Recombination and selection in the major histocompatibility complex of the endangered forest musk deer (Moschus berezovskii).

Ruibo Cai,Shuqiang Liu,Zhenzhen Lin,Alice Laguardia,Aaron B A Shafer,Defu Hu

doi:10.1038/srep17285

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.

Highlights

major histocompatibility complex (MHC) gene diversity is generated and maintained by point mutations and balancing selection, combined with translocations and gene duplications[10]
DRB sequences of forest musk deer along with standard Bos taurus DRB MHC loci (Bola DRB1, DRB2, DRB3) were included to examine whether all of the Mobe DRB sequences were derived from the same locus
Assessing the DRB amino acid structure of Li et al.[19], we found that our samples contain 5 of the 6 alleles observed in that population, suggesting we have captured a large portion of the MHC diversity seen in the species for this region

Summary

Introduction

MHC gene diversity is generated and maintained by point mutations and balancing selection, combined with translocations and gene duplications[10]. It has been proposed that MHC genes, due to their important biological functions, should play a role in the design of programs to conserve genetic diversity in captive populations of endangered species, and generally be maintained in natural populations[14,15]. Previous studies have described the variation of MHC DRB genes of forest musk deer[19,20], but these data are not in public data repositories nor have been examined in a broader context (i.e. estimate species wide functional genetic diversity). We genotyped the MHC class II locus in a captive forest musk deer population, and analyzed patterns of genetic diversity and molecular evolution of DRB exon 2, focusing on inferring how recombination and selection shape genetic diversity. We compared our diversity data to additional species to put our data in context with other ungulate MHC diversity estimates, and discussed the conservation and evolutionary potential of forest musk deer

Methods

Results

Conclusion