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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

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
Authors: Trombetta, B
D'Atanasio, E
Massaia, A
Ippoliti, M
Coppa, A
Candilio, F
Coia, V
Russo, G
Dugoujon, J-M
Moral, P
Akar, N
Sellitto, D
Valesini, G
Novelletto, A
Scozzari, R
Cruciani, F
Item Type: Journal Article
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.
Issue Date: 1-Jul-2015
Date of Acceptance: 19-Jun-2015
URI: http://hdl.handle.net/10044/1/58161
DOI: https://dx.doi.org/10.1093/gbe/evv118
ISSN: 1759-6653
Publisher: Oxford University Press
Start Page: 1940
End Page: 1950
Journal / Book Title: Genome Biology and Evolution
Volume: 7
Issue: 7
Copyright Statement: © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: Science & Technology
Life Sciences & Biomedicine
Evolutionary Biology
Genetics & Heredity
human Y chromosome
African prehistory
MSY phylogeny
dispersal of early pastoralists
next generation sequencing
SNP-based dating
Chromosomes, Human, Y
Evolution, Molecular
Genotyping Techniques
Human Migration
Polymorphism, Single Nucleotide
0604 Genetics
0603 Evolutionary Biology
Developmental Biology
Publication Status: Published
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