A Back Migration from Asia to Sub-Saharan Africa Is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes

Abstract

The variation of 77 biallelic sites located in the nonrecombining portion of the Y chromosome was examined in 608 male subjects from 22 African populations. This survey revealed a total of 37 binary haplotypes, which were combined with microsatellite polymorphism data to evaluate internal diversities and to estimate coalescence ages of the binary haplotypes. The majority of binary haplotypes showed a nonuniform distribution across the continent. Analysis of molecular variance detected a high level of interpopulation diversity (PhiST=0.342), which appears to be partially related to the geography (PhiCT=0.230). In sub-Saharan Africa, the recent spread of a set of haplotypes partially erased pre-existing diversity, but a high level of population (PhiST=0.332) and geographic (PhiCT=0.179) structuring persists. Correspondence analysis shows that three main clusters of populations can be identified: northern, eastern, and sub-Saharan Africans. Among the latter, the Khoisan, the Pygmies, and the northern Cameroonians are clearly distinct from a tight cluster formed by the Niger-Congo-speaking populations from western, central western, and southern Africa. Phylogeographic analyses suggest that a large component of the present Khoisan gene pool is eastern African in origin and that Asia was the source of a back migration to sub-Saharan Africa. Haplogroup IX Y chromosomes appear to have been involved in such a migration, the traces of which can now be observed mostly in northern Cameroon.

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.…”

“…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.…”

“…[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.…”