Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences.
Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences.
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DOI：
10.1186/2041-2223-5-13
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发表时间：
2014
期刊：
影响因子：
--
通讯作者：
Stoneking M
中科院分区：
文献类型：
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作者：
Lippold S;Xu H;Ko A;Li M;Renaud G;Butthof A;Schröder R;Stoneking M
母系遗传的线粒体DNA（mtDNA）和父系遗传的非重组Y染色体（NRY）变异的比较为性别偏见过程（如迁移、居住模式等）对人类遗传变异的影响提供了重要的见解。然而，这种比较受到通常用于测定mtDNA和NRY变异的不同分子方法的限制（例如，对mtDNA的控制区的高变区段进行测序，而对NRY的SNP和/或STR基因座进行基因分型）。在这里，我们报告了一种简单的捕获阵列方法来富集Illumina测序文库中约500 kb的NRY序列，我们使用该序列从CEPH人类基因组多样性小组（HGDP）中的51个群体的623名男性中生成NRY序列。我们还从同一个体中获得了完整的mtDNA基因组序列，使我们能够比较没有任何确定偏差的母系和父系历史。我们在NRY序列中鉴定了2，228个SNP，在mtDNA序列中鉴定了2，163个SNP。我们的研究结果证实了一个有争议的论断，即在全球范围内，人类群体之间的遗传差异在NRY上比在mtDNA上更大，尽管这种差异并不像以前认为的那么大。更重要的是，我们发现大量的区域变化模式的mtDNA与NRY变异。基于模型的模拟表明，非洲以外的移徙以及许多人口的祖先有效人口规模非常小（<100）。我们还发现，女性有效人口规模与男性有效人口规模之比（Nf/Nm）在整个现代人类历史上一直大于1，并且最近由于Nf的增长速度比Nm更快而有所增加。NRY和mtDNA序列提供了新的见解人类群体的父系和母系的历史，我们在这里介绍的方法应该广泛适用于进一步的研究。
Comparisons of maternally-inherited mitochondrial DNA (mtDNA) and paternally-inherited non-recombining Y chromosome (NRY) variation have provided important insights into the impact of sex-biased processes (such as migration, residence pattern, and so on) on human genetic variation. However, such comparisons have been limited by the different molecular methods typically used to assay mtDNA and NRY variation (for example, sequencing hypervariable segments of the control region for mtDNA vs. genotyping SNPs and/or STR loci for the NRY). Here, we report a simple capture array method to enrich Illumina sequencing libraries for approximately 500 kb of NRY sequence, which we use to generate NRY sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). We also obtained complete mtDNA genome sequences from the same individuals, allowing us to compare maternal and paternal histories free of any ascertainment bias. We identified 2,228 SNPs in the NRY sequences and 2,163 SNPs in the mtDNA sequences. Our results confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA, although the differences are not as large as previously suggested. More importantly, we find substantial regional variation in patterns of mtDNA versus NRY variation. Model-based simulations indicate very small ancestral effective population sizes (<100) for the out-of-Africa migration as well as for many human populations. We also find that the ratio of female effective population size to male effective population size (Nf/Nm) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in Nf than Nm. The NRY and mtDNA sequences provide new insights into the paternal and maternal histories of human populations, and the methods we introduce here should be widely applicable for further such studies.