Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences

Genome Biol Evol. 2020 Jul 1;12(7):1031-1039. doi: 10.1093/gbe/evaa098.

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.

Keywords: Khoe-San; Y chromosome; haplogroups; next-generation sequencing; southern Africa.

Publication types

  • Comparative Study
  • Letter
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Africa, Southern
  • Chromosomes, Human, Y*
  • Female
  • Genetic Variation
  • Genome, Human*
  • Haplotypes
  • Humans
  • Male
  • Phylogeny
  • Whole Genome Sequencing