Phylogeographic Refinement and Large Scale Genotyping of Human Y Chromosome Haplogroup E Provide New Insights into the Dispersal of Early Pastoralists in the African Continent.
Bottom Line: 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 in previous studies.The phylogeny of haplogroup E showed novel features compared with the previous topology, including a new basal dichotomy.In addition, our results increase the discriminative power of the E-M35 haplogroup for use in forensic genetics through the identification of new ancestry-informative markers.
Affiliation: Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy.Show MeSH
Mentions: The incorporation of the information obtained from this analysis into the previously reported E-M35 tree (Karafet et al. 2008; Trombetta et al. 2011) produced an extensively revised phylogeny for this clade, resulting in the detection of several new lineages (fig. 2). The E-M35 polytomy reported by Trombetta et al. (2011), not fully resolved in successive studies due to the lack of informative lineages (Francalacci et al. 2013; Poznik et al. 2013; Wei et al. 2013; Lippold et al. 2014; Scozzari et al. 2014; Van Geystelen et al. 2014; van Oven et al. 2014; Hallast et al. 2015), is here completely resolved (fig. 2 and supplementary fig. S2, Supplementary Material online). Haplogroup E-M35 is bifurcated in two sister branches which are defined by Z827 and V68, respectively. Within E-Z827 we identified a new clade (E-V1515), which includes all the sub-Saharan haplogroups (E-V42, E-M293, E-V92, and E-V6) reported as E-M35 basal clades in the phylogeny by Trombetta et al. (2011) (supplementary fig. S2A, Supplementary Material online), as well as six new subhaplogroups. All the chromosomes previously referred to as paragroup E-M35*(×V92, V42, V6, M123, V68, M293, and V257) are now assigned to five different branches all belonging to haplogroup E-V1515 (fig. 2). This clade shows a tripartite structure, with a rare E-V1515* paragroup and two clades defined by V1486 and V1700 mutations (fig. 2). The V1486 haplogroup grouped six clades: E-M293, E-V92, and four new branches. A nested bifurcated structure is observed for the E-V1700 clade which contains the V42 branch and a sister clade (defined by V1785 and other three mutations), which joins the V6 chromosomes and 12 (former) E-M35* samples now indicated as V1785*. Haplogroup E-V1515 is mainly restricted to eastern Africa (supplementary table S7, Supplementary Material online) with the exception of the terminal clade E-M293, which has been proposed to mark an eastern to southern Africa migration (Henn et al. 2008), and V6, which we report at low frequency also in northeastern Africa.Fig. 2.
Affiliation: Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy.