Abstract Reproductive isolation is a fundamental step in speciation. While sex chromosomes have been linked to reproductive isolation in many model systems, including hominids, genetic studies of the contribution of sex chromosome loci to speciation for natural populations are relatively sparse. Natural hybrid zones can help identify genomic regions contributing to reproductive isolation, like hybrid incompatibility loci, since these regions exhibit reduced introgression between parental species. Here, we use a primate hybrid zone (Alouatta palliata × Alouatta pigra) to test for reduced introgression of X-linked SNPs compared to autosomal SNPs. To identify X-linked sequence in A. palliata, we used a sex-biased mapping approach with whole-genome re-sequencing data. We then used genomic cline analysis with reduced-representation sequence data for parental A. palliata and A. pigra individuals and hybrids (n = 88) to identify regions with non-neutral introgression. We identified ~26 Mb of non-repetitive, putatively X-linked genomic sequence in A. palliata, most of which mapped collinearly to the marmoset and human X chromosomes. We found that X-linked SNPs had reduced introgression and an excess of ancestry from A. palliata as compared to autosomal SNPs. One outlier region with reduced introgression overlaps a previously described “desert” of archaic hominin ancestry on the human X chromosome. These results are consistent with a large role for the X chromosome in speciation across animal taxa and further, suggest shared features in the genomic basis of the evolution of reproductive isolation in primates.

中文翻译：

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人类生殖隔离的 X 连锁特征反映在吼猴杂交区

摘要 生殖隔离是物种形成的一个基本步骤。虽然在包括原始人类在内的许多模型系统中，性染色体与生殖隔离有关，但关于性染色体位点对自然种群物种形成贡献的遗传研究相对较少。自然杂交区可以帮助识别导致生殖隔离的基因组区域，如杂交不相容性基因座，因为这些区域表现出亲本物种之间的基因渗入减少。在这里，我们使用灵长类动物杂交区（Alouatta palliata × Alouatta pigra）来测试与常染色体 SNP 相比，X 连锁 SNP 的基因渗入减少。为了识别 A. palliata 中的 X 连锁序列，我们使用了一种具有全基因组重测序数据的性别偏向制图方法。然后，我们对亲本 A. palliata 和 A.pigra 个体和杂种（n = 88）使用具有减少代表性序列数据的基因组克隆分析来识别具有非中性基因渗入的区域。我们在 A. palliata 中鉴定了约 26 Mb 的非重复性、推定的 X 连锁基因组序列，其中大部分与狨猴和人类 X 染色体共线定位。我们发现，与常染色体 SNP 相比，X 连锁 SNP 减少了 A. palliata 的基因渗入和过多的祖先。一个基因渗入减少的异常区域与先前描述的人类 X 染色体上古老的人类祖先的“沙漠”重叠。这些结果与 X 染色体在跨动物分类群的物种形成中的重要作用一致，并进一步表明灵长类动物生殖隔离进化的基因组基础的共同特征。