Whole Y-chromosome sequences reveal an extremely recent origin of the most common North African paternal lineage E-M183 (M81)

Abstract

E-M183 (E-M81) is the most frequent paternal lineage in North Africa and thus it must be considered to explore past historical and demographical processes. Here, by using whole Y chromosome sequences from 32 North African individuals, we have identified five new branches within E-M183. The validation of these variants in more than 200 North African samples, from which we also have information of 13 Y-STRs, has revealed a strong resemblance among E-M183 Y-STR haplotypes that pointed to a rapid expansion of this haplogroup. Moreover, for the first time, by using both SNP and STR data, we have provided updated estimates of the times-to-the-most-recent-common-ancestor (TMRCA) for E-M183, which evidenced an extremely recent origin of this haplogroup (2,000-3,000 ya). Our results also showed a lack of population structure within the E-M183 branch, which could be explained by the recent and rapid expansion of this haplogroup. In spite of a reduction in STR heterozygosity towards the West, which would point to an origin in the Near East, ancient DNA evidence together with our TMRCA estimates point to a local origin of E-M183 in NW Africa.

Figure 1

Maximum parsimony tree. Phylogenetic relations among (a) all samples included in the project (in blue the E-M183 branch) and (b) individuals within E-M183 branch are shown, coloured by its North African origin. Branch lengths are proportional to the number of SNPs on the branch.

Figure 2

Distribution of E-M183 subclades among North Africa, the Near East and the Iberian Peninsula. Pie chart sectors areas are proportional to haplogroup frequency and are coloured according to haplogroup in the schematic tree to the right. n: sample size. Map was generated using R software.

Figure 3

Median-joining network based on 13 Y-STRs: DYS19, DYS389I, DYS390, DYS391, DYS393, DYS438, DYS439, DYS437, DYS448, DYS456, DYS458, Y GATA H4, and DYS635. Each circle represents a haplotype with its size proportional to frequency and has been coloured according to (a) populations and (b) haplogroups (see key). The lines between them indicate the Y-STR mutational steps.

Figure 4

Principal component analysis based on Y-STRs. Coloured by (a) population and (b) by haplogroup (see key). Squares represent mean values of each component in the PCA coloured by (a) population and (b) haplogroup.

Figure 5

Bayesian skyline plots. Two different mutation rates have been used: (a) a ‘slow’ rate of 6.17 × 10⁻¹⁰ substitutions/site/year and (b) a ‘fast’ rate of 10⁻⁹ substitutions/site/ year. Black lines indicate the median effective population size (Ne) and discontinuous grey lines the 95% higher posterior density intervals. Vertical grey line indicate the TMRCA estimated using each substitution rate.