Many species are threatened with extinction as their population sizes decrease with changing environments or face novel pathogenic threats. A reduction of genetic diversity at major histocompatibility complex (MHC) genes may have dramatic effects on populations’ survival, as these genes play a key role in adaptive immunity. This might be the case for chimpanzees, the MHC genes of which reveal signatures of an ancient selective sweep likely due to a viral epidemic that reduced their population size a few million years ago. To better assess how this past event affected MHC variation in chimpanzees compared to humans, we analysed several indexes of genetic diversity and linkage disequilibrium across seven MHC genes on four cohorts of chimpanzees and we compared them to those estimated at orthologous HLA genes in a large set of human populations. Interestingly, the analyses uncovered similar patterns of both molecular diversity and linkage disequilibrium across the seven MHC genes in chimpanzees and humans. Indeed, in both species the greatest allelic richness and heterozygosity were found at loci A, B, C and DRB1, the greatest nucleotide diversity at loci DRB1, DQA1 and DQB1, and both significant global linkage disequilibrium and the greatest proportions of haplotypes in linkage disequilibrium were observed at pairs DQA1 ~ DQB1, DQA1 ~ DRB1, DQB1 ~ DRB1 and B ~ C. Our results also showed that, despite some differences among loci, the levels of genetic diversity and linkage disequilibrium observed in contemporary chimpanzees were globally similar to those estimated in small isolated human populations, in contrast to significant differences compared to large populations. We conclude, first, that highly conserved mechanisms shaped the diversity of orthologous MHC genes in chimpanzees and humans. Furthermore, our findings support the hypothesis that an ancient demographic decline affecting the chimpanzee populations – like that ascribed to a viral epidemic – exerted a substantial effect on the molecular diversity of their MHC genes, albeit not more pronounced than that experienced by HLA genes in human populations that underwent rapid genetic drift during humans’ peopling history. We thus propose a model where chimpanzees’ MHC genes regenerated molecular variation through recombination/gene conversion and/or balancing selection after the selective sweep.

中文翻译：

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西方黑猩猩（盘古猿verus）和人类的遗传多样性和连锁不平衡的相似模式表明MHC分子进化的高度保守的机制。

随着物种数量随着环境变化而减少或面临新的致病性威胁，许多物种面临灭绝的威胁。主要组织相容性复合体（MHC）基因的遗传多样性降低可能对人群的生存产生巨大影响，因为这些基因在适应性免疫中起关键作用。黑猩猩可能就是这种情况，黑猩猩的MHC基因揭示了一种古老的选择性扫描的特征，这可能是由于几百万年前减少了人口规模的病毒流行所致。为了更好地评估过去的事件与人类相比如何影响黑猩猩的MHC变化，我们分析了四个黑猩猩群体中七个MHC基因的遗传多样性和连锁不平衡的几个指标，并将它们与大范围直系同源HLA基因的估计值进行了比较人口。有趣的是，这些分析揭示了黑猩猩和人类中七个MHC基因之间分子多样性和连锁不平衡的相似模式。的确，在这两个物种中，在基因座A，B，C和DRB1处发现了最大的等位基因富集度和杂合性，在基因座DRB1，DQA1和DQB1处发现了最大的核苷酸多样性，并且显着的整体连锁不平衡和连锁不平衡中单倍型的比例最大分别在DQA1〜DQB1，DQA1〜DRB1，DQB1〜DRB1和B〜C对中观察到。与人口众多的人群相比，在孤立的人口较少的人群中存在显着差异。我们首先得出结论，高度保守的机制影响了黑猩猩和人类直系同源MHC基因的多样性。此外，我们的发现支持以下假设：影响黑猩猩种群的古代人口下降（如归因于病毒流行）对他们的MHC基因的分子多样性产生了实质性影响，尽管没有人类中HLA基因经历的更为明显在人类历史上经历过快速遗传漂移的人群。因此，我们提出了一个模型，其中黑猩猩的MHC基因通过选择性扫描后的重组/基因转换和/或平衡选择来再生分子变异。我们的发现支持以下假设：影响黑猩猩种群的古代人口下降（如归因于病毒流行）对他们的MHC基因的分子多样性产生了实质性影响，尽管没有比人类HLA基因经历的更为明显。在人类的历史上经历了快速的基因漂移。因此，我们提出了一个模型，其中黑猩猩的MHC基因通过选择性扫描后的重组/基因转换和/或平衡选择来再生分子变异。我们的发现支持以下假设：影响黑猩猩种群的古代人口下降（如归因于病毒流行）对他们的MHC基因的分子多样性产生了实质性影响，尽管没有比人类HLA基因经历的更为明显。在人类的历史上经历了快速的基因漂移。因此，我们提出了一个模型，其中黑猩猩的MHC基因通过选择性扫描后的重组/基因转化和/或平衡选择来再生分子变异。尽管没有比人类中人类经历HLA基因经历过快速遗传漂移的人类群体更为明显。因此，我们提出了一个模型，其中黑猩猩的MHC基因通过选择性扫描后的重组/基因转换和/或平衡选择来再生分子变异。尽管没有比人类中人类经历HLA基因经历过快速遗传漂移的人类群体更为明显。因此，我们提出了一个模型，其中黑猩猩的MHC基因通过选择性扫描后的重组/基因转换和/或平衡选择来再生分子变异。