Evolution of MHC class I genes in the European badger (Meles meles)

Authors

  • Yung Wa Sin,

    1. Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon, Oxfordshire OX13 5QL, United Kingdom
    2. NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, South Yorkshire, S10 2TN, United Kingdom
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  • Hannah L. Dugdale,

    1. NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, South Yorkshire, S10 2TN, United Kingdom
    2. Behavioural Ecology and Self-Organization, University of Groningen, P.O. Box 11103, 9700 CC Groningen, The Netherlands
    3. Theoretical Biology, University of Groningen, P.O. Box 11103, 9700 CC Groningen, The Netherlands
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  • Chris Newman,

    1. Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon, Oxfordshire OX13 5QL, United Kingdom
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  • David W. Macdonald,

    1. Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon, Oxfordshire OX13 5QL, United Kingdom
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  • Terry Burke

    1. NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, South Yorkshire, S10 2TN, United Kingdom
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  • Funded by the Croucher Foundation (Hong Kong), Natural Environment Research Council (NERC) Biomolecular Analysis Facility and the Netherlands Organisation for Scientific Research.

Yung Wa Sin, Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon, Oxfordshire, OX13 5QL, United Kingdom. Tel: +44 (0)1865 393 127; Fax: +44 (0)1865 393 101; E-mail: yungwa.sin@zoo.ox.ac.uk

Abstract

The major histocompatibility complex (MHC) plays a central role in the adaptive immune system and provides a good model with which to understand the evolutionary processes underlying functional genes. Trans-species polymorphism and orthology are both commonly found in MHC genes; however, mammalian MHC class I genes tend to cluster by species. Concerted evolution has the potential to homogenize different loci, whereas birth-and-death evolution can lead to the loss of orthologs; both processes result in monophyletic groups within species. Studies investigating the evolution of MHC class I genes have been biased toward a few particular taxa and model species. We present the first study of MHC class I genes in a species from the superfamily Musteloidea. The European badger (Meles meles) exhibits moderate variation in MHC class I sequences when compared to other carnivores. We identified seven putatively functional sequences and nine pseudogenes from genomic (gDNA) and complementary (cDNA) DNA, signifying at least two functional class I loci. We found evidence for separate evolutionary histories of the α1 and α2/α3 domains. In the α1 domain, several sequences from different species were more closely related to each other than to sequences from the same species, resembling orthology or trans-species polymorphism. Balancing selection and probable recombination maintain genetic diversity in the α1 domain, evidenced by the detection of positive selection and a recombination event. By comparison, two recombination breakpoints indicate that the α2/α3 domains have most likely undergone concerted evolution, where recombination has homogenized the α2/α3 domains between genes, leading to species-specific clusters of sequences. Our findings highlight the importance of analyzing MHC domains separately.

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