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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptNIH Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
Curr Biol. Author manuscript; available in PMC Jul 10, 2012.
Published in final edited form as:
PMCID: PMC3319444

A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks


Genes underlying repeated adaptive evolution in natural populations are still largely unknown. Stickleback fish (Gasterosteus aculeatus) have undergone a recent dramatic evolutionary radiation, generating numerous examples of marine–freshwater species-pairs, and a small number of benthic–limnetic species-pairs found within single lakes []. We have developed a new genome-wide SNP genotyping array to study patterns of genetic variation in sticklebacks over a wide geographic range, and to scan the genome for regions that contribute to repeated evolution of marine–freshwater or benthic–limnetic species-pairs. Surveying 34 global populations with 1159 informative markers revealed substantial genetic variation, with predominant patterns reflecting demographic history and geographic structure. After correcting for geographic structure and filtering for neutral markers, we detect large repeated shifts in allele frequency at some loci, identifying both known and novel loci likely contributing to marine–freshwater and benthic–limnetic divergence. Several novel loci fall close to genes implicated in epithelial barrier or immune functions, which have likely changed as sticklebacks adapt to contrasting environments. Specific alleles differentiating sympatric benthic–limnetic species-pairs are shared in nearby solitary populations, suggesting an allopatric origin for adaptive variants, and selection pressures unrelated to sympatry in the initial formation of these classic vertebrate species-pairs.


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