , et al.
- 1994. Widespread occurrence of the TC1 transposon family - TC1-like transposons from teleost fish. Molecular & General Genetics 244:606–612. , , , and
- 1997. Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences of the United States of America 94:9197–9201. , and
- 2012. Genome-wide patterns of divergence during speciation: the lake whitefish case study. Philosophical Transactions of the Royal Society B-Biological Sciences 367:354–363. , , , , , , and
- 2012. Uninformative polymorphisms bias genome scans for signatures of selection. BMC Evolutionary Biology 12:94. , , and
- 2008. GENEPOP ' 007: a complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources 8:103–106.
- 2012. Detection of outlier loci and their utility for fisheries management. Evolutionary Applications 5:39–52. , , , and
- 1995. Anvik River salmon escapement study, 1994 [online]. Alaska Department of Fish and Game, Regional Information Report No. 3A95-08. Available from http://www.sf.adfg.state.ak.us/FedAidPDFs/RIR.3A.1995.08.pdf (accessed on 30 January 2013). .
- 2010. Population diversity and the portfolio effect in an exploited species. Nature 465:609–612. , , , , , , and
- 1999. High genetic heterogeneity in chum salmon in western Alaska, the contact zone between northern and southern lineages. Transactions of the American Fisheries Society 128:58–87. , and
- 2000. Genetic diversity of sockeye salmon of Cook Inlet, Alaska, and its application to management of populations affected by the Exxon Valdez oil spill. Transactions of the American Fisheries Society 129:1223–1249. , , , , , , and
- 2011. Transcriptome sequencing and high-resolution melt analysis advance single nucleotide polymorphism discovery in duplicated salmonids. Molecular Ecology Resources 11:335–348. , , , , , , and
- 1999. Managing fisheries using genetic data: case studies from four species of Pacific salmon. Fisheries Research 43:45–78. , , , and
- 2005. Single nucleotide polymorphisms provide rapid and accurate estimates of the proportions of US and Canadian Chinook salmon caught in Yukon River fisheries. North American Journal of Fisheries Management 25:944–953. , , , and
- 2013. Estimating effective population size from linkage disequilibrium between unlinked loci: theory and application to fruit fly outbreak populations. PLoS ONE 8:e69078. , , and
- 1997. Postglacial genetic differentiation of reproductive ecotypes of kokanee Oncorhynchus nerka in Okanagan Lake. British Columbia. Molecular Ecology 6:503–517. , , , and
- 2011. Genetic differentiation of Alaska Chinook salmon: the missing link for migratory studies. Molecular Ecology Resources 11:226–246. , , , , and
- 2007. Recent human effective population size estimated from linkage disequilibrium. Genome Research 17:520–526. , , , , , , and
- 1993. Genetic markers and mixed stock fisheries. Fisheries 18:11–21. , and
- 1974. Biochemical genetic studies of fishes: potentialities and limitations. In D. C. Malins, and J. R. Sargents, eds. Biochemical and biophysical perspectives in marine biology, vol. 1, pp. 213–238. Academic Press, San Francisco, CA. , , and
- 1990. Conservation genetics of Pacific salmon. 3. Estimating effective population-size. Journal of Heredity 81:277–289.
- 1998. Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. Journal of Heredity 89:438–450.
- 2006. A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conservation Genetics 7:167–184.
- 2010. Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evolutionary Applications 3:244–262. , and
- 2008. Six decades of fishery genetics: taking stock. Fisheries 33:76–79. , , , and
- 1984. Estimating F-statistics for the analysis of population-structure. Evolution 38:1358–1370. , and
- 2011. Kogrukluk River salmon studies, 2010 [online]. Alaska Department of Fish and Game, Fishery Data Series No. 11-49. http://www.adfg.alaska.gov/FedAidpdfs/FDS11-49.pdf (accessed on 30 January 2012). , and
- 1994. What DNA can do for you. Fisheries 19:16–27. , and
- 2012. Assessing reliability of Pebble Limited Partnership's salmon escapement studies [online]. Fisheries research and consulting, Anchorage, Alaska. http://www.pebblescience.org/pdfs/Woody_EBD_EscapementFINAL27June2012.pdf (accessed on 30 January 2012).
- 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18:821–829. , and