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      Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians

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          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.

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          Inferring human population size and separation history from multiple genome sequences

          The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) analyses the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago, and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe.
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            Bayesian inference of ancient human demography from individual genome sequences

            Besides their value for biomedicine, individual genome sequences are a rich source of information about human evolution. Here we describe an effort to estimate key evolutionary parameters from sequences for six individuals from diverse human populations. We use a Bayesian, coalescent-based approach to extract information about ancestral population sizes, divergence times, and migration rates from inferred genealogies at many neutrally evolving loci from across the genome. We introduce new methods for accommodating gene flow between populations and integrating over possible phasings of diploid genotypes. We also describe a custom pipeline for genotype inference to mitigate biases from heterogeneous sequencing technologies and coverage levels. Our analysis indicates that the San of Southern Africa diverged from other human populations 108–157 thousand years ago (kya), that Eurasians diverged from an ancestral African population 38–64 kya, and that the effective population size of the ancestors of all modern humans was ~9,000.
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              African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping.

              Comparative studies of ethnically diverse human populations, particularly in Africa, are important for reconstructing human evolutionary history and for understanding the genetic basis of phenotypic adaptation and complex disease. African populations are characterized by greater levels of genetic diversity, extensive population substructure, and less linkage disequilibrium (LD) among loci compared to non-African populations. Africans also possess a number of genetic adaptations that have evolved in response to diverse climates and diets, as well as exposure to infectious disease. This review summarizes patterns and the evolutionary origins of genetic diversity present in African populations, as well as their implications for the mapping of complex traits, including disease susceptibility.
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                Author and article information

                Contributors
                Journal
                Am J Hum Genet
                Am. J. Hum. Genet
                American Journal of Human Genetics
                Elsevier
                0002-9297
                1537-6605
                04 June 2015
                04 June 2015
                : 96
                : 6
                : 986-991
                Affiliations
                [1 ]The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
                [2 ]Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
                [3 ]Department of Biological, Geological, and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
                [4 ]Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
                [5 ]The Lebanese American University, Chouran, Beirut 1102 2801, Lebanon
                [6 ]Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
                [7 ]University of Addis Ababa and Center of Human Genetic Diversity, PO Box 1176, Ethiopia
                [8 ]Henry Stewart Group, 28/30 Little Russell Street, London WC1A 2HN, UK
                [9 ]Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
                Author notes
                []Corresponding author lp.lucapagani@ 123456gmail.com
                Article
                S0002-9297(15)00156-1
                10.1016/j.ajhg.2015.04.019
                4457944
                26027499
                2d3dc0e4-8397-40ff-abc7-1df159b62b28
                © 2015 The Authors

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

                History
                : 21 January 2015
                : 29 April 2015
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                Genetics
                Genetics

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