He Ke, Liu Hong-Yi, Ge Yun-Fa, Wu Shao-Ying, Wan Qiu-Hong
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 310058, China; College of Animal Science and Technology, Zhejiang A&F University, Lin'an 311300, China.
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 310058, China.
Mol Phylogenet Evol. 2017 May;110:93-103. doi: 10.1016/j.ympev.2017.03.009. Epub 2017 Mar 7.
Major histocompatibility complex (MHC) is a good marker system for geographical genetics since they are functional genes in the immune system that are likely to affect the fitness of the individual, and the survival and evolutionary potential of a population in a changing environment. Golden pheasant (Chrysolophus pictus) is a wild Phasianidae distributed in central and north China. In this study, we used a locus-specific genotyping technique for MHC IIB genes of golden pheasant. Combining with microsatellites (simple sequence repeat, SSR) and mitochondrial DNA (mtDNA) D-loop region, we investigated the demographic history and illuminate genetic structure of this bird in detail. SYR (south of Yangtze river) - NYR (north of Yangtze river) lineages, separated by Yangtze River, were defined in genetic structure of MHC IIB. NYR was supposed as refuge during glacial period, suggested by diversity parameters and more ancient alleles in this region. Based on this hypothesis, there was gene flow from NYR to SYR, which was proved by three pieces of evidence: (1) distinct demographic histories of SYR (kept stable) and NYR (experienced expansion); (2) specific affiliation of LC in genetic structure of SSR and MHC genes; (3) significant gene flow from NYR to SYR. Moreover, we also found balancing selection by combination of three Grouping A2's regions (SC, QL and North) into one in Grouping B4 (NYR) and no pattern of isolation by distance (IBD) found in MHC IIB, whereas for SSR we found a relatively strong and significant IBD. Several mechanisms in the evolution of MHC IIB genes, including recombination, historically positive selection, trans-species evolution and concerted evolution, were shown by molecular and phylogenetic analysis. Overall these results suggest the Yangtze River was inferred to be a geological barrier for this avian and NYR might experience population expansion, which invaded into a neighboring region. This study contributes to the understanding of the effects of geographic features on contemporary patterns of genetic variation in the golden pheasant in China, and helps us to define the adaptive unite (AU) for this avian.
主要组织相容性复合体（MHC）是地理遗传学中一个很好的标记系统，因为它们是免疫系统中的功能基因，可能会影响个体的适应性以及种群在不断变化的环境中的生存和进化潜力。红腹锦鸡（Chrysolophus pictus）是一种分布于中国中部和北部的野生雉科鸟类。在本研究中，我们对红腹锦鸡的MHC IIB基因采用了位点特异性基因分型技术。结合微卫星（简单序列重复，SSR）和线粒体DNA（mtDNA）D-loop区域，我们详细研究了该鸟类的种群历史并阐明了其遗传结构。在MHC IIB的遗传结构中定义了由长江分隔的SYR（长江以南）-NYR（长江以北）谱系。根据多样性参数以及该区域中更古老的等位基因推测，NYR在冰川期被认为是避难所。基于这一假设，存在从NYR到SYR的基因流，这由三条证据证明：（1）SYR（保持稳定）和NYR（经历扩张）不同的种群历史；（2）SSR和MHC基因遗传结构中LC的特定归属；（3）从NYR到SYR的显著基因流。此外，我们还通过将三个A2组区域（SC、QL和北部）合并为B4组（NYR）中的一个发现了平衡选择，并且在MHC IIB中未发现距离隔离模式（IBD），而对于SSR我们发现了相对较强且显著的IBD。分子和系统发育分析显示了MHC IIB基因进化中的几种机制，包括重组、历史上的正选择、跨物种进化和协同进化。总体而言，这些结果表明长江被推断为这种鸟类的地理屏障，并且NYR可能经历了种群扩张，并侵入了邻近区域。本研究有助于理解地理特征对中国红腹锦鸡当代遗传变异模式的影响，并有助于我们确定这种鸟类的适应单元（AU）。
