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

Genome Biology and Evolution
Thijessen NaidooCarina M Schlebusch

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 linke...Continue Reading

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Citations

Jul 23, 2020·Molecular Biology and Evolution·Carina M SchlebuschMattias Jakobsson

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Methods Mentioned

BETA
chip

Software Mentioned

BWA
TMRCA
BEAUti
ISOGG
LogCombiner
GATK
Tracer
VCFtools
TreeAnnotator
BEAST

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