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Am J Hum Genet. 2015 Jun 4;96(6):986-91. doi: 10.1016/j.ajhg.2015.04.019. Epub 2015 May 28.

Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians.

Author information

1
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK; Department of Biological, Geological, and Environmental Sciences, University of Bologna, 40126 Bologna, Italy. Electronic address: lp.lucapagani@gmail.com.
2
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
3
Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.
4
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; The Lebanese American University, Chouran, Beirut 1102 2801, Lebanon.
5
Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK.
6
University of Addis Ababa and Center of Human Genetic Diversity, PO Box 1176, Ethiopia.
7
Department of Biological, Geological, and Environmental Sciences, University of Bologna, 40126 Bologna, Italy.
8
Henry Stewart Group, 28/30 Little Russell Street, London WC1A 2HN, UK.
9
The Lebanese American University, Chouran, Beirut 1102 2801, Lebanon; Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
10
Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK.

Abstract

The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative routes, via Egypt and Sinai or across the Bab el Mandeb strait into Arabia, have traditionally been proposed as feasible gateways in light of geographic, paleoclimatic, archaeological, and genetic evidence. Distinguishing among these alternatives has been difficult. We generated 225 whole-genome sequences (225 at 8× depth, of which 8 were increased to 30×; Illumina HiSeq 2000) from six modern Northeast African populations (100 Egyptians and five Ethiopian populations each represented by 25 individuals). West Eurasian components were masked out, and the remaining African haplotypes were compared with a panel of sub-Saharan African and non-African genomes. We showed that masked Northeast African haplotypes overall were more similar to non-African haplotypes and more frequently present outside Africa than were any sets of haplotypes derived from a West African population. Furthermore, the masked Egyptian haplotypes showed these properties more markedly than the masked Ethiopian haplotypes, pointing to Egypt as the more likely gateway in the exodus to the rest of the world. Using five Ethiopian and three Egyptian high-coverage masked genomes and the multiple sequentially Markovian coalescent (MSMC) approach, we estimated the genetic split times of Egyptians and Ethiopians from non-African populations at 55,000 and 65,000 years ago, respectively, whereas that of West Africans was estimated to be 75,000 years ago. Both the haplotype and MSMC analyses thus suggest a predominant northern route out of Africa via Egypt.

PMID:
26027499
PMCID:
PMC4457944
DOI:
10.1016/j.ajhg.2015.04.019
[Indexed for MEDLINE]
Free PMC Article

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