Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages

Abstract

Although human Y chromosomes belonging to haplogroup R1b are quite rare in Africa, being found mainly in Asia and Europe, a group of chromosomes within the paragroup R-P25* are found concentrated in the central-western part of the African continent, where they can be detected at frequencies as high as 95%. Phylogenetic evidence and coalescence time estimates suggest that R-P25* chromosomes (or their phylogenetic ancestor) may have been carried to Africa by an Asia-to-Africa back migration in prehistoric times. Here, we describe six new mutations that define the relationships among the African R-P25* Y chromosomes and between these African chromosomes and earlier reported R-P25 Eurasian sub-lineages. The incorporation of these new mutations into a phylogeny of the R1b haplogroup led to the identification of a new clade (R1b1a or R-V88) encompassing all the African R-P25* and about half of the few European/west Asian R-P25* chromosomes. A worldwide phylogeographic analysis of the R1b haplogroup provided strong support to the Asia-to-Africa back-migration hypothesis. The analysis of the distribution of the R-V88 haplogroup in 41800 males from 69 African populations revealed a striking genetic contiguity between the Chadic-speaking peoples from the central Sahel and several other Afroasiatic-speaking groups from North Africa. The R-V88 coalescence time was estimated at 9200-5600 kya, in the early mid Holocene. We suggest that R-V88 is a paternal genetic record of the proposed mid-Holocene migration of proto-Chadic Afroasiatic speakers through the Central Sahara into the Lake Chad Basin, and geomorphological evidence is consistent with this view.

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

“…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. 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.…”

“…[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.…”

“…[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. Blench's theory (the 'inter-Saharan' hypothesis) 8 suggests that Chadic speakers arrived at the Chad Basin through an east to west migration through the Sahel, whereas Ehret's theory (the 'Trans-Saharan' hypothesis) 9 suggests that they arrived from the north through a migration across the Sahara desert.…”

“…The latter hypothesis has been used as the explanation for the high frequencies of the R1b1-P25 haplogroup in Central-West Africa, mainly due to its presence in speakers of other Afro-Asiatic languages in North Africa. 7,10 Nevertheless, there is still an on-going debate about the most suitable explanation for these observations. 10,11 To obtain a better and deeper understanding about this migration, a more detailed study of populations in all of the regions across the proposed paths is necessary.…”

“…The Y-SNP haplogroups in this country are still uncharacterised, although it borders Gabon and Cameroon, where the highest frequencies of the R1b1 haplogroup in Africa have been found. 7 The main objective of the present work is to better characterise the male lineages from Equatorial Guinea, particularly lineages of the Y chromosome haplogroup R1b1, to investigate the Chadic migration route hypothesis. The comparison of our results with previously published data will hopefully contribute not only to a better characterisation of the still understudied African genetic diversity but also to a better understanding of the unexpectedly high frequencies of the R1b1 haplogroup in this region of Africa.…”