title: The genomic basis of adaptive evolution in threespine sticklebacks.
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.
authors.affiliation: Department of Developmental Biology, Beckman Center B300, Stanford University School of Medicine, Stanford California 94305, USA.
authors.forename: Felicity C
authors.initials: FC
authors.lastname: Jones
authors.forename: Manfred G
authors.initials: MG
authors.lastname: Grabherr
authors.forename: Yingguang Frank
authors.initials: YF
authors.lastname: Chan
authors.forename: Pamela
authors.initials: P
authors.lastname: Russell
authors.forename: Evan
authors.initials: E
authors.lastname: Mauceli
authors.forename: Jeremy
authors.initials: J
authors.lastname: Johnson
authors.forename: Ross
authors.initials: R
authors.lastname: Swofford
authors.forename: Mono
authors.initials: M
authors.lastname: Pirun
authors.forename: Michael C
authors.initials: MC
authors.lastname: Zody
authors.forename: Simon
authors.initials: S
authors.lastname: White
authors.forename: Ewan
authors.initials: E
authors.lastname: Birney
authors.forename: Stephen
authors.initials: S
authors.lastname: Searle
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.forename: Mark C
authors.initials: MC
authors.lastname: Dickson
authors.forename: Richard M
authors.initials: RM
authors.lastname: Myers
authors.forename: Craig T
authors.initials: CT
authors.lastname: Miller
authors.forename: Brian R
authors.initials: BR
authors.lastname: Summers
authors.forename: Anne K
authors.initials: AK
authors.lastname: Knecht
authors.forename: Shannon D
authors.initials: SD
authors.lastname: Brady
authors.forename: Haili
authors.initials: H
authors.lastname: Zhang
authors.forename: Alex A
authors.initials: AA
authors.lastname: Pollen
authors.forename: Timothy
authors.initials: T
authors.lastname: Howes
authors.forename: Chris
authors.initials: C
authors.lastname: Amemiya
authors.forename: Jen
authors.initials: J
authors.lastname: Baldwin
authors.forename: Toby
authors.initials: T
authors.lastname: Bloom
authors.forename: David B
authors.initials: DB
authors.lastname: Jaffe
authors.forename: Robert
authors.initials: R
authors.lastname: Nicol
authors.forename: Jane
authors.initials: J
authors.lastname: Wilkinson
authors.forename: Eric S
authors.initials: ES
authors.lastname: Lander
authors.forename: Federica
authors.initials: F
authors.lastname: Di Palma
authors.forename: Kerstin
authors.initials: K
authors.lastname: Lindblad-Toh
authors.forename: David M
authors.initials: DM
authors.lastname: Kingsley
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000413:Alaska; D000818:Animals; D059001:Aquatic Organisms / Q000235:genetics; D005075:Biological Evolution; D007446:Chromosome Inversion / Q000235:genetics; D002875:Chromosomes / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D060146:Ecotype; D005260:Female; D005618:Fresh Water; D014644:Genetic Variation / Q000235:genetics; D016678:Genome / Q000235:genetics*; D023281:Genomics; D008969:Molecular Sequence Data; D012623:Seawater; D017422:Sequence Analysis, DNA; D023701:Smegmamorpha / Q000235:genetics*