Genetic variation of the major histocompatibility complex (MHC class II B gene) in the threatened Hume's pheasant, Syrmaticus humiae.

Weicai Chen,Yongjian Bei,Hanhua Li,Michelle L Baker

doi:10.1371/journal.pone.0116499

Abstract

Major histocompatibility complex (MHC) genes are the most polymorphic genes in vertebrates and encode molecules that play a crucial role in pathogen resistance. As a result of their diversity, they have received much attention in the fields of evolutionary and conservation biology. Here, we described the genetic variation of MHC class II B (MHCIIB) exon 2 in a wild population of Hume’s pheasant (Syrmaticus humiae), which has suffered a dramatic decline in population over the last three decades across its ranges in the face of heavy exploitation and habitat loss. Twenty-four distinct alleles were found in 73 S. humiae specimens. We found seven shared alleles among four geographical groups as well as six rare MHCIIB alleles. Most individuals displayed between one to five alleles, suggesting that there are at least three MHCIIB loci of the Hume’s pheasant. The d N ⁄ d S ratio at putative antigen-binding sites (ABS) was significantly greater than one, indicating balancing selection is acting on MHCIIB exon 2. Additionally, recombination and gene conversion contributed to generating MHCIIB diversity in the Hume’s pheasant. One to three recombination events and seventy-five significant gene conversion events were observed within the Hume’s pheasant MHCIIB loci. The phylogenetic tree and network analysis revealed that the Hume’s pheasant alleles do not cluster together, but are scattered through the tree or network indicating a trans-species evolutionary mode. These findings revealed the evolution of the Hume’s pheasant MHC after suffering extreme habitat fragmentation.

Highlights

The Hume’s pheasant (Syrmaticus humiae) is considered an endangered species of the Phasianidae family, found in northeastern India, northern Myanmar, northwestern Thailand and southwestern China [1]
Total 1046 clones derived from genomic DNA of 73 S. humiae were sequenced and 24 distinct nucleotide variants of MHC class II B (MHCIIB) exon 2 were identified according to the criteria summarized by Kennedy et al [22]
Following Kennedy’s et al criteria [22], twenty-four distinct MHCIIB exon 2 alleles have been identified from 73 individuals, indicating that a relatively high level of MHCIIB variation was found in the S. humiae population

Summary

Introduction

The Hume’s pheasant (Syrmaticus humiae) is considered an endangered species of the Phasianidae family, found in northeastern India, northern Myanmar, northwestern Thailand and southwestern China [1]. In China, S. humiae is undergoing a decline across many of its ranges, due to heavy exploitation and habitat loss over the last three decades [5, 6]. The wild population has been decreasing dramatically Due to these severe declines in geographic range and abundance, S. humiae is listed as a Grade I National Protected Wildlife in China [7] as well as a globally near threatened (NT) species by the IUCN (International Union for Conservation of Nature) [2]. Suffering a dramatic reduction, several previous studies following a neutral genetic marker (mitochondrial DNA D-Loop fragments) [8] revealed that a wild population of S. humiae collected from Guangxi and Guizhou Provinces did not display lower genetic diversity or significant genetic differentiation. Combined neutral and selective markers can deliver more information on evolutionary history of species [12,13,14]

Methods

Results

Conclusion