Sex-biased evolutionary forces shape genomic patterns of human diversity.
Sex-biased evolutionary forces shape genomic patterns of human diversity.
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DOI：
10.1371/journal.pgen.1000202
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发表时间：
2008-09-26
期刊：
影响因子：
4.5
通讯作者：
Wall JD
中科院分区：
文献类型：
--
作者：
Hammer MF;Mendez FL;Cox MP;Woerner AE;Wall JD
常染色体和X染色体上的变异水平的比较可以用来检验关于影响基因组变异模式的因素的假设。虽然现在有大量来自多个人类群体的基因组的核苷酸序列数据，但还没有系统的努力来检查X染色体与常染色体上中性多态性的相对水平。我们分析了来自6个地理上不同的人群的90个人中的每一个的40个独立的非编码区的常染色体和X染色体上的210 kb的DNA测序数据。我们通过考虑人类内部多样性与人类-猩猩分歧的比率来校正男性和女性之间突变率的差异。我们发现，在所有六个人类群体中，X染色体上遗传变异的相对水平高于预期。我们测试了一些替代假设来解释X染色体上的过度多态性，包括背景选择模型，人口规模的变化，以及结构化人口中的性别特异性迁移。虽然这些过程中的每一个可能有一个小的影响，X-连锁的常染色体多样性的相对比例，我们的研究结果指出，在生殖成功的方差性别之间的系统差异，即，在人类群体中的广泛影响一夫多妻制。我们的结论是，在努力构建人类人口历史模型和了解人类基因组变异的力量塑造模式时，必须将导致男性与女性有效人口规模较低的因素视为重要的人口变量。像许多灵长类物种一样，人类的交配系统被认为是适度的一夫多妻制（即，雄性在繁殖成功率方面比雌性表现出更高的差异）。因此，男性预计将有一个较低的有效人口规模（Ne）比女性，和中性遗传变异的比例在X染色体（相对于常染色体）应高于预期的假设下，严格的中性和一个平等的育种性别比。我们通过测量六个人类群体X染色体和常染色体上40个独立位点的中性多态性水平来测试一夫多妻制的影响。为了校正基因座之间的突变率异质性，我们将人类种群内的多样性估计值除以每个基因座与猩猩的差异。根据一夫多妻制模型的预期一致，我们发现X连锁与常染色体多样性的水平升高。虽然多个人口统计过程可能有助于观察到的基因组多样性模式（即，背景选择，种群规模的变化，和性别特异性迁移），我们得出结论，繁殖雌性数量超过繁殖雄性数量的历史性过剩本身可以解释大多数观察到的X染色体有效种群规模的增加。
Comparisons of levels of variability on the autosomes and X chromosome can be used to test hypotheses about factors influencing patterns of genomic variation. While a tremendous amount of nucleotide sequence data from across the genome is now available for multiple human populations, there has been no systematic effort to examine relative levels of neutral polymorphism on the X chromosome versus autosomes. We analyzed ∼210 kb of DNA sequencing data representing 40 independent noncoding regions on the autosomes and X chromosome from each of 90 humans from six geographically diverse populations. We correct for differences in mutation rates between males and females by considering the ratio of within-human diversity to human-orangutan divergence. We find that relative levels of genetic variation are higher than expected on the X chromosome in all six human populations. We test a number of alternative hypotheses to explain the excess polymorphism on the X chromosome, including models of background selection, changes in population size, and sex-specific migration in a structured population. While each of these processes may have a small effect on the relative ratio of X-linked to autosomal diversity, our results point to a systematic difference between the sexes in the variance in reproductive success; namely, the widespread effects of polygyny in human populations. We conclude that factors leading to a lower male versus female effective population size must be considered as important demographic variables in efforts to construct models of human demographic history and for understanding the forces shaping patterns of human genomic variability. Like many primate species, the mating system of humans is considered to be moderately polygynous (i.e., males exhibit a higher variance in reproductive success than females). As a consequence, males are expected to have a lower effective population size (Ne) than females, and the proportion of neutral genetic variation on the X chromosome (relative to the autosomes) should be higher than expected under the assumption of strict neutrality and an equal breeding sex ratio. We test for the effects of polygyny by measuring levels of neutral polymorphism at 40 independent loci on the X chromosome and autosomes in six human populations. To correct for mutation rate heterogeneity among loci, we divide our diversity estimates within human populations by divergence with orangutan at each locus. Consistent with expectations under a model of polygyny, we find elevated levels of X-linked versus autosomal diversity. While it is possible that multiple demographic processes may contribute to the observed patterns of genomic diversity (i.e., background selection, changes in population size, and sex-specific migration), we conclude that an historical excess of breeding females over the number of breeding males can by itself explain most of the observed increase in effective population size of the X chromosome.
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64.8
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