A genome-wide SNP genotyping array reveals patterns of global and repeated 
species-pair divergence in sticklebacks

Jones, Felicity C.; Chan, Yingguang Frank; Schmutz, Jeremy; Grimwood, Jane; Brady, Shannon D.; Southwick, Audrey M.; Absher, Devin M.; Myers, Richard M.; Reimchen, Thomas E.; Deagle, Bruce E.; Schluter, Dolph; Kingsley, David M.

doi:10.1016/j.cub.2011.11.045

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A genome-wide SNP genotyping array reveals patterns of global and repeated species-pair divergence in sticklebacks

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Chan, Yingguang Frank
Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Citation

Jones, F. C., Chan, Y. F., Schmutz, J., Grimwood, J., Brady, S. D., Southwick, A. M., et al. (2012). A genome-wide SNP genotyping array reveals patterns of global and repeated species-pair divergence in sticklebacks. Current Biology, 22, 83-90. doi:10.1016/j.cub.2011.11.045.

Cite as: https://hdl.handle.net/11858/00-001M-0000-000F-D341-0

Abstract

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
[1]. 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 marinefreshwater
or benthic-limnetic species pairs. Surveying 34
global populations with 1,159 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 detected large repeated shifts in allele
frequency at some loci, identifying both known and novel
loci likely contributing to marine-freshwater and benthiclimnetic
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