Data from: Shared evolutionary origin of MHC polymorphism in sympatric lemurs

Genes of the Major Histocompatibility Complex (MHC) play a central role in adaptive immune responses of vertebrates. They exhibit remarkable polymorphism, often crossing species boundaries with similar alleles or allelic motifs shared across species. This pattern may reflect parallel parasite-mediated selective pressures, either favouring the long maintenance of ancestral MHC allelic lineages across successive speciation events by balancing selection (‘trans-species polymorphism’), or alternatively favouring the independent emergence of functionally similar alleles post-speciation via convergent evolution. Here we investigate the origins of MHC similarity across several species of dwarf and mouse lemurs (Cheirogaleidae). We examined MHC class II variation in two highly polymorphic loci (DRB, DQB) and evaluated the overlap of gut-parasite communities in four sympatric lemurs. We tested for parasite-MHC associations across species to determine whether similar parasite pressures may select for similar MHC alleles in different species. Next, we integrated our MHC data with those previously obtained from other Cheirogaleidae to investigate the relative contribution of convergent evolution and co-ancestry to shared MHC polymorphism by contrasting patterns of codon usage at functional versus neutral sites. Our results indicate that parasites shared across species may select for functionally similar MHC alleles, implying that the dynamics of MHC-parasite co-evolution should be envisaged at the community level. We further show that balancing selection maintaining trans-species polymorphism, rather than convergent evolution, is the primary mechanism explaining shared MHC sequence motifs between species that diverged up to 30 million years ago.

主要组织相容性复合体（Major Histocompatibility Complex, MHC）基因在脊椎动物的适应性免疫应答中发挥核心作用。该类基因具有显著的多态性，且常跨越物种界限，不同物种间可共享相似的等位基因或等位基因基序。这一现象可能源于寄生虫介导的平行选择压力：一类是通过平衡选择在多次物种形成事件中维持祖先MHC等位基因谱系的长期存续，即跨物种多态性（trans-species polymorphism）；另一类则是在物种形成后通过趋同演化独立产生功能相似的等位基因。本研究聚焦倭狐猴科（Cheirogaleidae）下数种倭狐猴与鼠狐猴的MHC相似性起源问题。我们对两个高多态性MHC II类基因座（DRB、DQB）的变异情况进行了检测，并评估了4种同域分布狐猴的肠道寄生虫群落重叠度。我们跨物种检测了寄生虫与MHC的关联，以明确相似的寄生虫压力是否会在不同物种中选择出功能相似的MHC等位基因。随后，我们将本次获得的MHC数据与此前从其他倭狐猴科物种获取的数据相结合，通过对比功能位点与中性位点的密码子使用模式，探究趋同演化与共同祖先起源对共享MHC多态性的相对贡献度。研究结果表明，跨物种共享的寄生虫可能会选择出功能相似的MHC等位基因，这意味着MHC-寄生虫协同演化的动态过程应在群落层面进行考量。我们进一步证实，维持跨物种多态性的平衡选择而非趋同演化，是解释分化时长可达3000万年的物种间共享MHC序列基序的核心机制。