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International audience; Burkina Faso is located in the heart of West Africa and is a representative of the local structured patterns of human variability. Here, different cultures and languages are found in a geographic contiguity, as a result of several waves of migration and the succession of long- and short-term empires. However, historical documentation for this area is only partial, focusing predominantly on the recent empires, and linguistic surveys lack the power to fully elucidate the social context of the contact-induced changes. In this paper, we report Y-chromosomal data and complete mtDNA genome sequences for ten populations from Burkina Faso whose languages belong to two very distantly related branches of the Niger-Congo phylum, the Gur and Mande language families. In addition, two further populations, the Mande-speaking Mandenka from Senegal and the Yoruba from Nigeria, were included for regional comparison. We focus on the different historical trajectories undergone by the maternal and paternal lineages. Our results reveal a striking structure in the paternal line, which matches the linguistic affiliation of the ethnolinguistic groups, in contrast to the near-complete homogeneity of the populations in the maternal line. However, while the ancient structure along the linguistic lines is apparent in the Y-chromosomal haplogroup affiliation, this has clearly been overlain by more recent migrations, as shown by significant correlations between the genetic distances based on Y chromosome short tandem repeats and geographic distances between the populations, as well as by the patterns of shared haplotypes. Using the complete mtDNA sequences, we are able to reconstruct population size variation in the past, showing a strong sign of expansion in the concomitance with the Holocene Climate Optimum approximately 12,000-10,000 years ago, which has been suggested as the cause of the spread of the Niger-Congo phylum in the area. However, subsequent climatic fluctuations do not appear to have had an impact on the demography of the inhabitants of West Africa, probably reflecting the adaptive advantages of cultural innovations, such as pastoralism and agriculture.

International audience; 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.