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Refining the Y chromosome phylogeny with southern African sequences.

Barbieri C, Hübner A, Macholdt E, Ni S, Lippold S, Schröder R, Mpoloka SW, Purps J, Roewer L, Stoneking M, Pakendorf B - Hum. Genet. (2016)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany. barbieri.chiara@gmail.com.

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.

No MeSH data available.


Distances to the A2-T node in number of mutations. a Distribution of distances from each tip to the A2-T node. b Density distribution of distances to the A2-T node for each major haplogroup. Haplogroups are color-coded as in Fig. 1 (color figure online)
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Fig4: Distances to the A2-T node in number of mutations. a Distribution of distances from each tip to the A2-T node. b Density distribution of distances to the A2-T node for each major haplogroup. Haplogroups are color-coded as in Fig. 1 (color figure online)

Mentions: An analysis of the distribution of the number of mutations from each tip to the A2-T node (Fig. 4a) demonstrates considerable heterogeneity in branch length, with a bimodal distribution. Furthermore, the branch lengths differ strikingly among haplogroups (Fig. 4b): A, B, E2, and E1b1b are characterized by shorter than average branch lengths, while the E1b1a subgroups all have significantly longer branches (Wilcoxon test W = 71048, p value <0.001).Fig. 4


Refining the Y chromosome phylogeny with southern African sequences.

Barbieri C, Hübner A, Macholdt E, Ni S, Lippold S, Schröder R, Mpoloka SW, Purps J, Roewer L, Stoneking M, Pakendorf B - Hum. Genet. (2016)

Distances to the A2-T node in number of mutations. a Distribution of distances from each tip to the A2-T node. b Density distribution of distances to the A2-T node for each major haplogroup. Haplogroups are color-coded as in Fig. 1 (color figure online)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4835522&req=5

Fig4: Distances to the A2-T node in number of mutations. a Distribution of distances from each tip to the A2-T node. b Density distribution of distances to the A2-T node for each major haplogroup. Haplogroups are color-coded as in Fig. 1 (color figure online)
Mentions: An analysis of the distribution of the number of mutations from each tip to the A2-T node (Fig. 4a) demonstrates considerable heterogeneity in branch length, with a bimodal distribution. Furthermore, the branch lengths differ strikingly among haplogroups (Fig. 4b): A, B, E2, and E1b1b are characterized by shorter than average branch lengths, while the E1b1a subgroups all have significantly longer branches (Wilcoxon test W = 71048, p value <0.001).Fig. 4

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany. barbieri.chiara@gmail.com.

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.

No MeSH data available.