Data from: MHC structuring and divergent allele advantage in a urodele amphibian: a hierarchical multi-scale approach

The proteins encoded by extraordinarily polymorphic major
histocompatibility complex (MHC) genes are involved in the adaptive immune
response. Balancing selection is believed to maintain MHC polymorphism in
the long-term, although neutral processes also play a role in shaping MHC
diversity. However, the relative contribution of these processes is poorly
understood. Here we characterized MHC class II variation of a
low-dispersal, pond-breeding newt (Triturus carnifex) over a restricted,
geographically structured area. We aimed to: (1) evaluate the contribution
of selection and neutral processes to shaping MHC diversity at two
geographic scales; and (2) test for signatures of divergent allele
advantage (DAA), a potentially important mechanism of balancing selection.
The dominant role of selection in shaping MHC variation was suggested by
the lack of correlation between MHC and neutral (microsatellite)
variation. Although most variation occurred within populations for both
types of markers, they differed in the extent of structuring at the two
spatial scales. MHC structuring was more pronounced at local scales,
suggesting the role of local selection, while structuring was not
detectable at a larger scale, possibly an effect of balancing selection.
Microsatellites showed the opposite pattern. As expected under DAA, the
observed genotypes combined more sequence diversity than expected under
random association of alleles. Thus, DAA may contribute to maintaining MHC
polymorphism, which is ancient, as supported by signatures of historical
positive selection and trans-species polymorphism. Our results point to
the importance of a multi-scale approach in studying MHC variation,
especially in low-dispersal taxa, genetically structured at fine spatial
scales.

极端多态的主要组织相容性复合体（major histocompatibility complex, MHC）基因所编码的蛋白参与适应性免疫应答。尽管中性过程在塑造MHC多样性中同样发挥作用，但长期以来学界普遍认为平衡选择是维持MHC多态性的核心机制。然而，目前对于这两类过程的相对贡献仍知之甚少。本研究针对一处受限制且具有地理结构的区域内的低扩散性、池塘繁殖的蝾螈（Triturus carnifex），对其MHC II类基因的变异特征进行了表征。本研究的目标在于：(1) 在两个地理尺度下评估选择作用与中性过程对MHC多样性塑造的贡献；(2) 检测趋异等位基因优势（divergent allele advantage, DAA）的特征信号——这是平衡选择的一类潜在重要机制。MHC变异与中性（微卫星）变异之间不存在相关性，这一结果提示选择作用在塑造MHC变异中占据主导地位。尽管两类分子标记的绝大多数变异均存在于种群内部，但二者在两种空间尺度下的群体分化程度存在显著差异。MHC的群体分化在局域尺度上更为显著，提示局域选择发挥了作用；而在更大尺度上则未检测到群体分化，这可能是平衡选择作用的结果。微卫星标记则呈现出相反的分布模式。正如趋异等位基因优势理论所预期的那样，观测到的基因型所整合的序列多样性，高于等位基因随机组合下的预期值。因此，趋异等位基因优势可能有助于维持古老的MHC多态性，这一结论得到了历史正向选择特征与跨物种多态性信号的支持。本研究结果表明，采用多尺度方法研究MHC变异具有重要意义，这一点在精细空间尺度下存在遗传结构的低扩散类群中尤为突出。