Journal
GENOME BIOLOGY AND EVOLUTION
Volume 7, Issue 7, Pages 1940-1950Publisher
OXFORD UNIV PRESS
DOI: 10.1093/gbe/evv118
Keywords
human Y chromosome; African prehistory; MSY phylogeny; dispersal of early pastoralists; next generation sequencing; SNP-based dating
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Funding
- Italian Ministry of Education [2012JA4BTY_004, 2012JA4BTY_003]
- Sapienza University of Rome [C26A13S9AR]
- Inserm Reseau Nord/Sud [490NS1]
- Region Midi-Pyrenees (Toulouse, France)
- CNRS
- E.C. [ERASCT-2003-980409]
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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 12ka. 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.
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