title: Refining the Y chromosome phylogeny with southern African sequences.
abstract: The recent availability of large-scale sequence data for the human Y chromosome has revolutionized analyses of and insights gained from this non-recombining, paternally inherited chromosome. However, the studies to date focus on Eurasian variation, and hence the diversity of early-diverging branches found in Africa has not been adequately documented. Here, we analyze over 900 kb of Y chromosome sequence obtained from 547 individuals from southern African Khoisan- and Bantu-speaking populations, identifying 232 new sequences from basal haplogroups A and B. We identify new clades in the phylogeny, an older age for the root, and substantially older ages for some individual haplogroups. Furthermore, while haplogroup B2a is traditionally associated with the spread of Bantu speakers, we find that it probably also existed in Khoisan groups before the arrival of Bantu speakers. Finally, there is pronounced variation in branch length between major haplogroups; in particular, haplogroups associated with Bantu speakers have significantly longer branches. Technical artifacts cannot explain this branch length variation, which instead likely reflects aspects of the demographic history of Bantu speakers, such as recent population expansion and an older average paternal age. The influence of demographic factors on branch length variation has broader implications both for the human Y phylogeny and for similar analyses of other species.
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany. barbieri.chiara@gmail.com.|Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. barbieri.chiara@gmail.com.
authors.forename: Chiara
authors.identifier: http://orcid.org/0000-0001-8827-5655
authors.initials: C
authors.lastname: Barbieri
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Hübner
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
authors.forename: Enrico
authors.initials: E
authors.lastname: Macholdt
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
authors.forename: Shengyu
authors.initials: S
authors.lastname: Ni
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Lippold
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
authors.forename: Roland
authors.initials: R
authors.lastname: Schröder
authors.affiliation: Department of Biological Sciences, University of Botswana, Gaborone, Botswana.
authors.forename: Sununguko Wata
authors.initials: SW
authors.lastname: Mpoloka
authors.affiliation: Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, 10559, Berlin, Germany.
authors.forename: Josephine
authors.initials: J
authors.lastname: Purps
authors.affiliation: Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, 10559, Berlin, Germany.
authors.forename: Lutz
authors.initials: L
authors.lastname: Roewer
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
authors.forename: Mark
authors.initials: M
authors.lastname: Stoneking
authors.affiliation: Dynamique du Langage, UMR5596, CNRS & Université Lyon 2, 69363, Lyon Cedex 07, France. brigitte.pakendorf@cnrs.fr.
authors.forename: Brigitte
authors.initials: B
authors.lastname: Pakendorf
mesh_terms: D000349:Africa; D044383:Black People / Q000235:genetics*; D041322:Chromosomes, Human, Y / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D005828:Genetics, Population; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D010802:Phylogeny