Data from: Microsatellite and major histocompatibility complex variation in an endangered rattlesnake, the Eastern Massasauga (Sistrurus catenatus)

Genetic diversity is fundamental to maintaining the long-term viability of populations, yet reduced genetic variation is often associated with small, isolated populations. To examine the relationship between demography and genetic variation, variation at hypervariable loci (e.g., microsatellite DNA loci) is often measured. However, these loci are selectively neutral (or near neutral) and may not accurately reflect genomewide variation. Variation at functional trait loci, such as the major histocompatibility complex (MHC), can provide a better assessment of adaptive genetic variation in fragmented populations. We compared patterns of microsatellite and MHC variation across three Eastern Massasauga (Sistrurus catenatus) populations representing a gradient of demographic histories to assess the relative roles of natural selection and genetic drift. Using 454 deep amplicon sequencing, we identified 24 putatively functional MHC IIB exon 2 alleles belonging to a minimum of six loci. Analysis of synonymous and nonsynonymous substitution rates provided evidence of historical positive selection at the nucleotide level, and Tajima's D provided support for balancing selection in each population. As predicted, estimates of microsatellite allelic richness, observed, heterozygosity, and expected heterozygosity varied among populations in a pattern qualitatively consistent with demographic history and abundance. While MHC allelic richness at the population and individual levels revealed similar trends, MHC nucleotide diversity was unexpectedly high in the smallest population. Overall, these results suggest that genetic variation in the Eastern Massasauga populations in Illinois has been shaped by multiple evolutionary mechanisms. Thus, conservation efforts should consider both neutral and functional genetic variation when managing captive and wild Eastern Massasauga populations.

遗传多样性是维持种群长期存续的核心基础，而遗传变异水平降低则常与小型、隔离种群相关联。为探究种群统计学与遗传变异之间的关联，研究人员常对高变位点（如微卫星DNA位点）的变异情况进行检测。然而，这类位点多为选择中性（或近选择中性），无法准确反映全基因组范围内的遗传变异水平。而功能性状位点（如主要组织相容性复合体（MHC））的变异，则能更精准地评估破碎化种群的适应性遗传变异。本研究针对3个具有不同种群动态历史梯度的东部马萨索加响尾蛇（Sistrurus catenatus）种群，比较了其微卫星与MHC的变异模式，以评估自然选择与遗传漂变的相对作用。本研究采用454深度扩增子测序技术，共鉴定出至少6个位点的24个假定功能性MHC IIB外显子2等位基因。对同义替换与非同义替换速率的分析，在核苷酸水平上找到了历史正向选择的证据；而塔伊马D（Tajima's D）统计量则证明所有种群均存在平衡选择现象。正如预期，不同种群的微卫星等位基因丰富度、观测杂合度与期望杂合度的估计值存在差异，且其变化模式与种群动态历史及种群丰度在定性上保持一致。尽管种群与个体水平的MHC等位基因丰富度呈现出相似的变化趋势，但最小种群的MHC核苷酸多样性却出乎意料地偏高。总体而言，本研究结果表明，伊利诺伊州东部马萨索加响尾蛇种群的遗传变异受到多种进化机制的共同塑造。因此，在管理圈养与野生东部马萨索加响尾蛇种群时，保护工作应同时兼顾选择中性与功能性遗传变异。