Abstract
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 comparisonwith existingwholeY-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 Ychromosome phylogeny. The distribution ofmajor 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 Africanmigrations, B-M112 linked to earlier east-south gene flow, A-M14 linked to shared ancestrywith central African rainforest hunter-gatherers, and A-M51 potentially unique to the Khoe-San.