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Genome Biol Evol. 2015 Jun 24;7(7):1940-50. doi: 10.1093/gbe/evv118.

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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Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy.
Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy Present address: The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom.
Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Italy.
Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy.
Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, Italy.
Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique (CNRS), Université Toulouse-3-Paul-Sabatier, Toulouse, France.
Department of Animal Biology-Anthropology, Biodiversity Research Institute, University of Barcelona, Spain.
Pediatrics Department, TOBB-Economy and Technology University Hospital, Ankara, Turkey.
Istituto di Biologia e Patologia Molecolari, CNR, Rome Italy.
Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Italy.
Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy Istituto di Biologia e Patologia Molecolari, CNR, Rome Italy


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.


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

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