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  • Speciation with gene flow in equids despite extensive chromosomal plasticity

    Author(s)
    Jonsson, Hakon
    Schubert, Mikkel
    Seguin-Orlando, Andaine
    Ginolhac, Aurelien
    Petersen, Lillian
    Fumagalli, Matteo
    Albrechtsen, Anders
    Petersen, Bent
    Korneliussen, Thorfinn S.
    Vilstrup, Julia T.
    Lear, Teri
    Myka, Jennifer Leigh
    Lundquist, Judith
    Miller, Donald C.
    Alfarhan, Ahmed H.
    Alquraishi, Saleh A.
    Al-Rasheid, Khaled A. S.
    Stagegaard, Julia
    Strauss, Gunter
    Bertelsen, Mads Frost
    Sicheritz-Ponten, Thomas
    Antczak, Douglas F.
    Bailey, Ernest
    Nielsen, Rasmus
    Willerslev, Eske
    Orlando, Ludovic
    Griffith University Author(s)
    Willerslev, Eske
    Year published
    2014
    Metadata
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    Abstract
    Horses, asses, and zebras belong to a single genus, Equus, which emerged 4.0–4.5 Mya. Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here we present six genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto represented only by the horse and the domestic donkey. In addition, we used a museum specimen to characterize the genome of the quagga zebra, which was driven to extinction in the early 1900s. ...
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    Horses, asses, and zebras belong to a single genus, Equus, which emerged 4.0–4.5 Mya. Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here we present six genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto represented only by the horse and the domestic donkey. In addition, we used a museum specimen to characterize the genome of the quagga zebra, which was driven to extinction in the early 1900s. We scan the genomes for lineage-specific adaptations and identify 48 genes that have evolved under positive selection and are involved in olfaction, immune response, development, locomotion, and behavior. Our extensive genome dataset reveals a highly dynamic demographic history with synchronous expansions and collapses on different continents during the last 400 ky after major climatic events. We show that the earliest speciation occurred with gene flow in Northern America, and that the ancestor of present-day asses and zebras dispersed into the Old World 2.1–3.4 Mya. Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 pairs to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation, and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow, and, ultimately, speciation.
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    Journal Title
    Proceedings of the National Academy of Sciences of the United States of America
    Volume
    111
    Issue
    52
    DOI
    https://doi.org/10.1073/pnas.1412627111
    Subject
    Genetics not elsewhere classified
    Publication URI
    http://hdl.handle.net/10072/172189
    Collection
    • Journal articles

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