In human populations, the relative levels of neutral diversity on the X and autosomes differ markedly from each other and from the naïve theoretical expectation of 3/4. Here we propose an explanation for these differences based on new theory about the effects of sex-specific life history and given pedigree-based estimates of the dependence of human mutation rates on sex and age. We demonstrate that life history effects, particularly longer generation times in males than in females, are expected to have had multiple effects on human X-to-autosome (X:A) diversity ratios, as a result of male-biased mutation rates, the equilibrium X:A ratio of effective population sizes, and the differential responses to changes in population size. We also show that the standard approach of using divergence between species to correct for male mutation bias results in biased estimates of X:A effective population size ratios. We obtain alternative estimates using pedigree-based estimates of the male mutation bias, which reveal that X:A ratios of effective population sizes are considerably greater than previously appreciated. Finally, we find that the joint effects of historical changes in life history and population size can explain the observed X:A diversity ratios in extant human populations. Our results suggest that ancestral human populations were highly polygynous, that non-African populations experienced a substantial reduction in polygyny and/or increase in the male-to-female ratio of generation times around the Out-of-Africa bottleneck, and that current diversity levels were affected by fairly recent changes in sex-specific life history.

在人群中，X和常染色体上的中性多样性的相对水平彼此之间显着不同，并且与3/4的天真理论预期值也存在显着差异。在这里，我们基于有关特定性别的生活史影响的新理论，并基于谱系估计的人类突变率对性别和年龄的依赖性，对这些差异提出了解释。我们证明，由于男性偏见的突变率，生活史的影响，尤其是男性的产生时间比女性更长，对人类的X染色体常染色体（X：A）多样性比率产生了多重影响。均衡X：有效人口规模与人口规模变化的差异响应之比。我们还表明，使用物种之间的差异来校正男性突变偏倚的标准方法会导致对X：A有效种群规模比的偏倚估计。我们使用基于谱系的男性突变偏倚的估计值获得替代估计值，该估计值表明有效人群规模的X：A比值明显大于以前的估计。最后，我们发现生活史和人口规模的历史变化的共同影响可以解释现存人口中X：A的多样性比率。我们的结果表明，祖先的人口具有高度多性，多族裔，非非洲人口在非洲瓶颈附近经历了一夫多妻制的大幅减少和/或世代男女比例的增加，