Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences. (22nd July 2020)

• Record Type: Journal Article
• Authors: Naidoo, Thijessen; Xu, Jingzi; Vicente, Mário; Malmström, Helena; Soodyall, Himla; Jakobsson, Mattias; Schlebusch, Carina M
• Editors: Majumder, Partha T E
• Is Part Of: Genome biology and evolution. Volume 12:Number 7(2020)
• Page Start: 1031
• Page End: 1039
• Publication Date: 2020-07-22
• Subjects: Y chromosome -- next-generation sequencing -- haplogroups -- Khoe-San -- southern Africa; Genomics -- Periodicals; Genes -- Periodicals; 572.8605
• DOI: 10.1093/gbe/evaa098
• Languages: English
• ISSNs: 1759-6653

Abstract

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 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.