Large scale genotyping of the human Y chromosome provides new insights into the dispersal of early pastoralists in the African continent
Haplogroup E is the most common human Y chromosome clade within Africa and its internal branches have been linked to a wide range of human movements. To increase the level of resolution of haplogroup E, we disclosed the phylogenetic relationships among 729 mutations found in 33 haplogroup DE Y chromosomes sequenced at high coverage (50×) in previous studies and further dissected the E-M35 subclade by genotyping 62 informative markers in about 5000 samples from 118 worldwide populations. The phylogeny of haplogroup E showed novel features compared to the previous topology, including a new basal clade. Within haplogroup E-M35, we resolved basal polytomies and assigned all the E-M35* chromosomes to different new monophyletic clades. Through a Bayesian phylogeographic analysis, we associated each node of the tree to specific geographic areas. By this analysis, we identified a new E-M35 sub-Saharan clade, which originated about 11 kya in the northern part of the Horn of Africa. SNP-based dating, phylogenetic structuring and geographic distribution of this clade are consistent with a multistep dispersal of herders within eastern Africa and its subsequent diffusion to sub-equatorial areas. Our results provide new insights into the evolutionary hypotheses about the spread of pastoralism in Africa and increase the discriminative power of the E-M35 haplogroup for use in forensic genetics through the identification of new ancestry-informative markers.