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, 7 (7), 1940-50

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

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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

Beniamino Trombetta et al. Genome Biol Evol.

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.

Keywords: African prehistory; MSY phylogeny; SNP-based dating; dispersal of early pastoralists; human Y chromosome; next generation sequencing.

Figures

F<sc>ig</sc>. 1.
Fig. 1.
— MP tree of haplogroup E obtained with 729 variable positions. Above each branch are reported the haplogroup nomenclature used in the main text (in square brackets) and the number of mutational events defining each branch. Few internal key mutations are indicated as an aid to the reader. Dating estimates are reported in boxes near each node (the values on top and on bottom were obtained with BEAST and rho method, respectively). At the tip of each terminal branch, the haplogroup affiliation of the sequenced sample is reported, using a mutation-based nomenclature according to Trombetta et al. (2011). The ID of the samples from Complete Genomics is also indicated (in parentheses). Colored belts indicate major lineages.
F<sc>ig</sc>. 2.
Fig. 2.
—Molecular dissection of haplogroup E-M35. All the 62 mutations shown have been genotyped. New mutations and branches are in blue. Previously known mutations are underlined. At the bottom of each branch are reported: The number of samples carrying the haplogroup, the former mutation-based nomenclature (according to Trombetta et al. [2011]), and the new mutation-based nomenclature. Chromosomes E-V1785* are ancestral for V1472, V1617, V2793, V2684, V2727, V2802, and V2927 (not shown).
F<sc>ig</sc>. 3.
Fig. 3.
—Maps of the observed frequencies for haplogroup E-V1515 and its major subhaplogroups. (A) Haplogroup E-V1515, (B) haplogroup E-V1700, (C) haplogroup E-V1486, (D) haplogroup E-V2881, (E) haplogroup E-M293, (F) simplified phylogeny of E-V1515, showing the estimated age of the nodes (ky). Place of sampling of chromosomes carrying rare paragroups E-V1515*, E-V1785*, and E-V1486* is shown as blue asterisks in panels (A), (B), and (C), respectively. The sampling locations for the populations used in this analysis are shown in supplementary figure S5, Supplementary Material online.

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