title: Recombination and selection in the major histocompatibility complex of the endangered forest musk deer (Moschus berezovskii).
abstract: The forest musk deer (Moschus berezovskii) is a high elevation species distributed across western China and northern Vietnam. Once abundant, habitat loss and poaching has led to a dramatic decrease in population numbers prompting the IUCN to list the species as endangered. Here, we characterized the genetic diversity of a Major Histocompatibility Complex (MHC) locus and teased apart driving factors shaping its variation. Seven DRB exon 2 alleles were identified among a group of randomly sampled forest musk deer from a captive population in the Sichuan province of China. Compared to other endangered or captive ungulates, forest musk deer have relatively low levels of MHC genetic diversity. Non-synonymous substitutions primarily occurred in the putative peptide-binding region (PBR), with analyses suggesting that recombination and selection has shaped the genetic diversity across the locus. Specifically, inter-allelic recombination generated novel allelic combinations, with evidence for both positive selection acting on the PBR and negative selection on the non-PBR. An improved understanding of functional genetic variability of the MHC will facilitate better design and management of captive breeding programs for this endangered species.
authors.affiliation: College of Nature Conservation, Beijing Forestry University, China.
authors.forename: Ruibo
authors.initials: R
authors.lastname: Cai
authors.affiliation: Department of Ecology and Genetics, Uppsala University, Sweden.
authors.forename: Aaron B A
authors.initials: AB
authors.lastname: Shafer
authors.affiliation: College of Nature Conservation, Beijing Forestry University, China.
authors.forename: Alice
authors.initials: A
authors.lastname: Laguardia
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Zhenzhen
authors.initials: Z
authors.lastname: Lin
authors.affiliation: College of Nature Conservation, Beijing Forestry University, China.
authors.forename: Shuqiang
authors.initials: S
authors.lastname: Liu
authors.affiliation: College of Nature Conservation, Beijing Forestry University, China.
authors.forename: Defu
authors.initials: D
authors.lastname: Hu
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D000818:Animals; D002681:China; D003670:Deer / Q000235:genetics*; D056727:Endangered Species; D005091:Exons; D056426:Genetic Loci; D014644:Genetic Variation; D005838:Genotype; D006239:Haplotypes; D006649:Histocompatibility Antigens / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic; D012641:Selection, Genetic; D016415:Sequence Alignment; D014744:Vietnam
chemical_list: D006649:Histocompatibility Antigens