Genetic structure and sex‐biased gene flow in the history of southern African populations

Abstract

Objectives: We investigated the genetic history of southern African populations with a special focus on their paternal history. We reexamined previous claims that the Y-chromosome haplogroup E1b1b (E-M293) was brought to southern Africa by pastoralists from eastern Africa, and investigated patterns of sex-biased gene flow in southern Africa. Materials and methods:We analyzed previously published complete mtDNA genome sequences and 900 kb of NRY sequences from 23 populations from Namibia, Botswana, and Zambia, as well as haplogroup frequencies from a large sample of southern African populations and 23 newly genotyped Y-linked STR loci for samples assigned to haplogroup E1b1b. Results:Our results support an eastern African origin for Y-chromosome haplogroup E1b1b (E-M293); however, its current distribution in southern Africa is not strongly associated with pastoralism, suggesting more complex demographic events and/or changes in subsistence practices in this region. The Bantu expansion in southern Africa had a notable genetic impact and was probably a rapid, male-dominated expansion. Our finding of a significant increase in the intensity of the sex-biased gene flow from north to south may reflect changes in the social dynamics between Khoisan and Bantu groups over time.Conclusions: Our study shows that the population history of southern Africa has been complex, with different immigrating groups mixing to different degrees with the autochthonous populations. The Bantu expansion led to heavily sex-biased admixture as a result of interactions between Khoisan females and Bantu males, with a geographic gradient which may reflect changes in the social dynamics between Khoisan and Bantu groups over time.

The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola

“…2 of ref. [9]), similar to the reported male-biased patterns of gene flow from Bantu to "Khoisan"-speaking groups [34], and from non-Pygmies to Pygmies in Central Africa [38]. A comparable trend involving the introgression of MSY eastern African lineages was also found in the !Xun, who exhibit high frequencies of haplogroup E-M293 (25%) while retaining the mtDNA profile characteristic of southern African "Khoisan" populations [9].…”

“…In Bantu speakers, MSY vs. mtDNA diversity ratios accounting for differences in mutation rates of the two chromosomes (π MSY /π mtDNA ) range from 0.09 to 0.5 (Table S1), indicating that Bantu peoples, like many other human populations, display less MSY diversity relative to mtDNA than expected in neutral demographic models without sex-biased processes [4,6,27,34]. In contrast, the !Xun resemble other "Khoisan" groups in displaying comparable levels of diversity in both sexes (π MSY /π mtDNA = 1.11) [6,27].…”

Contrasting Paternal and Maternal Genetic Histories of Thai and Lao Populations

“…Analyzing partial sequences of the MSY and complete mtDNA genome sequences provides more insight into genetic history, especially sex-biased practices that can influence genetic variation, as well as the role of geography and language (Arias et al. 2018; Bajic et al. 2018; Kutanan, Kampuansai, Changmai, et al.…”

Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences

“…This E-M35 subclade was previously linked to the movement of pastoralist groups from eastern Africa to southern Africa ∼2,000 years ago ( Henn et al. 2008 ; Bajic et al. 2018 ).…”

“…2014 ; Skoglund et al. 2017 ; Bajic et al. 2018 ; Schlebusch and Jakobsson 2018 ) indicate that B2b1a2b2∼ in the Khoe-San may have come from eastern Africa.…”