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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.


Values of TMRCA for the A2-T node from the present study. The dates are obtained by direct count and by BEAST analysis, for four different mutation rates (indicated with different colors); both median and mean estimates are indicated. The dates are compared with estimates from other studies (indicated by the name of the first author), which variously dated the same A2-T node (not explicitly labeled in the figure) or the A00-T or A0-T nodes (identified above the bars) (color figure online)
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Fig3: Values of TMRCA for the A2-T node from the present study. The dates are obtained by direct count and by BEAST analysis, for four different mutation rates (indicated with different colors); both median and mean estimates are indicated. The dates are compared with estimates from other studies (indicated by the name of the first author), which variously dated the same A2-T node (not explicitly labeled in the figure) or the A00-T or A0-T nodes (identified above the bars) (color figure online)

Mentions: Estimates of the time to the most recent common ancestor (TMRCA) were obtained with two different methods: count of mutations (corresponding to the rho statistic) and BEAST analysis. The TMRCA for the deepest node found in our dataset (A2-T) is 218 kyrs based on counting mutations and 248 kyrs based on BEAST analyses (Fig. 3). As shown by the comparison with TMRCA estimates for various nodes obtained by other studies (Fig. 3), our estimates are always older than those published previously.Fig. 3


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)

Values of TMRCA for the A2-T node from the present study. The dates are obtained by direct count and by BEAST analysis, for four different mutation rates (indicated with different colors); both median and mean estimates are indicated. The dates are compared with estimates from other studies (indicated by the name of the first author), which variously dated the same A2-T node (not explicitly labeled in the figure) or the A00-T or A0-T nodes (identified above the bars) (color figure online)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig3: Values of TMRCA for the A2-T node from the present study. The dates are obtained by direct count and by BEAST analysis, for four different mutation rates (indicated with different colors); both median and mean estimates are indicated. The dates are compared with estimates from other studies (indicated by the name of the first author), which variously dated the same A2-T node (not explicitly labeled in the figure) or the A00-T or A0-T nodes (identified above the bars) (color figure online)
Mentions: Estimates of the time to the most recent common ancestor (TMRCA) were obtained with two different methods: count of mutations (corresponding to the rho statistic) and BEAST analysis. The TMRCA for the deepest node found in our dataset (A2-T) is 218 kyrs based on counting mutations and 248 kyrs based on BEAST analyses (Fig. 3). As shown by the comparison with TMRCA estimates for various nodes obtained by other studies (Fig. 3), our estimates are always older than those published previously.Fig. 3

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.