TY - JOUR
T1 - Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians
AU - Pagani, Luca
AU - Schiffels, Stephan
AU - Gurdasani, Deepti
AU - Danecek, Petr
AU - Scally, Aylwyn
AU - Chen, Yuan
AU - Xue, Yali
AU - Haber, Marc
AU - Ekong, Rosemary
AU - Oljira, Tamiru
AU - Mekonnen, Ephrem
AU - Luiselli, Donata
AU - Bradman, Neil
AU - Bekele, Endashaw
AU - Zalloua, Pierre
AU - Durbin, Richard
AU - Kivisild, Toomas
AU - Tyler-Smith, Chris
N1 - Funding Information:
The authors would like to acknowledge all the donors who kindly contributed samples to this study. L.P., S.S., D.G., P.D., Y.C., Y.X., M.H., R.D., and C.T.-S. were funded by Wellcome Trust grant 098051. T.K. was funded by European Research Council (ERC) Starting Grant FP7-261213, and D.L. was funded by ERC Advanced Grant FP7-295733. R.D. is a founder and non-executive director of Congenica. N.B. is the senior trustee, settlor, and principal donor of Melford Charitable Trust and the director and beneficial owner of the entire share capital of Cordell Homes, a company that provided the financial support for the collection of the Ethiopian samples analyzed in this paper.
Publisher Copyright:
© 2015 The Authors
PY - 2015/6/4
Y1 - 2015/6/4
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84991608013&partnerID=8YFLogxK
U2 - 10.1016/j.ajhg.2015.04.019
DO - 10.1016/j.ajhg.2015.04.019
M3 - Article
C2 - 26027499
AN - SCOPUS:84991608013
SN - 0002-9297
VL - 96
SP - 986
EP - 991
JO - American Journal of Human Genetics
JF - American Journal of Human Genetics
IS - 6
ER -