A role for migration-linked genes and genomic islands in divergence of a songbird

Authors

  • Kristen Ruegg,

    Corresponding author
    1. Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
    2. Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
    • Correspondence: Kristen Ruegg, Fax: (831) 459-5353;

      E-mail: kruegg@ucsc.edu

    Search for more papers by this author
  • Eric C. Anderson,

    1. Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
    2. Department of Applied Mathematics and Statistics, University of California, Santa Cruz, CA, USA
    Search for more papers by this author
  • Jason Boone,

    1. Floragenex, Inc., Eugene, OR, USA
    Search for more papers by this author
  • Jazz Pouls,

    1. Pacific Collegiate School, Santa Cruz, CA, USA
    Search for more papers by this author
  • Thomas B. Smith

    1. Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
    2. Department of Ecology and Evolutionary Biology, University of California, Los Angles, CA, USA
    Search for more papers by this author

Abstract

Next-generation sequencing has made it possible to begin asking questions about the process of divergence at the level of the genome. For example, recently, there has been a debate around the role of ‘genomic islands of divergence’ (i.e. blocks of outlier loci) in facilitating the process of speciation-with-gene-flow. The Swainson's thrush, Catharus ustulatus, is a migratory songbird with two genetically distinct subspecies that differ in a number of traits known to be involved in reproductive isolation in birds (plumage coloration, song and migratory behaviour), despite contemporary gene flow along a secondary contact zone. Here, we use RAD-PE sequencing to test emerging hypotheses about the process of divergence at the level of the genome and identify genes and gene regions involved in differentiation in this migratory songbird. Our analyses revealed distinct genomic islands on 15 of the 23 chromosomes and an accelerated rate of divergence on the Z chromosome, one of the avian sex chromosomes. Further, an analysis of loci linked to traits known to be involved in reproductive isolation in songbirds showed that genes linked to migration are significantly more differentiated than expected by chance, but that these genes lie primarily outside the genomic islands. Overall, our analysis supports the idea that genes linked to migration play an important role in divergence in migratory songbirds, but we find no compelling evidence that the observed genomic islands are facilitating adaptive divergence in migratory behaviour.

Ancillary