Although the human Y chromosome has effectively shown utility in uncovering facets of human evolution and population histories, the ascertainment bias present in early Y-chromosome variant data sets limited the accuracy of diversity and TMRCA estimates obtained from them. The advent of next-generation sequencing, however, has removed this bias and allowed for the discovery of thousands of new variants for use in improving the Y-chromosome phylogeny and computing estimates that are more accurate. Here, we describe the high-coverage sequencing of the whole Y chromosome in a data set of 19 male Khoe-San individuals in comparison with existing whole Y-chromosome sequence data. Due to the increased resolution, we potentially resolve the source of haplogroup B-P70 in the Khoe-San, and reconcile recently published haplogroup A-M51 data with the most recent version of the ISOGG Y-chromosome phylogeny. Our results also improve the positioning of tentatively placed new branches of the ISOGG Y-chromosome phylogeny. The distribution of major Y-chromosome haplogroups in the Khoe-San and other African groups coincide with the emerging picture of African demographic history; with E-M2 linked to the agriculturalist Bantu expansion, E-M35 linked to pastoralist eastern African migrations, B-M112 linked to earlier east-south gene flow, A-M14 linked to shared ancestry with central African rainforest hunter-gatherers, and A-M51 potentially unique to the Khoe-San.

中文翻译：

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基于全基因组序列的南部非洲 Khoe-San 人群的 Y 染色体变异。


尽管人类 Y 染色体在揭示人类进化和人口历史方面有效地显示出实用性，但早期 Y 染色体变异数据集中存在的确定偏差限制了多样性和从中获得的 TMRCA 估计的准确性。然而，下一代测序的出现消除了这种偏差，并允许发现数千种新变异，用于改进 Y 染色体系统发育和计算更准确的估计。在这里，我们描述了 19 名男性 Khoe-San 个体的数据集中的整个 Y 染色体的高覆盖率测序，并与现有的整个 Y 染色体序列数据进行了比较。由于分辨率的提高，我们有可能解决 Khoe-San 中单倍群 B-P70 的来源，并将最近发布的单倍群 A-M51 数据与最新版本的 ISOGG Y 染色体系统发育相一致。我们的结果还改善了 ISOGG Y 染色体系统发育中暂定新分支的定位。 Khoe-San 和其他非洲族群中主要 Y 染色体单倍群的分布与非洲人口历史的新图景相吻合；其中E-M2与农业班图人扩张有关，E-M35与东非牧民迁徙有关，B-M112与早期东南基因流动有关，A-M14与中非雨林狩猎采集者的共同祖先有关，A-M14与中非雨林狩猎采集者的共同祖先有关-M51 可能是 Khoe-San 独有的。