Polymorphism in the major histocompatibility complex (MHC class II B) genes of the Rufous-backed Bunting (Emberiza jankowskii)

Abstract

Genetic diversity is one of the pillars of conservation biology research. High genetic diversity and abundant genetic variation in an organism may be suggestive of capacity to adapt to various environmental changes. The major histocompatibility complex (MHC) is known to be highly polymorphic and plays an important role in immune function. It is also considered an ideal model system to investigate genetic diversity in wildlife populations. The Rufous-backed Bunting (Emberiza jankowskii) is an endangered species that has experienced a sharp decline in both population and habitat size. Many historically significant populations are no longer present in previously populated regions, with only three breeding populations present in Inner Mongolia (i.e., the Aolunhua, Gahaitu and Lubei557 populations). Efforts focused on facilitating the conservation of the Rufous-backed Bunting (Emberiza jankowskii) are becoming increasingly important. However, the genetic diversity of E. jankowskii has not been investigated. In the present study, polymorphism in exon 2 of the MHCIIB of E. jankowskii was investigated. This polymorphism was subsequently compared with a related species, the Meadow Bunting (Emberiza cioides). A total of 1.59 alleles/individual were detected in E. jankowskii and 1.73 alleles/individual were identified in E. cioides. The maximum number of alleles per individual from the three E. jankowskii populations suggest the existence of at least three functional loci, while the maximum number of alleles per individual from the three E. cioides populations suggest the presence of at least four functional loci. Two of the alleles were shared between the E. jankowskii and E. cioides. Among the 12 unique alleles identified in E. jankowskii, 10.17 segregating sites per allele were detected, and the nucleotide diversity was 0.1865. Among the 17 unique alleles identified in E. cioides, eight segregating sites per allele were detected, and the nucleotide diversity was 0.1667. Overall, compared to other passerine birds, a relatively low level of MHC polymorphism was revealed in E. jankowskii, which was similar to that in E. cioides. Positive selection was detected by PAML/SLAC/FEL analyses in the region encoding the peptide-binding region in both species, and no recombination was detected. Phylogenetic analysis showed that the alleles from E. jankowskii and E. cioides belong to the same clade and the two species shared similar alleles, suggesting the occurrence of a trans-species polymorphism between the two Emberiza species.

Keywords: Emberiza cioides; Emberiza jankowskii; MHC; Positive selection; Trans-species polymorphism.

Figure 1. Sample distribution of Emberiza jankowskii and Emberiza cioides.

GHT represents Gahaitu, LB represents Lubei557, ALH represents Aolunhua, and BYTL represents Bayantala. The sample distribution map was generated with QGIS 2.16 (http://www.qgis.org) and Natural Earth public domain map data (http://www.naturalearthdata.com/about/terms-of-use/), and modified in Adobe Illustrator.

Figure 2. Alignment of MHCIIB exon 2 amino acid sequences.

Emberiza jankowskii and Emberiza cioides were the two species selected for this analysis. Periods and dots indicate identity with the Emja01 or Emci01 sequence. Emja04 = Emci03, Emja05 = Emja07 = Emci11, Emja01 = Emja12. Emja represents Emberiza jankowskii, Emci represents Emberiza cioides. * represents putative peptide-binding sites based on Tong et al. (2006); + represents sites identified by SLAC in this study; - represents sites identified by FEL in this study; 1represents Luscinia svecica (FJ529861; Anmarkrud et al., 2010); 2 represents Ficedula albicollis (HQ678311; Zagalska-Neubauer et al., 2010); 3 represents Philesturnus carunculatus (KF225737; Sutton et al., 2013); 4 represents Passer domesticus (Pado-DAB*301; Borg et al., 2011). Sites identified by CODEML as being under positive selection by model M8 are shaded gray.

Figure 3. Emberiza jankowskii and Emberiza cioides MHCIIB exon 2 tree.

HLA-DRB*04 is the human MHCIIB exon 2 allele (GenBank Accession No.: NM_021983), and Game is the Gallinago media MHCIIB exon 2 allele (GenBank Accession No.: AF485413); these were used as outgroups. The tree constructed by the contiguous 270 bp fragment of exon 2. All the clades were labeled, including bootstrap support and posterior probabilities (BI and NJ). Emja07/Emci11 and Emja04/Emci03 represent identical alleles from Emberiza jankowskii and Emberiza cioides. Emja, Emberiza jankowskii; Emci, Emberiza cioides.

Figure 4. Neighbor joining trees of all MHCIIB exon 2 variants in Emberiza jankowskii and Emberiza cioides.

(A) Tree constructed by comparing synonymous substitutions/synonymous site from codon positions identified as the peptide binding region (putative non-PBR) in HLA (Tong et al., 2006) (74 codons). (B) Tree constructed by comparing non-synonymous substitutions/nonsynonymous site at remaining (putative PBR) sites (15 codons). Black rectangle indicates supported interspecific clades in (A) and (B). Emja, Emberiza jankowskii; Emci, Emberiza cioides.