The hidden history of the snowshoe hare, Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation

Authors

  • José Melo-Ferreira,

    Corresponding author
    1. CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
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    • These authors contributed equally.
  • Fernando A. Seixas,

    1. CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
    2. Departamento Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
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    • These authors contributed equally.
  • Ellen Cheng,

    1. Wildlife Biology, University of Montana, Missoula, MT, USA
    2. Ugyen Wangchuck Institute for Conservation and Environment, Bumthang, Bhutan
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  • L. Scott Mills,

    1. Wildlife Biology, University of Montana, Missoula, MT, USA
    2. Fisheries, Wildlife and Conservation Biology Program, North Carolina State University, Raleigh, NC, USA
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  • Paulo C. Alves

    1. CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
    2. Departamento Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
    3. Wildlife Biology, University of Montana, Missoula, MT, USA
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Abstract

Hybridization drives the evolutionary trajectory of many species or local populations, and assessing the geographic extent and genetic impact of interspecific gene flow may provide invaluable clues to understand population divergence or the adaptive relevance of admixture. In North America, hares (Lepus spp.) are key species for ecosystem dynamics and their evolutionary history may have been affected by hybridization. Here we reconstructed the speciation history of the three most widespread hares in North America – the snowshoe hare (Lepus americanus), the white-tailed jackrabbit (L. townsendii) and the black-tailed jackrabbit (L. californicus) – by analysing sequence variation at eight nuclear markers and one mitochondrial DNA (mtDNA) locus (6240 bp; 94 specimens). A multilocus–multispecies coalescent-based phylogeny suggests that L. americanus diverged ~2.7 Ma and that L. californicus and L. townsendii split more recently (~1.2 Ma). Within L. americanus, a deep history of cryptic divergence (~2.0 Ma) was inferred, which coincides with major speciation events in other North American species. While the isolation-with-migration model suggested that nuclear gene flow was generally rare or absent among species or major genetic groups, coalescent simulations of mtDNA divergence revealed historical mtDNA introgression from L. californicus into the Pacific Northwest populations of L. americanus. This finding marks a history of past reticulation between these species, which may have affected other parts of the genome and influence the adaptive potential of hares during climate change.

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