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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.


Maximum parsimony (MP) tree for the southern African dataset, rooted with A00. The width of the triangles is proportional to the number of individuals included. Previously unreported lineages are highlighted. Branches are numbered to identify them in Table S1 (Online Resource 2), where information on the defining mutations and comparison with other nomenclature systems are reported. Branch number 1 indicates the branch shared by A2 and A3b1, which is not visible as a separate branch in the MP reconstruction
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Fig1: Maximum parsimony (MP) tree for the southern African dataset, rooted with A00. The width of the triangles is proportional to the number of individuals included. Previously unreported lineages are highlighted. Branches are numbered to identify them in Table S1 (Online Resource 2), where information on the defining mutations and comparison with other nomenclature systems are reported. Branch number 1 indicates the branch shared by A2 and A3b1, which is not visible as a separate branch in the MP reconstruction

Mentions: The major haplogroups found in our dataset are A2, A3b1, B2a, B2b, and E (including E1a1a, E1a1b, and E2); furthermore, individual sequences belonging to haplogroups G, I, O, T, and R1 were found. The phylogeny reconstructed with a maximum parsimony tree (Fig. 1) and verified by means of network analysis (Figures S4–S7 in Online Resource 1) corresponds to that of the ISOGG consortium (International Society of Genetic Genealogy 2014, Version: 10.101, Date: 8 December 2015), as summarized in van Oven et al. (2014); however, we identify additional branches that have not yet been reported. Table S1 in Online Resource 2 summarizes information about the major branches reported in Fig. 1, such as the different nomenclatures used and the mutations defining each branch. The haplogroup assignment for each individual is listed in Table S2 (Online Resource 2), while haplogroup frequencies and measures of diversity are shown in Table 1.Fig. 1


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)

Maximum parsimony (MP) tree for the southern African dataset, rooted with A00. The width of the triangles is proportional to the number of individuals included. Previously unreported lineages are highlighted. Branches are numbered to identify them in Table S1 (Online Resource 2), where information on the defining mutations and comparison with other nomenclature systems are reported. Branch number 1 indicates the branch shared by A2 and A3b1, which is not visible as a separate branch in the MP reconstruction
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig1: Maximum parsimony (MP) tree for the southern African dataset, rooted with A00. The width of the triangles is proportional to the number of individuals included. Previously unreported lineages are highlighted. Branches are numbered to identify them in Table S1 (Online Resource 2), where information on the defining mutations and comparison with other nomenclature systems are reported. Branch number 1 indicates the branch shared by A2 and A3b1, which is not visible as a separate branch in the MP reconstruction
Mentions: The major haplogroups found in our dataset are A2, A3b1, B2a, B2b, and E (including E1a1a, E1a1b, and E2); furthermore, individual sequences belonging to haplogroups G, I, O, T, and R1 were found. The phylogeny reconstructed with a maximum parsimony tree (Fig. 1) and verified by means of network analysis (Figures S4–S7 in Online Resource 1) corresponds to that of the ISOGG consortium (International Society of Genetic Genealogy 2014, Version: 10.101, Date: 8 December 2015), as summarized in van Oven et al. (2014); however, we identify additional branches that have not yet been reported. Table S1 in Online Resource 2 summarizes information about the major branches reported in Fig. 1, such as the different nomenclatures used and the mutations defining each branch. The haplogroup assignment for each individual is listed in Table S2 (Online Resource 2), while haplogroup frequencies and measures of diversity are shown in Table 1.Fig. 1

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.