Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes

Abstract

To investigate associations between genetic, linguistic, and geographic variation in Africa, we type 50 Y chromosome SNPs in 1122 individuals from 40 populations representing African geographic and linguistic diversity. We compare these patterns of variation with those that emerge from a similar analysis of published mtDNA HVS1 sequences from 1918 individuals from 39 African populations. For the Y chromosome, Mantel tests reveal a strong partial correlation between genetic and linguistic distances (r ¼ 0.33, P ¼ 0.001) and no correlation between genetic and geographic distances (r ¼ À0.08, P40.10). In contrast, mtDNA variation is weakly correlated with both language (r ¼ 0.16, P ¼ 0.046) and geography (r ¼ 0.17, P ¼ 0.035). AMOVA indicates that the amount of paternal among-group variation is much higher when populations are grouped by linguistics (U CT ¼ 0.21) than by geography (U CT ¼ 0.06). Levels of maternal genetic among-group variation are low for both linguistics and geography (U CT ¼ 0.03 and 0.04, respectively). When Bantu speakers are removed from these analyses, the correlation with linguistic variation disappears for the Y chromosome and strengthens for mtDNA. These data suggest that patterns of differentiation and gene flow in Africa have differed for men and women in the recent evolutionary past. We infer that sex-biased rates of admixture and/or language borrowing between expanding Bantu farmers and local hunter-gatherers played an important role in influencing patterns of genetic variation during the spread of African agriculture in the last 4000 years.

The genetic landscape of Equatorial Guinea and the origin and migration routes of the Y chromosome haplogroup R-V88

“…2,5,18,21 The major haplogroup E, the most diverse clade in the Y chromosome tree, is widespread across the African continent, where its highest frequencies are found and is also present in the Middle East, southern Europe, and Central and South Asia. 17 This clade was the most frequent in our sample, representing almost 80% of all the chromosomes, similar to results for other sub-Saharan populations (for example, reference 5,30 ). The most frequent sub-lineage found in our sample inside this clade was the haplogroup E1b1a-M2, proposed as a marker of Bantu expansion.…”

“…The most frequent sub-lineage found in our sample inside this clade was the haplogroup E1b1a-M2, proposed as a marker of Bantu expansion. 22,30 Nevertheless, some other typically non-Bantu lineages were also found in our sample. One is the E1a-M33 haplogroup, which is usually not found further South in the Bantu expansion route (for example, Angola 18 ) but is detected at higher frequencies above the starting point of these migrations (for example, Guinea-Bissau 31 ).…”

“…Nevertheless, high frequencies of these lineages in some African populations have been previously reported by several authors. [5][6][7]29,30 Lineages in clade A, although almost entirely restricted to Africa, have been described in Bantu populations at low frequencies. These lineages are mostly present in Nilo-Saharan speakers Figure 1 Phylogenetic tree of the Y chromosome haplogroups studied.…”

“…[5][6][7]29,30 This haplogroup is thought to have originated in Central Asia approximately 40 000 years BP and then migrated westward into Europe, achieving its highest frequencies in the western region of this continent. 39,40 Although Balaresque et al 41 proposed the hypothesis of a European spread of haplogroup R1b1b2-M269 during the Neolithic, the distribution of the M269 sub-haplogroups and their Y-STR diversities proved to be compatible with a pre-Neolithic diffusion of M269 in Europe.…”

Population differences in the postcrania of modern South Africans and the implications for ancestry estimation

“…Because of socio-political regimes and the colonization history of South Africa, the black and coloured groups would be expected to have more similarities to one another than either group would have to white South Africans. For instance, numerous examples of intermarriage between the historic Khoesan and Bantu-speaking groups are noted within the literature [19,65].…”