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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.


Related in: MedlinePlus

Diversity and distribution of haplogroup B2a. a Network of B2a sequences color coded by linguistic affiliation (Khoisan vs. Bantu speaking individuals). The dashed line indicates the position of branch 21 from Fig. 1, which leads to the root of B2a. b Schematic distribution of haplogroup B2a in Africa: the more intense the color, the higher the frequency in the population. Small crosses mark the locations of the 146 African populations included in the analysis (see Supplemental Table S3)
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Fig2: Diversity and distribution of haplogroup B2a. a Network of B2a sequences color coded by linguistic affiliation (Khoisan vs. Bantu speaking individuals). The dashed line indicates the position of branch 21 from Fig. 1, which leads to the root of B2a. b Schematic distribution of haplogroup B2a in Africa: the more intense the color, the higher the frequency in the population. Small crosses mark the locations of the 146 African populations included in the analysis (see Supplemental Table S3)

Mentions: Whereas most African haplogroups differ significantly in frequency between the Khoisan- and Bantu-speaking groups in our study, thereby showing a signature of having a Khoisan vs. Bantu origin in southern Africa, haplogroup B2a does not (Table 1). Moreover, haplogroup B2a is characterized by long branches radiating from a core haplotype found in both Khoisan and Bantu speakers (Fig. 2a). As shown by the map in Fig. 2b, which visualizes frequency data from these and other African populations (Table S3 in Online Resource 2), this haplogroup is widespread over the continent, with the highest frequencies found in populations from Botswana and Cameroon. From these data, it is not clear if haplogroup B2a is an autochthonous Khoisan haplogroup, or a haplogroup brought to southern Africa by Bantu speakers, or both. To further investigate this haplogroup, we generated STR haplotypes based on 16 loci and compared these to published data; the network generated from these STR haplotypes (Table S4 in Online Resource 2; Figure S8 in Online Resource 1) shows haplotypes of southern African Khoisan and Bantu speakers located toward the core, and two separate clusters of haplotypes from central Africa and elsewhere at the periphery. Hence, the STR data also do not provide a clear signal of the origin of this haplogroup.Fig. 2


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)

Diversity and distribution of haplogroup B2a. a Network of B2a sequences color coded by linguistic affiliation (Khoisan vs. Bantu speaking individuals). The dashed line indicates the position of branch 21 from Fig. 1, which leads to the root of B2a. b Schematic distribution of haplogroup B2a in Africa: the more intense the color, the higher the frequency in the population. Small crosses mark the locations of the 146 African populations included in the analysis (see Supplemental Table S3)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Diversity and distribution of haplogroup B2a. a Network of B2a sequences color coded by linguistic affiliation (Khoisan vs. Bantu speaking individuals). The dashed line indicates the position of branch 21 from Fig. 1, which leads to the root of B2a. b Schematic distribution of haplogroup B2a in Africa: the more intense the color, the higher the frequency in the population. Small crosses mark the locations of the 146 African populations included in the analysis (see Supplemental Table S3)
Mentions: Whereas most African haplogroups differ significantly in frequency between the Khoisan- and Bantu-speaking groups in our study, thereby showing a signature of having a Khoisan vs. Bantu origin in southern Africa, haplogroup B2a does not (Table 1). Moreover, haplogroup B2a is characterized by long branches radiating from a core haplotype found in both Khoisan and Bantu speakers (Fig. 2a). As shown by the map in Fig. 2b, which visualizes frequency data from these and other African populations (Table S3 in Online Resource 2), this haplogroup is widespread over the continent, with the highest frequencies found in populations from Botswana and Cameroon. From these data, it is not clear if haplogroup B2a is an autochthonous Khoisan haplogroup, or a haplogroup brought to southern Africa by Bantu speakers, or both. To further investigate this haplogroup, we generated STR haplotypes based on 16 loci and compared these to published data; the network generated from these STR haplotypes (Table S4 in Online Resource 2; Figure S8 in Online Resource 1) shows haplotypes of southern African Khoisan and Bantu speakers located toward the core, and two separate clusters of haplotypes from central Africa and elsewhere at the periphery. Hence, the STR data also do not provide a clear signal of the origin of this haplogroup.Fig. 2

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.


Related in: MedlinePlus