Integrating sex-bias into studies of archaic introgression on chromosome X.
Integrating sex-bias into studies of archaic introgression on chromosome X.
复制标题
DOI：
10.1371/journal.pgen.1010399
复制
发表时间：
2023-08
期刊：
影响因子：
4.5
通讯作者：
中科院分区：
文献类型：
--
作者：
古人类与人类杂交的证据来自于推断古人类单倍型片段位置的方法，或者使用生活在今天的人的基因组来推断“古人类覆盖范围”的方法。随着越来越多的古代覆盖范围的估计出现，很明显，大多数覆盖范围都在常染色体上，很少保留在X染色体上。在这里，我们总结了从现存人类样本中发表的关于常染色体和X染色体的古代覆盖范围的估计。我们发现，在常染色体上的古老覆盖率平均是X染色体的7倍，并确定了这一比例的广泛大陆模式：在欧洲样本中最大，在南亚样本中最少。我们还进行了广泛的模拟研究，以调查古文覆盖的数量、覆盖的长度和古文覆盖的清除率如何受到古文渗入子内性别比例不平等引起的性别偏见的影响。我们的研究结果普遍证实，随着男性性别偏见的增加，x染色体上保留的古人类覆盖范围越来越少。我们的研究首次明确地模拟了这种性别偏见及其在造成x染色体上古人类覆盖范围缺乏的潜在作用。数万年前，人类与我们的近亲（如尼安德特人）杂交，我们通过在我们的基因组中发现古人类DNA片段而了解到这一点。高达4%的人类基因组可能是古老的DNA，但大部分古老的部分都在常染色体上（非性染色体）。X染色体所含的原始DNA通常比常染色体少3到10倍。也不像常染色体，它总是由母亲遗传，但有时只是由父亲遗传。关于为什么X染色体的古老DNA比常染色体少，有几种假设；一个尚未被充分探索的问题是，与我们祖先杂交的古人类主要是男性还是女性，这被称为“性别偏见”。在本文中，我们使用模拟来研究性别偏见是否会减少X染色体上的古代DNA。通过模拟研究，我们发现，当古代人主要是男性时，与存在女性偏见或没有性别偏见的情况相比，现代人最终在X染色体上的古代DNA少于他们的常染色体。因此，男性的性别偏见可能是导致X染色体上古代DNA数量与常染色体数量差异的原因。当然，关于人口和自然选择如何塑造我们的DNA，还有很多其他因素有待探索。研究这样的模式有助于我们更多地了解早期人类的自然历史，并将古代的杂交事件与人类历史上其他性别偏见事件联系起来。
Evidence of interbreeding between archaic hominins and humans comes from methods that infer the locations of segments of archaic haplotypes, or ‘archaic coverage’ using the genomes of people living today. As more estimates of archaic coverage have emerged, it has become clear that most of this coverage is found on the autosomes— very little is retained on chromosome X. Here, we summarize published estimates of archaic coverage on autosomes and chromosome X from extant human samples. We find on average 7 times more archaic coverage on autosomes than chromosome X, and identify broad continental patterns in this ratio: greatest in European samples, and least in South Asian samples. We also perform extensive simulation studies to investigate how the amount of archaic coverage, lengths of coverage, and rates of purging of archaic coverage are affected by sex-bias caused by an unequal sex ratio within the archaic introgressors. Our results generally confirm that, with increasing male sex-bias, less archaic coverage is retained on chromosome X. Ours is the first study to explicitly model such sex-bias and its potential role in creating the dearth of archaic coverage on chromosome X. Tens of thousands of years ago, humans interbred with our close hominin relatives (e.g. Neanderthals), which we know from finding segments of archaic hominin DNA in our genomes. Up to 4% of a human genome may be archaic DNA, but most of that archaic part is on the autosomes (the non-sex chromosomes). Chromosome X usually contains 3 to 10 times less archaic DNA than the autosomes. Also unlike the autosomes, it is always passed down by mothers, but only sometimes by fathers. There are several hypotheses for why chromosome X has less archaic DNA than the autosomes; one that has not been fully explored is whether the archaic hominins that interbred with our ancestors were mostly male or mostly female, known as ‘sex-bias’. In this paper, we use simulations to investigate whether sex-bias could produce less archaic DNA on chromosome X. Using simulation studies, we find that when the archaics are mostly male, modern humans end up with less archaic DNA on chromosome X than their autosomes, compared to when there is a female-bias or no sex-bias. Therefore, male sex-bias could be contributing to the difference in the amount of archaic DNA on chromosome X versus the autosomes. Of course, there are still plenty of other factors to be explored about how demography and selection have shaped our DNA. Studying patterns like this helps us learn more about early hominin natural history, and contextualizes archaic interbreeding events among other sex-biased events in human history.
登录
查看更多内容
影响因子：
4.5
作者：
Kim BY;Huber CD;Lohmueller KE
通讯作者：
Lohmueller KE
影响因子：
5.3
作者：
Lind, Joanne M.;Hutcheson-Dilks, Holli B.;Smith, Michael W.
通讯作者：
Smith, Michael W.
影响因子：
3.3
作者：
Goldberg, Amy;Rosenberg, Noah A.
通讯作者：
Rosenberg, Noah A.
影响因子：
4.5
作者：
Hubisz, Melissa J.;Williams, Amy L.;Siepel, Adam
通讯作者：
Siepel, Adam
影响因子：
64.8
作者：
通讯作者：
--