Additional file 6: Figure S3. of Variation in NAT2 acetylation phenotypes is associated with differences in food-producing subsistence modes and ecoregions in Africa

Plot of the number of alleles (distinct NAT2 sequence haplotypes) observed in samples as a function of sample size. The dashed line shows the linear regression of number of haplotypes on sample size, and Pearson’s product–moment correlation coefficient is shown in the bottom-right caption. (PDF 2 kb

<i>Alu</i> insertion polymorphisms in the African Sahel and the origin of Fulani pastoralists

<p><b>Background:</b> The origin of Western African pastoralism, represented today by the Fulani nomads, has been a highly debated issue for the past decades, and has not yet been conclusively resolved.</p> <p><b>Aim:</b> This study focused on <i>Alu</i> polymorphisms in sedentary and nomadic populations across the African Sahel to investigate patterns of diversity that can complement the existing results and contribute to resolving issues concerning the origin of West African pastoralism.</p> <p><b>Subjects and methods:</b> A new dataset of 21 <i>Alu</i> biallelic markers covering a substantial part of the African Sahel has been analysed jointly with several published North African populations.</p> <p><b>Results:</b> Interestingly, with regard to <i>Alu</i> variation, the relationship of Fulani pastoralists to North Africans is not as evident as was earlier revealed by studies of uniparental loci such as mtDNA and NRY. <i>Alu</i> insertions point rather to an affinity of Fulani pastoralists to Eastern Africans also leading a pastoral lifestyle.</p> <p><b>Conclusions:</b> It is suggested that contemporary Fulani pastoralists might be descendants of an ancestral Eastern African population that, while crossing the Sahara in the Holocene, admixed slightly with a population of Eurasian (as evidenced by uniparental polymorphisms) ancestry. It seems that, in the Fulani pastoralists, <i>Alu</i> elements reflect more ancient genetic relationships than do uniparental genetic systems.</p

Additional file 11: Figure S8. of Variation in NAT2 acetylation phenotypes is associated with differences in food-producing subsistence modes and ecoregions in Africa

MDS plot of pairwise Reynolds genetic distances between the 29 populations of the FP dataset. The Stress value is 0.045. The same plot is reproduced 4 times, with populations color-coded according to: (a) geographical region, (b) linguistic affiliation, (c) subsistence mode, and (d) biome (see text). (PDF 11 kb

Additional file 3: Figure S2. of Variation in NAT2 acetylation phenotypes is associated with differences in food-producing subsistence modes and ecoregions in Africa

Schematic diagram of the NAT2 870 bp-long single protein-coding Exon (Exon 2) on 8p22. The first (+1) and last positions (+873) of the ORF are indicated on top of it. The positions of the 30 polymorphic sites (SNPs) observed among the 1192 individuals from the 39 African samples analyzed in this study are shown as heavy-black (non-synonymous mutations) or light-gray (synonymous mutations) vertical bars below the diagram. Segments link the SNPs positions to the list of 61 haplotypes inferred from the combination of the 30 SNPs. Haplotypes’ associated acetylation activity (taken from the official NAT2 gene nomenclature, http://nat.mbg.duth.gr/ ) and average frequency among the 39 population samples are shown on the left and right sides of the list, respectively. (PDF 21 kb

Additional file 4: Table S1. of Variation in NAT2 acetylation phenotypes is associated with differences in food-producing subsistence modes and ecoregions in Africa

NAT2 coding-exon SNPs and haplotypes observed in all sequenced African population samples. (XLSX 32 kb

Additional file 1: Figure S1. of Variation in NAT2 acetylation phenotypes is associated with differences in food-producing subsistence modes and ecoregions in Africa

Map showing the location of African populations screened for sequence variation in NAT2, including the six Sahelian populations of this study. The ASW sample of African Americans from the 1000 Genomes Project is not located on this map. Map created with the QGis open source software [98]. (PDF 2240 kb

Matrices of <i>F</i>_<i>ST</i> distances.

<p>Matrices of <i>F</i>_<i>ST</i> values between ADMIXTURE components (A) and Arabian and Near Eastern populations (B).</p

Founder analysis results on JT lineages.

<p>Probabilistic distribution of founder clusters across migration times, with time scanned at 200 year intervals from 0–60 ka, using <i>f1</i> (blue line) and <i>f2</i> criteria (red line), when considering putative migrations from the Near East, Iran and Pakistan to Arabia for (A) whole-mtDNA genomes or (C) HVS-I for haplogroups J and T; and probabilistic proportion of founder clusters considering different migration events, using <i>f1</i> (blue bar) and <i>f2</i> criteria (red bar), when considering putative migrations from the Near East, Iran and Pakistan to Arabia for (B) whole-mtDNA genomes or (D) HVS-I for haplogroups J and T.</p

Founder analysis results.

<p>Probabilistic distribution of founder clusters across migration times, with time scanned at 200 year intervals from 0–60 ka, using <i>f1</i> (blue line) and <i>f2</i> criteria (red line), when considering putative migrations: (A) from the Near East, Iran and Pakistan to Arabia; (C) from Africa into Arabia plus the Near East and Iran; (E) Arabia plus the Near East and Iran into eastern Africa; (G) Arabia plus the Near East and Iran into North Africa; and probabilistic proportion of founder clusters considering different migration events, using <i>f1</i> (blue bar) and <i>f2</i> criteria (red bar), when considering putative migrations: (B) from the Near East, Iran and Pakistan to Arabia; (D) from African into Arabia plus the Near East and Iran; (F) Arabia plus the Near East and Iran into eastern Africa; (H) Arabia plus the Near East and Iran into North Africa.</p

ADMIXTURE results.

<p>Population structure inferred by ADMIXTURE analysis. Each individual is represented by a vertical (100%) stacked column of genetic components proportions shown in colour for K = 6.</p