Data from: Neutral genetic processes influence MHC evolution in threatened gopher tortoises (Gopherus polyphemus)

Levels of adaptive genetic variation influence how species deal with environmental and ecological change, but these levels are frequently inferred using neutral genetic markers. Major histocompatibility complex (MHC) genes play a key role in the adaptive branch of the immune system and have been used extensively to estimate levels of adaptive genetic variation. Parts of the peptide binding region, sites where MHC molecules directly interact with pathogen and self-proteins, were sequenced from a MHC class I (95/441 tortoises) and class II (245/441 tortoises) gene in threatened and non-threatened populations of gopher tortoises (<i>Gopherus polyphemus</i>), and adaptive genetic variation at MHC genes was compared to neutral genetic variation derived from 10 microsatellite loci (441 tortoises). Genetic diversity at the MHC class II locus and microsatellites was greater in populations in the non-threatened portion of the gopher tortoise’s range (MHC class II difference in mean <i>A</i> = 8.11, <i>A_R</i> = 0.79, <i>H_O</i> = 0.51, and <i>H_E</i> = 0.16; microsatellite difference in mean <i>A</i> = 1.05 and <i>A_R</i> = 0.47). Only MHC class II sequences showed evidence of positive selection (d_N/d_S > 1, <i>Z</i> = 1.81, <i>P</i> = 0.04). Historical gene flow as estimated with Migrate-N was greater than recent migration estimated with BayesAss, suggesting that populations were better connected in the past when habitat was less fragmented. MHC genetic differentiation was correlated with microsatellite differentiation (Mantel r = 0.431, <i>P</i> = 0.001) suggesting neutral genetic processes are influencing MHC evolution, and advantageous MHC alleles could be lost due to genetic drift.

适应性遗传变异水平会影响物种应对环境与生态变化的能力，但这类变异水平的推断往往通过中性遗传标记完成。主要组织相容性复合体（Major histocompatibility complex, MHC）基因在免疫系统的适应性分支中扮演核心角色，已被广泛用于估算适应性遗传变异水平。研究针对地鼠龟（<i>Gopherus polyphemus</i>）受威胁与非受威胁种群的MHC I类（95/441只陆龟）和II类（245/441只陆龟）基因，对其肽结合区——即MHC分子直接与病原体及自身蛋白结合的区域——的部分序列进行了测序，并将MHC基因的适应性遗传变异与基于10个微卫星位点（441只陆龟）得到的中性遗传变异进行了对比。在地鼠龟分布区非受威胁区域的种群中，MHC II类位点以及微卫星的遗传多样性更高（MHC II类的平均差异：等位基因数<italic>A</italic> = 8.11、等位基因丰富度<italic>A_R</italic> = 0.79、观测杂合度<italic>H_O</italic> = 0.51、期望杂合度<italic>H_E</italic> = 0.16；微卫星的平均差异：等位基因数<italic>A</italic> = 1.05、等位基因丰富度<italic>A_R</italic> = 0.47）。仅MHC II类序列呈现出正选择信号（非同义替换速率与同义替换速率的比值<italic>d_N/d_S</italic> > 1，<italic>Z</italic> = 1.81，<italic>P</italic> = 0.04）。基于Migrate-N软件估算的历史基因流水平高于基于BayesAss软件得到的近期迁移水平，这表明在过去生境碎片化程度更低的时期，种群间的连通性更佳。MHC遗传分化与微卫星遗传分化呈显著相关（Mantel检验相关系数<italic>r</italic> = 0.431，<italic>P</italic> = 0.001），提示中性遗传过程可对MHC进化产生影响，且适应性MHC等位基因可能因遗传漂变而丢失。