Genetic and Demographic Implications of the Bantu Expansion: Insights from Human Paternal Lineages

Abstract

The expansion of Bantu languages, which started around 5,000 years before present in west/central Africa and spread all throughout sub-Saharan Africa, may represent one of the major and most rapid demographic movements in the history of the human species. Although the genetic footprints of this expansion have been unmasked through the analyses of the maternally inherited mitochondrial DNA lineages, information on the genetic impact of this massive movement and on the genetic composition of pre-Bantu populations is still scarce. Here, we analyze an extensive collection of Y-chromosome markers--41 single nucleotide polymorphisms and 18 short tandem repeats--in 883 individuals from 22 Bantu-speaking agriculturalist populations and 3 Pygmy hunter-gatherer populations from Gabon and Cameroon. Our data reveal a recent origin for most paternal lineages in west Central African populations most likely resulting from the expansion of Bantu-speaking farmers that erased the more ancient Y-chromosome diversity found in this area. However, some traces of ancient paternal lineages are observed in these populations, mainly among hunter-gatherers. These results are at odds with those obtained from mtDNA analyses, where high frequencies of ancient maternal lineages are observed, and substantial maternal gene flow from hunter-gatherers to Bantu farmers has been suggested. These differences are most likely explained by sociocultural factors such as patrilocality. We also find the intriguing presence of paternal lineages belonging to Eurasian haplogroup R1b1*, which might represent footprints of demographic expansions in central Africa not directly related to the Bantu expansion.

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

“…Biallelic markers are displayed in each branch. Haplogroups are named according to Karafet et al 17 Y haplogroup R in Central-West Africa M González et al (for example, reference 2,5,6,21 ) and therefore, a high frequency was not expected in our sample. This expectation was confirmed; only one of the chromosomes in our sample belongs to this haplogroup, more specifically to the haplogroup A3b2-M13, which is more frequently observed among Nilotes than other African groups.…”

“…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.…”

“…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.…”

“…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 ).…”

“…[2][3][4] Apart from the aforementioned haplogroups, some studies have reported unexpectedly high frequencies of haplogroup R1b1-P25 in some African populations. [5][6][7] This haplogroup is thought to have originated in Europe, and its high frequencies in Central-West African countries have been explained through a migration back to Africa in prehistoric times, mediated in Africa by speakers of the Chadic family of Afro-Asiatic languages. 6,7 The arrival of this ethnic group to Lake Chad from the Proto-Afro-Asiatic homeland in Eastern Africa has been explained by two different hypotheses.…”