Abstract
Patterns of genetic variation in human populations across the African continent are still not well studied in comparison with Eurasia and America, despite the high genetic and cultural diversity among African populations. In population and forensic genetic studies a single sample is often used to represent a complete African region. In such a scenario, inappropriate sampling strategies and/or the use of local, isolated populations may bias interpretations and pose questions of representativeness at a macrogeographic-scale. The non-recombining region of the Y-chromosome (NRY) has great potential to reveal the regional representation of a sample due to its powerful phylogeographic information content. An area poorly characterized for Y-chromosomal data is the West-African region along the Bight of Benin, despite its important history in the trans-Atlantic slave trade and its large number of ethnic groups, languages and lifestyles. In this study, Y-chromosomal haplotypes from four Beninese populations were determined and a global meta-analysis with available Y-SNP and Y-STR data from populations along the Bight of Benin and surrounding areas was performed. A thorough methodology was developed allowing comparison of population samples using Y-chromosomal lineage data based on different Y-SNP panels and phylogenies. Geographic proximity turned out to be the best predictor of genetic affinity between populations along the Bight of Benin. Nevertheless, based on Y-chromosomal data from the literature two population samples differed strongly from others from the same or neighbouring areas and are not regionally representative within large-scale studies. Furthermore, the analysis of the HapMap sample YRI of a Yoruban population from South-western Nigeria based on Y-SNPs and Y-STR data showed for the first time its regional representativeness, a result which is important for standard population and forensic genetic applications using the YRI sample. Therefore, the uniquely and powerful geographical information carried by the Y-chromosome makes it an important locus to test the representativeness of a certain sample even in the genomic era, especially in poorly investigated areas like Africa.
Highlights
Human populations in the African continent exhibit a high linguistic, cultural, genetic and phenotypic diversity
The correspondence analyses (CA)-plot and the Principal component analyses (PCAs)-plot showed that D3 was the most differentiated population sample whereas Dendi (D4) and Fon (D5) were the samples most similar to each other (S7 Fig)
Based on the five additional phylogenies defined (S2–S5 Figs), the Y-SNP data of the Beninese samples were compared with published data for other West African populations
Summary
Human populations in the African continent exhibit a high linguistic, cultural, genetic and phenotypic diversity. The genetic diversity in African populations is higher than in non-African populations due to the recent African origin of modern humans, yet it is still poorly studied in comparison with populations of Eurasia and the Americas [3] Such a multifaceted and fragmented pattern of variation, often amplified by the presence of clans or other substructures within a local population, can lead to issues of representativeness of a single sample included for a specific African region in macro-geographic population genetic and forensic studies. The recent discovery of the lineage A00 within a Bantu-population in North Cameroon, which introduced an extremely ancient root to the Ychromosomal phylogenetic tree, testifies to the still limited knowledge of Y-chromosomal variation in Africa [20]
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