Major histocompatibility complex (MHC) genes are critical for disease resistance or susceptibility responsible for host-pathogen interactions determined mainly by extensive polymorphisms in the MHC genes. Here, we examined the diversity and phylogenetic pattern of MHC haplotypes reconstructed using three MHC-linked microsatellite markers in 55 populations of five Bovidae species and compared them with those based on neutral autosomal microsatellite markers (NAMs). Three-hundred-and-forty MHC haplotypes were identified in 1453 Bovidae individuals, suggesting significantly higher polymorphism and heterozygosity compared with those based on NAMs. The ambitious boundaries in population differentiation (phylogenetic network, pairwise F_ST and STRUCTURE analyses) within and between species assessed using the MHC haplotypes were different from those revealed by NAMs associated closely with speciation, geographical distribution, domestication and management histories. In addition, the mean F_ST was significantly correlated negatively with the number of observed alleles (N_A), observed (H_O) and expected (H_E) heterozygosity and polymorphism information content (PIC) (P < 0.05) in the MHC haplotype dataset while there was no correction of the mean F_ST estimates (P> 0.05) between the MHC haplotype and NAMs datasets. Analysis of molecular variance (AMOVA) revealed a lower percentage of total variance (PTV) between species/groups based on the MHC-linked microsatellites than NAMs. Therefore, it was inferred that individuals within populations accumulated as many MHC variants as possible to increase their heterozygosity and thus the survival rate of their affiliated populations and species, which eventually reduced population differentiation and thereby complicated their classification and phylogenetic relationship inference. In summary, host-pathogen coevolution and heterozygote advantage, rather than demographic history, act as key driving forces shaping the MHC diversity within the populations and determining the interspecific MHC diversity.

主要的组织相容性复合体（MHC）基因对于疾病抗性或易感性至关重要，这种疾病或易感性主要是由MHC基因中广泛的多态性决定的宿主-病原体相互作用。在这里，我们研究了在五个牛科物种的55个种群中使用三个MHC连锁微卫星标记重建的MHC单倍型的多样性和系统发育模式，并将其与基于中性常染色体微卫星标记（NAM）的单体型进行了比较。340个MHC在1453个牛科个体中鉴定出单倍型，表明与基于NAM的个体相比，多态性和杂合性显着更高。使用MHC单倍型评估的物种内部和物种之间的种群分化（系统进化网络，成对F _ST和STRUCTURE分析）的宏大边界不同于NAM揭示的与物种形成，地理分布，驯化和管理历史密切相关的边界。此外，平均F _ST与观察到的等位基因（N _A），观察到的（H _O）和预期的（H _E）数量显着负相关。）杂合度和多态性信息含量（PIC）（P <0.05）在MHC单倍型的数据集而没有平均的F校正_ST估计（P>之间0.05）MHC单倍型和NAMs中的数据集。分子方差分析（AMOVA）显示，与MAM关联的基于MHC的微卫星物种/组之间的总方差（PTV）百分比较低。因此，可以推断出人群中的个体积累了尽可能多的MHC变体尽可能增加其杂合性，从而增加其相关种群和物种的存活率，最终减少种群分化，从而使它们的分类和系统发育关系推断复杂化。总之，宿主-病原体的协同进化和杂合子优势，而不是人口历史，是塑造种群内MHC多样性并确定种间MHC多样性的主要驱动力。