Title: Genotyping‐by‐sequencing in ecological and conservation genomics
Abstract: Molecular EcologyVolume 22, Issue 11 p. 2841-2847 Introduction Genotyping-by-sequencing in ecological and conservation genomics Shawn R. Narum, Corresponding Author Shawn R. Narum Department of Fisheries and Wildlife, University of Idaho, Moscow, ID, USA Columbia River Inter-Tribal Fish Commission, Hagerman Fish Culture Experiment Station, Hagerman, ID, USACorrespondence: Shawn R. Narum, Fax: 208-837-6047; E-mail: [email protected]Search for more papers by this authorC. Alex Buerkle, C. Alex Buerkle Department of Botany, University of Wyoming, Laramie, WY, USASearch for more papers by this authorJohn W. Davey, John W. Davey Department of Zoology, University of Cambridge, Cambridge, UKSearch for more papers by this authorMichael R. Miller, Michael R. Miller Department of Animal Science, University of California, Davis, CA, USASearch for more papers by this authorPaul A. Hohenlohe, Paul A. Hohenlohe Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USASearch for more papers by this author Shawn R. Narum, Corresponding Author Shawn R. Narum Department of Fisheries and Wildlife, University of Idaho, Moscow, ID, USA Columbia River Inter-Tribal Fish Commission, Hagerman Fish Culture Experiment Station, Hagerman, ID, USACorrespondence: Shawn R. Narum, Fax: 208-837-6047; E-mail: [email protected]Search for more papers by this authorC. Alex Buerkle, C. Alex Buerkle Department of Botany, University of Wyoming, Laramie, WY, USASearch for more papers by this authorJohn W. Davey, John W. Davey Department of Zoology, University of Cambridge, Cambridge, UKSearch for more papers by this authorMichael R. Miller, Michael R. Miller Department of Animal Science, University of California, Davis, CA, USASearch for more papers by this authorPaul A. Hohenlohe, Paul A. Hohenlohe Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USASearch for more papers by this author First published: 25 May 2013 https://doi.org/10.1111/mec.12350Citations: 397Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat References Allendorf FW, Hohenlohe PA, Luikart G (2010) Genomics and the future of conservation genetics. Nature Reviews Genetics, 11, 697–709. Andolfatto PD, Davison D, Erezyilmaz TT et al. (2011) Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Research, 21, 610–617. Arnold B, Corbet-Detig RB, Hartl D, Bomblies K (2013) RAD-seq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. Molecular Ecology, 22, 3179–3190. Baird NA, Etter PD, Atwood TS, et al. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE, 3, e3376. Bonneaud C, Balenger S, Russell AF, Zhang J, Hill G, Edwards SV (2011) Rapid evolution of disease resistance is accompanied by functional changes in gene expression in a wild bird. Proceedings of the National Academy of Sciences USA, 108, 7866–7871. Buerkle CA, Gompert Z (2013) Population genomics based on low coverage sequencing: how low should we go? Molecular Ecology, 22, 3028–3035. Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH (2011) Stacks: building and genotyping loci de novo from short-read sequences. G3 (Bethesda), 1, 171–182. Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013a) Stacks: an analysis tool set for population genomics. Molecular Ecology, 22, 3124–3140. Catchen J, Bassham S, Wilson T et al. (2013b) The population structure and recent colonization history of Oregon threespine stickleback determined using RAD-seq. Molecular Ecology, 22, 2864–2883. Corander J, Majander KK, Cheng L, Merilä J (2013) High degree of cryptic population differentiation in the Baltic Sea herring Clupea harengus. Molecular Ecology, 22, 2931–2940. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12, 499–510. Davey JW, Cezard T, Fuentes-Utrilla P, Eland C, Gharbi K, Blaxter ML (2013) Special features of RAD sequencing data: implications for genotyping. Molecular Ecology, 22, 3151–3164. De Wit P, Palumbi SR (2013) Transcriptome-wide polymorphisms of red abalone (Haliotis rufescens) reveal patterns of gene flow and local adaptation. Molecular Ecology, 22, 2884–2897. Elshire RJ, Glaubitz JC, Sun Q et al. (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE, 6, e19379. Flint J, Eskin E (2012) Genome-wide association studies in mice. Nature Reviews Genetics, 13, 807–817. Gagnaire P-A, Normandeau E, Pavey SA, Bernatchez L (2013) Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis). Molecular Ecology, 22, 3036–3048. Gautier M, Gharbi K, Cezard T et al. (2013) The effect of RAD allele dropout on the estimation of genetic variation within and between populations. Molecular Ecology, 22, 3165–3178. Glenn TC (2011) Field guide to next generation DNA sequencers. Molecular Ecology Resources, 11, 759–769. Hecht BC, Campbell NR, Holecek DE, Narum SR (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. Hess JE, Campbell NR, Close DA, Docker MF, Narum SR (2013) Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species. Molecular Ecology, 22, 2898–2916. Hindorff LA, Sethupathy P, Junkins HA et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proceedings of the National Academy of Sciences USA, 106, 9362–9367. Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson E, Cresko WA (2010) Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genetics, 6, e1000862. Hohenlohe PA, Amish SJ, Catchen JM, Allendorf FW, Luikart G (2011) Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Molecular Ecology Resources, 11(Suppl. 1), 117–122. Hohenlohe PA, Day MD, Amish SJ et al. (2013) Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing. Molecular Ecology, 22, 3002–3013. Hyma KE, Fay JC (2013) Mixing of vineyard and oak-tree ecotypes of Saccharomyces cerevisiae in North American vineyards. Molecular Ecology, 22, 2917–2930. Jones JC, Shaohua F, Franchini P, Schartl M, Meyer A (2013) Hybridization and speciation in Xiphophorus fish: a genome wide approach using RAD sequencing. Molecular Ecology, in press. Keller I, Wagner CE, Greuter L et al. (2013) Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes. Molecular Ecology, 22, 2848–2863. Li J, Haipeng L, Jakobsson M, Sjodin P, Lascoux M (2012) Joint analysis of demography and selection in population genetics: where do we stand and where could we go? Molecular Ecology, 21, 28–44. Miller MR, Atwood TS, Eames BF et al. (2007) RAD marker microarrays enable rapid mapping of zebrafish mutations. Genome Biology, 8, R105. Narum SR, Campbell NR, Kozfkay CC, Meyer KA (2010) Adaptation of redband trout in desert and montane environments. Molecular Ecology, 19, 4622–4637. Narum SR, Campbell NR, Meyer KA, Miller MR, Hardy RW (2013) Thermal adaptation and acclimation of ectotherms from differing aquatic climates. Molecular Ecology, 22, 3090–3097. Ogden R, Gharbi K, Mugue N et al. (2013) Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing. Molecular Ecology, 22, 3112–3123. van Orsouw NJ, Hogers RCJ, Janssen A et al. (2007) Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS ONE, 2, e1172. Parchman TL, Gompert Z, Mudge J, Schilkey FD, Benkman CW, Buerkle CA (2012) Genome-wide association genetics of an adaptive trait in lodgepole pine. Molecular Ecology, 21, 2991–3005. Parchman TL, Gompert Z, Braun MJ et al. (2013) The genomic consequences of adaptive divergence and reproductive isolation between species of manakins. Molecular Ecology, doi:10.1111/mec.12201. Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE, 7, e37135. Reitzel AM, Herrera S, Layden MJ, Martindale MQ, Shank TM (2013) Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics. Molecular Ecology, 22, 2953–2970. Richards PM, Liu MM, Lowe N, Davey JW, Blaxter ML, Davison A (2013) A search for the Cepaea supergene: RAD-Seq derived markers bound tightly linked loci for shell colour and banding. Molecular Ecology, in press. Roda F, Ambrose L, Walter GM et al. (2013) Genomic evidence for the parallel evolution of coastal forms in the Senecio lautus complex. Molecular Ecology, 22, 2941–2952. Roesti M, Moser D, Berner D (2013) Recombination in the threespine stickleback genome – patterns and consequences. Molecular Ecology, 22, 3014–3027. Seeb JE, Carvalho G, Hauser L, Naish K, Roberts S, Seeb LW (2011) SNP discovery and applications of SNP genotyping in non-model organisms. Molecular Ecology Resources, 11, 1–8. Senn H, Ogden R, Cezard T et al. (2013) Reference-free SNP discovery for the Eurasian beaver from restriction site–associated DNA paired-end data. Molecular Ecology, 22, 3141–3150. Serang O, Mollinari M, Garcia AAF (2012) Efficient exact maximum a posteriori computation for bayesian SNP genotyping in polyploids. PLoS ONE, 7, e30906. Stapley J, Reger J, Feulner PGD et al. (2010) Adaptation genomics: the next generation. Trends Ecology and Evolution, 25, 705–712. Storz JF, Runck AM, Sabatino SJ et al. (2009) Evolutionary and functional insights into the mechanism underlying high-altitude adaptation of deer mouse hemoglobin. Proceedings of the National Academy of Sciences USA, 106, 14450–14455. Takahashi T, Sota T, Hori M (2013) Genetic basis of male colour dimorphism in a Lake Tanganyika cichlid fish. Molecular Ecology, 22, 3049–3060. Wang N, Thomson M, Bodles WJA et al. (2013) Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers. Molecular Ecology, 22, 3098–3111. White TA, Perkins SE, Heckel G, Searle J (2013) Adaptive evolution during an ongoing range expansion: the invasive bank vole (Myodes glareolus) in Ireland. Molecular Ecology, 22, 2971–2985. Citing Literature Volume22, Issue11Special Issue: GENOTYPING BY SEQUENCING IN ECOLOGICAL AND CONSERVATION GENOMICSJune 2013Pages 2841-2847 ReferencesRelatedInformation