{"entity": "publication", "iuid": "4f490df9d6fc4ab287ac10a2efd9faea", "timestamp": "2026-09-25T10:36:00.609Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4f490df9d6fc4ab287ac10a2efd9faea.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4f490df9d6fc4ab287ac10a2efd9faea"}}, "title": "Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences.", "authors": [{"family": "Naidoo", "given": "Thijessen", "initials": "T"}, {"family": "Xu", "given": "Jingzi", "initials": "J"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM"}], "type": "comparative study", "published": "2020-07-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "12", "issue": "7", "pages": "1031-1039", "issn-l": "1759-6653"}, "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.", "doi": "10.1093/gbe/evaa098", "pmid": "32697300", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7375190"}, {"db": "pii", "key": "5874966"}], "notes": [], "created": "2026-09-23T08:43:47.267Z", "modified": "2026-09-23T08:43:47.288Z"}