Frequency of the major Y-chromosome haplogroups in North Africa and surrounding regions.

<p>Intensity of the colors reflects the frequency of a haplogroup in the studied populations. A) Location of the analyzed populations. B–F) Frequency distribution of haplogroups E-M81, E-M78, E-M123, J-M267, and J-M172 respectively.</p

Y-chromosome population structure.

<p>A) Principal component analysis of haplogroups frequencies. B) Multidimensional scaling plot based on R_ST distances between populations derived from Y-STR data.</p

Genome-wide population structure.

<p>A) Principal component analysis of ∼44,000 SNPs showing the top two components. B) Maximum likelihood tree showing populations relationships.</p

Genetic polymorphisms of 17 X-STR loci in two Tunisian populations from Sousse and Makthar

Tunisia has a complex demographic history of migrations from within Africa, Europe, and the Middle East. However, only one population study based on X-STR markers has been reported so far. To investigate the genetic polymorphisms of 17 X-STRs in two Tunisian populations from the cities of Sousse and Makthar, and to reveal the genetic relationships with other reference populations. A total of 194 unrelated healthy individuals were analysed for 17 X-STR markers. Our results indicate that DXS6809 is the most polymorphic locus, whereas DXS6807 is the least informative marker in the populations of Sousse and Makthar. In addition, forensic statistical parameters, such as the power of discrimination in males and females, as well as the mean of exclusion in duos and trios, reveal that the panel of 17 X-STRs is highly informative and useful in different forensic applications. Overall, pairwise genetic distances (Fst) and non-metric MDS plots demonstrate clustering of different populations according to their geographic locations and their historical relationships. Overall, the study of X-STR markers of the Tunisian populations can help to promote the establishment of a forensic DNA reference database in Tunisia and provide reference for future anthropological research.</p

The genetic landscape of Mediterranean North African populations through complete mtDNA sequences

<p><b>Background:</b> The genetic composition of human North African populations is an amalgam of different ancestral components coming from the Middle East, Europe, south-Saharan Africa and autochthonous to North Africa. This complex genetic pattern is the result of migrations and admixtures in the region since Palaeolithic times.</p> <p><b>Aims:</b> The objective of the present study is to refine knowledge of the population history of North African populations through the analysis of complete mitochondrial sequences.</p> <p><b>Subjects and methods:</b> This study has sequenced complete mitochondrial DNAs (mtDNAs) in several North African and neighbouring individuals.</p> <p><b>Results:</b> The mtDNA haplogroup classification and phylogeny shows a high genetic diversity in the region as a result of continuous admixture. The phylogenetic analysis allowed us to identify a new haplogroup characterised by positions 10 101 C and 146 C (H1v2), a sub-branch of H1v, which is restricted to North Africa and whose origins are estimated as ∼4000 years ago.</p> <p><b>Conclusions:</b> The analysis of the complete mtDNA genome has allowed for the identification of a North African sub-lineage that might be ignored by the analysis of partial mtDNA control region sequences, highlighting the phylogeographic relevance of mtDNA complete sequence analysis.</p

North_African_Ychromosome_dataset.vcf

This file is a VCF (variant call format) that contains information the genotypes of each sample for each position

Divergence time estimates among European, Maghrebi, and Near Eastern ancestral populations.

<p>We use population-based F_st to estimate divergence time between each of the North African populations and the Qatari (green dots) and Tuscans (purple dots), respectively. We assume point estimates of effective population sizes based on autosomal haplotype heterozygosity estimates from Li et al. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002397#pgen.1002397-Li1" target="_blank">[17]</a> (<i>Material and Methods</i>). We further estimate ancestral population clusters assigned at <i>k</i> = 5–8 with ADMIXTURE. Assuming that the ancestral clustering procedure has removed, or at least mitigated, the effect of recent migrations into Mediterranean populations, we then use F_st to estimate divergence times between these ancestral clusters. The range of <i>k</i>-based estimates for Maghrebi versus Near Eastern ancestry is indicated with light green polygon. The range of <i>k</i>-based estimates for Magrebi versus European ancestry is indicated with light purple polygon.</p

Genome admixture deconvolution karyogram of an Egyptian.

<p>A single Egyptian individual is presented for ancestry assuming <i>k</i> = 4 source populations: Saharawi [SAH], Nilotic-speaking Maasai [MKK], Spanish Basque [BAS] and Arabic Qatari [QAT]. Maasai segments (which were inferred from <i>k</i> = 3 and were highly diverged from the SAH, QAT, BAS segments) are layered on top of the inferred Maghrebi/Qatari/Basque ancestral karyogram, for <i>k</i> = 4 putative source populations.</p

Correlation between ancestry proportions inferred from ADMIXTURE and PCADMIX.

<p>We compare the proportions of ancestry inferred from assuming 3 ancestral populations in individuals from South Morocco A) using a clustering algorithm set to <i>k</i> = 8 (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002397#pgen-1002397-g001" target="_blank">Figure 1</a>) summing the sub-Saharan ancestry, both Qatar and European ancestry, and Maghrebi ancestry. We compared these estimates (left bar) to our PCA-based local ancestry assignment estimates (right bar). The three ancestral populations were Saharawi [SAH], Bantu-speaking Luhya [LWK], and Spanish Basque [BAS]. B) Genome admixture deconvolution on chromosome 1 of sixteen South Moroccans. Using a principal component-based method of admixture deconvolution, we assign local ancestry to South Moroccan individuals. We implement our PCA-based method for k = 3, and choose the ancestral populations based on the three ancestral populations were Saharawi [SAH], Bantu-speaking Luhya [LWK], and Spanish Basque [BAS]. Chromosome 1 for all sixteen South Moroccans is presented for both the maternal and paternal haplotypes.</p

Map of samples and population structure of North Africa and neighboring populations.

<p>A) On the map, star symbols indicate the location of new population samples and circles indicate previously published samples. The decreasing proportions of Maghrebi ancestry is indicated in a west-to-east gradient of blue across North Africa. An unsupervised clustering algorithm, <i>ADMIXTURE </i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002397#pgen.1002397-Alexander1" target="_blank">[25]</a> was used to analyze population structure among 13 African, 2 European and 1 Near Eastern populations based on approximately 300 K autosomal SNP loci in common. The two main gradients of ancestry in North Africa (at <i>k</i> = 8), Maghrebi and Near Eastern, are emphasized with arrows. Other population colors in open circles match the colors displayed in the population structure analysis. B) We plot the full dataset assuming <i>k</i> = 2,4,6,8 ancestral populations. <i>k</i> = 10 and log likelihoods are presented in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002397#pgen.1002397.s001" target="_blank">Figure S1</a>.</p