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. 2015 Nov 6;10(11):e0141510.
doi: 10.1371/journal.pone.0141510. eCollection 2015.

The Paternal Landscape Along the Bight of Benin - Testing Regional Representativeness of West-African Population Samples Using Y-Chromosomal Markers

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Free PMC article

The Paternal Landscape Along the Bight of Benin - Testing Regional Representativeness of West-African Population Samples Using Y-Chromosomal Markers

Maarten H D Larmuseau et al. PLoS One. .
Free PMC article

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.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Geographic location of all population samples along the Bight of Benin and the rest of the West-African coast analysed in the study.
The nomenclature and the references of the population samples are available in S1 Table.
Fig 2
Fig 2. Principal component analysis (PCA), together with a biplot, of 14 West-African population samples, (a) inclusively and (b) exclusively the Ghanaian C1 population sample, based on the Y-SNP frequencies using the phylogeny given in S3 Fig.
The cumulative proportion of plot (a) is 0.92 for the first two principal components (PC1: 0.83; PC2: 0.09), and of plot (b) is 0.81 for the first two principal components (PC1: 0.45; PC2: 0.36). The nomenclature and the references of the population samples are available in S1 Table.
Fig 3
Fig 3. Principal component analysis (PCA) of ten West-African population samples and the HapMap YRI sample based on the Y-SNP frequencies using the phylogeny given in S2 Fig.
The cumulative proportion of the plot is 0.90 for the first two principal components (PC1: 0.63; PC2: 0.27). In this analysis the Ghanaian C1 population sample was excluded from the analysis. The nomenclature and the references of the population samples are available in S1 Table.

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