Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.
Am J Hum Genet. 2014 Jun 5;94(6):827-44. doi: 10.1016/j.ajhg.2014.04.011. Epub 2014 May 15.
Contrasting the genetic diversity of the human X chromosome (X) and autosomes has facilitated understanding historical differences between males and females and the influence of natural selection. Previous studies based on smaller data sets have left questions regarding how empirical patterns extend to additional populations and which forces can explain them. Here, we address these questions by analyzing the ratio of X-to-autosomal (X/A) nucleotide diversity with the complete genomes of 569 females from 14 populations. Results show that X/A diversity is similar within each continental group but notably lower in European (EUR) and East Asian (ASN) populations than in African (AFR) populations. X/A diversity increases in all populations with increasing distance from genes, highlighting the stronger impact of diversity-reducing selection on X than on the autosomes. However, relative X/A diversity (between two populations) is invariant with distance from genes, suggesting that selection does not drive the relative reduction in X/A diversity in non-Africans (0.842 ± 0.012 for EUR-to-AFR and 0.820 ± 0.032 for ASN-to-AFR comparisons). Finally, an array of models with varying population bottlenecks, expansions, and migration from the latest studies of human demographic history account for about half of the observed reduction in relative X/A diversity from the expected value of 1. They predict values between 0.91 and 0.94 for EUR-to-AFR comparisons and between 0.91 and 0.92 for ASN-to-AFR comparisons. Further reductions can be predicted by more extreme demographic events in excess of those captured by the latest studies but, in the absence of these, also by historical sex-biased demographic events or other processes.
比较人类 X 染色体(X)和常染色体的遗传多样性,有助于了解男性和女性之间的历史差异以及自然选择的影响。之前基于较小数据集的研究仍存在一些问题,例如经验模式如何扩展到其他群体,以及哪些因素可以解释这些模式。在这里,我们通过分析来自 14 个群体的 569 名女性的完整基因组中的 X 与常染色体(X/A)核苷酸多样性比来解决这些问题。结果表明,X/A 多样性在每个大陆群体内是相似的,但在欧洲(EUR)和东亚(ASN)群体中明显低于非洲(AFR)群体。X/A 多样性在所有群体中都随着与基因的距离增加而增加,这突出表明多样性降低选择对 X 染色体的影响大于对常染色体的影响。然而,相对 X/A 多样性(两个群体之间)与基因距离无关,表明选择不会导致非非洲人(EUR 与 AFR 相比为 0.842±0.012,ASN 与 AFR 相比为 0.820±0.032)的 X/A 多样性相对减少。最后,根据人类人口历史最新研究中具有不同种群瓶颈、扩张和迁移的一系列模型,可解释观察到的相对 X/A 多样性减少量的一半左右,而这些模型从预期值 1 中得出。这些模型预测 EUR 与 AFR 相比的数值在 0.91 到 0.94 之间,ASN 与 AFR 相比的数值在 0.91 到 0.92 之间。如果发生最新研究中未捕获的更极端的人口事件,或者历史上的性别偏向人口事件或其他过程,也可以预测进一步的减少。