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

Abstract

Haplogroup E, defined by mutation M40, is the most common human Y chromosome clade within Africa. 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. Additionally, we dissected the E-M35 subclade by genotyping 62 informative markers in 5,222 samples from 118 worldwide populations. The phylogeny of haplogroup E showed novel features compared with the previous topology, including a new basal dichotomy. Within haplogroup E-M35, we resolved all the previously known polytomies and assigned all the E-M35* chromosomes to five new different clades, all belonging to a newly identified subhaplogroup (E-V1515), which accounts for almost half of the E-M35 chromosomes from the Horn of Africa. Moreover, using a Bayesian phylogeographic analysis and a single nucleotide polymorphism-based approach we localized and dated the origin of this new lineage in the northern part of the Horn, about 12 ka. Time frames, phylogenetic structuring, and sociogeographic distribution of E-V1515 and its subclades are consistent with a multistep demic spread of pastoralism within north-eastern Africa and its subsequent diffusion to subequatorial areas. 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.

Genetic structure and sex‐biased gene flow in the history of southern African populations

“…This haplogroup is considered to have an East African origin, and it has been associated with the spread of pastoralism from East Africa to southern Africa (Henn et al, ; Trombetta et al, ). The sequence‐based network of this haplogroup shows a star‐like pattern with all language families represented in the core of the network (Supporting Information Figure S10A).…”

The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola

“…Reads that aligned to the MSY captured region are available in the European Nucleotide Archive (https://www.ebi.ac.uk/ena) with the study accession number PRJEB27776. Y chromosome haplogroups were determined using yhaplo [20], which is based on the International Society of Genetic Genealogy (ISOGG) nomenclature of January 2016 (https:// isogg.org/tree/index.html), with two modifications: (i) the SNP defining B-50f2(P) ( Table S2) was corrected according to a recent ISOGG update (August 6th, 2017); and (ii) instead of using variant NC_000024.9:g.16251357G>A (not typed in this study), we used variant NC_000024.9: g.7595638T>A [21,22] to define haplogroup E-V1245 (Table S2).…”

Carriers of mitochondrial DNA macrohaplogroup L3 basic lineages migrated back to Africa from Asia around 70,000 years ago

“…Against early studies that considered a Paleolithic implantation of E-M81 in the Maghreb [96, 97], it was suggested later that the low microsatellite diversity of this clade in northwest Africa could be better explained as the result of Neolithic or post-Neolithic gene flow episodes from the Near East [98]. However, after that, the discovery of a new sister branch of E-M81, named E-V257 [99], without Near Eastern roots but present in the European western and central Mediterranean shores and in Cameroon and Kenyan populations [99, 100], has weaken the suggested Levantine connection. Furthermore, E-M81 and E-M78 precursors are very old lineages that, respectively, accumulated 23 and 16 mutations in their basal branches.…”

“…The persistence of an even older male demographic substrate in this area has been evidenced by the detection in the region of representatives of the deepest Y phylogenetic clades A0 and A1a [103]. There is general consent in attributing an eastern African origin to the initial expansion of the NRY haplogroup E in the continent [100]. Curiously, ancestral E* lineages have been detected in the Arabian Peninsula [104] and the Levant [105].…”