The genomic basis of adaptive evolution in threespine sticklebacks

Felicity C. Jones, Manfred G. Grabherr, Yingguang Frank Chan, Pamela Russell, Evan Mauceli, Jeremy Johnson, Ross Swofford, Mono Pirun, Michael C. Zody, Simon White, Ewan Birney, Stephen Searle, Jeremy Schmutz, Jane Grimwood, Mark C. Dickson, Richard M. Myers, Craig T. Miller, Brian R. Summers, Anne K. Knecht, Shannon D. Brady, Haili Zhang, Alex A. Pollen, Timothy Howes, Chris Amemiya, Eric S. Lander, Federica Di Palma, Kerstin Lindblad-Toh () and David M. Kingsley ()
Additional contact information
Felicity C. Jones: Beckman Center B300, Stanford University School of Medicine
Manfred G. Grabherr: Broad Institute of MIT and Harvard, 7 Cambridge Center
Yingguang Frank Chan: Beckman Center B300, Stanford University School of Medicine
Pamela Russell: Broad Institute of MIT and Harvard, 7 Cambridge Center
Evan Mauceli: Broad Institute of MIT and Harvard, 7 Cambridge Center
Jeremy Johnson: Broad Institute of MIT and Harvard, 7 Cambridge Center
Ross Swofford: Broad Institute of MIT and Harvard, 7 Cambridge Center
Mono Pirun: Broad Institute of MIT and Harvard, 7 Cambridge Center
Michael C. Zody: Broad Institute of MIT and Harvard, 7 Cambridge Center
Simon White: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
Ewan Birney: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Stephen Searle: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
Jeremy Schmutz: HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35806, USA
Jane Grimwood: HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35806, USA
Mark C. Dickson: HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35806, USA
Richard M. Myers: HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35806, USA
Craig T. Miller: Beckman Center B300, Stanford University School of Medicine
Brian R. Summers: Beckman Center B300, Stanford University School of Medicine
Anne K. Knecht: Beckman Center B300, Stanford University School of Medicine
Shannon D. Brady: Beckman Center B300, Stanford University School of Medicine
Haili Zhang: Beckman Center B300, Stanford University School of Medicine
Alex A. Pollen: Beckman Center B300, Stanford University School of Medicine
Timothy Howes: Beckman Center B300, Stanford University School of Medicine
Chris Amemiya: Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle Washington 98101, USA
Eric S. Lander: Broad Institute of MIT and Harvard, 7 Cambridge Center
Federica Di Palma: Broad Institute of MIT and Harvard, 7 Cambridge Center
Kerstin Lindblad-Toh: Broad Institute of MIT and Harvard, 7 Cambridge Center
David M. Kingsley: Beckman Center B300, Stanford University School of Medicine

Nature, 2012, vol. 484, issue 7392, 55-61

Abstract: Abstract Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine–freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine–freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.

Date: 2012
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DOI: 10.1038/nature10944

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