Amos William
Department of Zoology, Cambridge University, Downing Street, Cambridge CB2 3EJ, UK.
R Soc Open Sci. 2021 Jun 16;8(6):201229. doi: 10.1098/rsos.201229.
Although the presence of archaic hominin legacies in humans is taken for granted, little attention has been given as to how the data fit with how humans colonized the world. Here, I show that Neanderthal and Denisovan legacies are strongly correlated and that inferred legacy size, like heterozygosity, exhibits a strong correlation with distance from Africa. Simulations confirm that, once created, legacy size is extremely stable: it may reduce through admixture with lower legacy populations but cannot increase significantly through neutral drift. Consequently, populations carrying the highest legacies are likely to be those whose ancestors inter-bred most with archaics. However, the populations with the highest legacies are globally scattered and are unified, not by having origins within the known Neanderthal range, but instead by living in locations that lie furthest from Africa. Furthermore, the Simons Genome Diversity Project data reveal two distinct correlations between Neanderthal and Denisovan legacies, one that starts in North Africa and increases west to east across Eurasia and into some parts of Oceania, and a second, much steeper trend that starts in Africa, peaking with the San and Ju/'hoansi and which, if extrapolated, predicts the large inferred legacies of both archaics found in Oceania/Australia. Similar 'double' trends are observed for the introgression statistic in a second large dataset published by Qin and Stoneking (Qin & Stoneking 2015 , 2665-2674 (doi:10.1093/molbev/msv141)). These trends appear at odds with simple models of how introgression occurred though more complicated patterns of introgression could potentially generate better fits. Moreover, substituting archaic genomes with those of great apes yields similar but biologically impossible signals of introgression, suggesting that the signals these metrics capture arise within humans and are largely independent of the test group. Interestingly, the data do appear to fit a speculative model in which the loss of diversity that occurred when humans moved further from Africa created a gradient in heterozygosity that in turn progressively reduced mutation rate such that populations furthest from Africa have diverged less from our common ancestor and hence from the archaics. In this light, the two distinct trends could be interpreted in terms of two 'out of Africa' events, an early one ending in Oceania and Australia and a later one that colonized Eurasia and the Americas.
尽管人类体内存在古老人类遗产这一点已被视为理所当然，但对于这些数据如何与人类殖民世界的方式相契合，却很少有人关注。在此，我表明尼安德特人和丹尼索瓦人的遗产具有很强的相关性，而且推断出的遗产规模，如同杂合度一样，与距非洲的距离呈现出很强的相关性。模拟结果证实，一旦形成，遗产规模极其稳定：它可能会因与遗产较少的群体混合而减少，但不会通过中性漂变显著增加。因此，携带最高遗产的群体很可能是那些祖先与古老人类杂交最多的群体。然而，遗产最高的群体在全球范围内分布零散，它们并非因起源于已知的尼安德特人活动范围而统一，而是因生活在距离非洲最远的地方而统一。此外，西蒙斯基因组多样性项目的数据揭示了尼安德特人和丹尼索瓦人遗产之间的两种不同相关性，一种始于北非，从西到东横跨欧亚大陆并延伸至大洋洲的一些地区，另一种则陡峭得多，始于非洲，在桑人和朱/霍安西人中达到峰值，若外推的话，预测在大洋洲/澳大利亚发现的两种古老人类都有大量推断出的遗产。在秦和斯托金发表的第二个大型数据集中（Qin & Stoneking 2015, 2665 - 2674 (doi:10.1093/molbev/msv141)），对于渗入统计量也观察到了类似的“双重”趋势。这些趋势似乎与渗入发生的简单模型不一致，不过更复杂的渗入模式可能会产生更好的拟合。此外，用大猩猩的基因组替代古老人类基因组会产生类似但生物学上不可能的渗入信号，这表明这些指标所捕捉到的信号是在人类内部产生的，并且在很大程度上与测试群体无关。有趣的是，这些数据似乎确实符合一个推测性模型，即当人类从非洲向外迁移时发生的多样性丧失创造了一个杂合度梯度，进而逐渐降低了突变率，使得距离非洲最远的群体与我们的共同祖先以及古老人类的差异更小。据此，这两种不同的趋势可以用两次“走出非洲”事件来解释，一次早期事件在大洋洲和澳大利亚结束，另一次后期事件则殖民了欧亚大陆和美洲。
