The genetic legacy of western Bantu migrations

Abstract

There is little knowledge on the demographic impact of the western wave of the Bantu expansion. Only some predictions could be made based mainly on indirect archaeological, linguistic, and genetic evidences. Apart from the very limited available data on the mitochondrial DNA (mtDNA) side, there are not, however, Y-chromosome studies revealing-if any-the male contribution of western Bantu-farmers. To elucidate the still poorly characterized western Bantu expansion, we analyzed Y-chromosome (25 biallelic polymorphisms and 15 microsatellite markers) and mtDNA (hypervariable control regions I and II and selected coding region RFLPs) variation in a population of 110 individuals from southwest Africa, and compared it with a database of 2,708 Y-chromosome profiles and of 2,565 mtDNAs from all other regions of Africa. This study reveals (1) a dramatic displacement of male and female Khoisan-speaking groups in the southwest, since both the maternal and the paternal genetic pools were composed exclusively by types carried by Bantu-speakers; (2) a clear bias in the admixture process towards the mating of male Europeans with female Sub-Saharan Africans; (3) the assimilation of east African lineages by the southwest (mainly mtDNA-L3f and Y-chromosome-B2a lineages); and (4) signatures of recent male and female gene flow from the southeast into the southwest. The data also indicate that the western stream of the Bantu expansion was a more gradual process than the eastern counterpart, which likely involved multiple short dispersals.

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

“…For the Y-SNP data, the haplogroup diversity of our sample (0.7526 ± 0.0261), although higher than that found in other West African populations, 18 is still lower than for other regions, a fact that has been explained by a loss of diversity during the Bantu migrations. 3,5,18 For the Y-STRs, high levels of haplotype diversity (0.9987±0.0014) and of the mean number of pairwise differences (9.5048 ± 4.3932) were found.…”

“…The SNP markers used in this study were selected based on the Y chromosome parsimony tree 17 to characterise the haplogroups most frequently found in sub-Saharan Africa as well as to identify those that are thought to have been brought by the Europeans to Africa during the last five centuries. 3,5,[18][19][20][21][22] Moreover, eight additional SNPs inside haplogroup R1b were also included in our set to increase the resolution of this haplogroup. 7 A hierarchical approach (Supplementary Figure S1) based on the phylogeny reported by Karafet et al 17 and M213 carried the derived allele, Multiplex 2 (described by Brió n et al 23 ) was performed under the same conditions used for the other three multiplexes; (ii) in chromosomes carrying the derived allele at marker P25, M269 was typed using the RFLP technique.…”

“…7 A hierarchical approach (Supplementary Figure S1) based on the phylogeny reported by Karafet et al 17 and M213 carried the derived allele, Multiplex 2 (described by Brió n et al 23 ) was performed under the same conditions used for the other three multiplexes; (ii) in chromosomes carrying the derived allele at marker P25, M269 was typed using the RFLP technique. The amplification PCR for this marker was conducted using the primers described by Beleza et al, 18 and the conditions were optimised from Gomes et al 3 for the multiplexes used. Touchdown PCR was performed with a first set of 5 cycles with a higher annealing temperature of 65 1C for 90 s and a second set of 30 cycles in which the temperature was decreased to 62 1C, also for 90 s. After confirming the amplification in a polyacrylamide gel using the silver staining method, 2 ml of the amplified product were incubated overnight at 371C with 0.05 ml of the restriction enzyme MvaI at a concentration of 10 U/ml, 0.5 ml of 10Â buffer R þ and 2.45 ml of water.…”

“…3 Similarly, only one chromosome in our sample was found to belong to haplogroup B, namely to the branch that is most common in Bantu individuals (defined by the derived allele at M150). 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 ).…”

Mitochondrial DNA control region data from indigenous Angolan Khoe-San lineages

“…The data set comprises 21 haplotypes occurring more than once and 17 unique haplotypes. Upon publication, haplotypes were incorporated in the EMPOP database (www.empop.org; Only few Angolan mtDNA sequences were available in the literature, which were typed for the first and second hypervariable segment of the control region [11][12][13]. The blood samples for this study came from 129 healthy randomly drawn volunteer donors of to our knowledge unrelated individuals collected in the Schmidtsdrift community.…”