Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation

Kira E. Delmore, Sariel Hübner, Nolan C. Kane, Richard Schuster, Rose L. Andrew, Francisco Câmara, Roderic Guigõ, Darren E. Irwin

Research output: Contribution to journalArticlepeer-review

Abstract

Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole-genome shotgun sequence data for populations adjacent to the hybrid zone between these groups. We documented substantial genomewide heterogeneity in relative estimates of genetic differentiation between the groups. Within population diversity was lower in areas of high relative differentiation, supporting a role for selective sweeps in generating this pattern. Absolute genetic differentiation was reduced in these areas, further suggesting that recurrent selective sweeps in the ancestral population and/or between divergent populations following secondary contact likely occurred. Relative genetic differentiation was also higher near centromeres and on the Z chromosome, suggesting that features of the genome also contribute to genomewide heterogeneity. Genes linked to migratory traits were concentrated in islands of differentiation, supporting previous suggestions that seasonal migration is under divergent selection between Swainson's thrushes. Differences in migratory behaviour likely play a central role in the speciation of many taxa; we developed the infrastructure here to permit future investigations into the role several candidate genes play in reducing gene flow between not only Swainson's thrushes but other species as well.

Original languageEnglish
Pages (from-to)1873-1888
Number of pages16
JournalMolecular Ecology
Volume24
Issue number8
DOIs
StatePublished - 1 Apr 2015
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2015 John Wiley & Sons Ltd.

Keywords

  • Catharus ustulatus
  • Swainson's thrush
  • candidate genes
  • migratory divide
  • next-generation DNA sequencing
  • population genomics
  • selective sweeps
  • speciation

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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