Dataset Information

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.

SUBMITTER: Jones FC

PROVIDER: S-EPMC3322419 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature

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The genomic basis of adaptive evolution in threespine sticklebacks.

Jones Felicity C FC Grabherr Manfred G MG Chan Yingguang Frank YF Russell Pamela P Mauceli Evan E Johnson Jeremy J Swofford Ross R Pirun Mono M Zody Michael C MC White Simon S Birney Ewan E Searle Stephen S Schmutz Jeremy J Grimwood Jane J Dickson Mark C MC Myers Richard M RM Miller Craig T CT Summers Brian R BR Knecht Anne K AK Brady Shannon D SD Zhang Haili H Pollen Alex A AA Howes Timothy T Amemiya Chris C Baldwin Jen J Bloom Toby T Jaffe David B DB Nicol Robert R Wilkinson Jane J Lander Eric S ES Di Palma Federica F Lindblad-Toh Kerstin K Kingsley David M DM

Nature 20120404 7392

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 consistentl ...[more]

PMID: 22481358

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Project description:Dorsal spine reduction in threespine sticklebacks (Gasterosteus aculeatus) is a classic example of recurrent skeletal evolution in nature. Sticklebacks in marine environments typically have long spines that form part of their skeletal armor. Many derived freshwater populations have evolved shorter spines. Changes in spine length are controlled in part by a quantitative trait locus (QTL) previously mapped to chromosome 4, but the causative gene and mutations underlying the repeated evolution of this interesting skeletal trait have not been identified.Refined mapping of the spine length QTL shows that it lies near the MSX2A transcription factor gene. MSX2A is expressed in developing spines. In F1 marine × freshwater fish, the marine allele is preferentially expressed. Differences in expression can be attributed to splicing regulation. Due to the use of an alternative 5 ' splice site within the first exon, the freshwater allele produces greater amounts of a shortened, non-functional transcript and makes less of the full-length transcript. Sequence changes in the MSX2A region are shared by many freshwater fish, suggesting that repeated evolution occurs by reuse of a spine-reduction variant. To demonstrate the effect of full-length MSX2A on spine length, we produced transgenic freshwater fish expressing a copy of marine MSX2A. The spines of the transgenic fish were significantly longer on average than those of their non-transgenic siblings, partially reversing the reduced spine lengths that have evolved in freshwater populations.MSX2A is a major gene underlying dorsal spine reduction in freshwater sticklebacks. The gene is linked to a separate gene controlling bony plate loss, helping explain the concerted effects of chromosome 4 on multiple armor-reduction traits. The nature of the molecular changes provides an interesting example of morphological evolution occurring not through a simple amino acid change, nor through a change only in gene expression levels, but through a change in the ratio of splice products encoding both normal and truncated proteins.

Dataset Information

The genomic basis of adaptive evolution in threespine sticklebacks.

Publications

The genomic basis of adaptive evolution in threespine sticklebacks.

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