Y-Chromosomal Variation in Sub-Saharan Africa: Insights Into the History of Niger-Congo Groups

Abstract

Technological and cultural innovations as well as climate changes are thought to have influenced the diffusion of major language phyla in sub-Saharan Africa. The most widespread and the richest in diversity is the Niger-Congo phylum, thought to have originated in West Africa ∼ 10,000 years ago (ya). The expansion of Bantu languages (a family within the Niger-Congo phylum) ∼ 5,000 ya represents a major event in the past demography of the continent. Many previous studies on Y chromosomal variation in Africa associated the Bantu expansion with haplogroup E1b1a (and sometimes its sublineage E1b1a7). However, the distribution of these two lineages extends far beyond the area occupied nowadays by Bantu-speaking people, raising questions on the actual genetic structure behind this expansion. To address these issues, we directly genotyped 31 biallelic markers and 12 microsatellites on the Y chromosome in 1,195 individuals of African ancestry focusing on areas that were previously poorly characterized (Botswana, Burkina Faso, Democratic Republic of Congo, and Zambia). With the inclusion of published data, we analyzed 2,736 individuals from 26 groups representing all linguistic phyla and covering a large portion of sub-Saharan Africa. Within the Niger-Congo phylum, we ascertain for the first time differences in haplogroup composition between Bantu and non-Bantu groups via two markers (U174 and U175) on the background of haplogroup E1b1a (and E1b1a7), which were directly genotyped in our samples and for which genotypes were inferred from published data using linear discriminant analysis on short tandem repeat (STR) haplotypes. No reduction in STR diversity levels was found across the Bantu groups, suggesting the absence of serial founder effects. In addition, the homogeneity of haplogroup composition and pattern of haplotype sharing between Western and Eastern Bantu groups suggests that their expansion throughout sub-Saharan Africa reflects a rapid spread followed by backward and forward migrations. Overall, we found that linguistic affiliations played a notable role in shaping sub-Saharan African Y chromosomal diversity, although the impact of geography is clearly discernible.

Bringing together linguistic and genetic evidence to test the Bantu expansion

“…However, this scenario of a slow and gradual process of diversification over short distances does not fit well with the evidence for a demic migration apparent in the reduction of diversity values for the genetic markers, nor with the low genetic distance values among geographically distant Bantu groups. An alternative explanation could be that the signal of the initial migration(s) might have been attenuated by later contact among peoples and languages, as suggested by previous genetic studies of mtDNA [35,36], Y-chromosomal [18] and autosomal [32] markers. This hypothesis finds some support in our data, since the linguistic distances between Eastern and Western languages belonging to adjacent Guthrie's zones (such as K versus M) are significantly smaller compared with those of non-adjacent zones (such as H-R versus G-P, K versus G-P and H-R versus M; all MWUs with one tail p , 10 214 ; data not shown).…”

“…Genetic studies have highlighted the strong demographic impact of the Bantu migration on the gene pool of Sub-Saharan African populations for mtDNA [15,16], the Y chromosome [17,18] and autosomes [19,20]. However, a recent study by Sikora et al [21] of approximately 2800 autosomal single nucleotide polymorphisms suggested that the spread of Bantu languages to southeastern Africa (i.e.…”

Composition of the Kirsten Skeletal Collection at Stellenbosch University

“…The Western Cape Province of South Africa has a rich genetic history, arising from many parts of the world including the local ancient Khoisan population [8][9][10][11] , the greater Bantu groups from the Niger-Congo phylum 12,[14][15][16] , European settlers 17,18 and slaves from the East 18,19 . Marriages amongst the different population groups were once common 17,20 , and produced a heterogeneous new and genetically unique population in the Western Cape, until apartheid was introduced and resulted in a drastic decrease in cross-population gene flow 6,20,25 .…”

“…12,13 Variants from this Bantu family in the south included the Nguni group (Xhosa, Zulu, Swati and Ndebele tribes) and the Southern (also called the Sotho-Tswana) groups (Southern Sotho, Northern Sotho, Tswana, Venda and Tsonga tribes). 12,14,15 The Nguni populations migrated southwards over many centuries with large herds of Nguni cattle. These migration patterns started around 2000 years ago followed by larger migration impressions around 1400 CE.…”

“…These migration patterns started around 2000 years ago followed by larger migration impressions around 1400 CE. 14,16 When entering southern Africa, settlement patterns among the different tribes formed as a result of the settling of some groups along the way, while others kept moving; for example the Ndebele stayed in the north, the Swazi in the northeast, the Zulu towards the east and the Xhosa in the south. 12 Historical documents indicate that Portuguese sailors in the 1400s were the first Europeans to have contact with these tribes.…”