title: 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.
authors.affiliation: Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy.
authors.forename: Beniamino
authors.initials: B
authors.lastname: Trombetta
authors.affiliation: Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy.
authors.forename: Eugenia
authors.initials: E
authors.lastname: D'Atanasio
authors.affiliation: Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy Present address: The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom.
authors.forename: Andrea
authors.initials: A
authors.lastname: Massaia
authors.affiliation: Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Ippoliti
authors.affiliation: Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Italy.
authors.forename: Alfredo
authors.initials: A
authors.lastname: Coppa
authors.affiliation: Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Candilio
authors.affiliation: Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy.
authors.forename: Valentina
authors.initials: V
authors.lastname: Coia
authors.affiliation: Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, Italy.
authors.forename: Gianluca
authors.initials: G
authors.lastname: Russo
authors.affiliation: Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique (CNRS), Université Toulouse-3-Paul-Sabatier, Toulouse, France.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Dugoujon
authors.affiliation: Department of Animal Biology-Anthropology, Biodiversity Research Institute, University of Barcelona, Spain.
authors.forename: Pedro
authors.initials: P
authors.lastname: Moral
authors.affiliation: Pediatrics Department, TOBB-Economy and Technology University Hospital, Ankara, Turkey.
authors.forename: Nejat
authors.initials: N
authors.lastname: Akar
authors.affiliation: Istituto di Biologia e Patologia Molecolari, CNR, Rome Italy.
authors.forename: Daniele
authors.initials: D
authors.lastname: Sellitto
authors.affiliation: Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Italy.
authors.forename: Guido
authors.initials: G
authors.lastname: Valesini
authors.affiliation: Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Novelletto
authors.affiliation: Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy.
authors.forename: Rosaria
authors.initials: R
authors.lastname: Scozzari
authors.affiliation: Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy Istituto di Biologia e Patologia Molecolari, CNR, Rome Italy fulvio.cruciani@uniroma1.it.
authors.forename: Fulvio
authors.initials: F
authors.lastname: Cruciani
mesh_terms: D000349:Africa; D041322:Chromosomes, Human, Y / Q000145:classification; D019143:Evolution, Molecular; D060005:Genotyping Techniques; D006239:Haplotypes; D063426:Human Migration; D006801:Humans; D008297:Male; D009154:Mutation; D010802:Phylogeny; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide
keywords: African prehistory; MSY phylogeny; SNP-based dating; dispersal of early pastoralists; human Y chromosome; next generation sequencing