title: Balancing selection and recombination as evolutionary forces caused population genetic variations in golden pheasant MHC class I genes.
abstract: BACKGROUND
  The major histocompatibility complex (MHC) genes are vital partners in the acquired immune processes of vertebrates. MHC diversity may be directly associated with population resistance to infectious pathogens. Here, we screened for polymorphisms in exons 2 and 3 of the IA1 and IA2 genes in 12 golden pheasant populations across the Chinese mainland to characterize their genetic variation levels, to understand the effects of historical positive selection and recombination in shaping class I diversity, and to investigate the genetic structure of wild golden pheasant populations.
  
  
  RESULTS
  Among 339 individual pheasants, we identified 14 IA1 alleles in exon 2 (IA1-E2), 11 IA1-E3 alleles, 27 IA2-E2 alleles, and 28 IA2-E3 alleles. The non-synonymous substitution rate was significantly greater than the synonymous substitution rate at sequences in the IA2 gene encoding putative peptide-binding sites but not in the IA1 gene; we also found more positively selected sites in IA2 than in IA1. Frequent recombination events resulted in at least 9 recombinant IA2 alleles, in accordance with the intermingling pattern of the phylogenetic tree. Although some IA alleles are widely shared among studied populations, large variation occurs in the number of IA alleles across these populations. Allele frequency analysis across 2 IA loci showed low levels of genetic differentiation among populations on small geographic scales; however, significant genetic differentiation was observed between pheasants from the northern and southern regions of the Yangtze River. Both STRUCTURE analysis and F-statistic (F ST ) value comparison classified those populations into 2 major groups: the northern region of the Yangtze River (NYR) and the southern region of the Yangtze River (SYR).
  
  
  CONCLUSIONS
  More extensive polymorphisms in IA2 than IA1 indicate that IA2 has undergone much stronger positive-selection pressure during evolution. Moreover, the recombination events detected between the genes and the intermingled phylogenetic pattern indicate that interlocus recombination accounts for much of the allelic variation in IA2. Analysis of the population differentiation implied that homogenous balancing selection plays an important part in maintaining an even distribution of MHC variations. The natural barrier of the Yangtze River and heterogeneous balancing selection might help shape the NYR-SYR genetic structure in golden pheasants.
authors.affiliation: The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China. sumenger@126.com.
authors.forename: Qian-Qian
authors.initials: QQ
authors.lastname: Zeng
authors.affiliation: The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China. heke@zafu.edu.cn.|College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang, 311300, China. heke@zafu.edu.cn.
authors.forename: Ke
authors.initials: K
authors.lastname: He
authors.affiliation: The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China. dandansun_4102@126.com.
authors.forename: Dan-Dan
authors.initials: DD
authors.lastname: Sun
authors.affiliation: The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China. ma_beauty@126.com.
authors.forename: Mei-Ying
authors.initials: MY
authors.lastname: Ma
authors.affiliation: The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China. yunfa_ge@163.com.
authors.forename: Yun-Fa
authors.initials: YF
authors.lastname: Ge
authors.affiliation: The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China. sgfanglab@zju.edu.cn.
authors.forename: Sheng-Guo
authors.initials: SG
authors.lastname: Fang
authors.affiliation: The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China. qiuhongwan@zju.edu.cn.
authors.forename: Qiu-Hong
authors.initials: QH
authors.lastname: Wan
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019143:Evolution, Molecular; D005091:Exons; D046094:Galliformes / Q000235:genetics*; D005787:Gene Frequency; D005805:Genes, MHC Class I; D040961:Genetic Drift; D014644:Genetic Variation; D005828:Genetics, Population; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic; D012641:Selection, Genetic