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Nature. 2016 Oct 13;538(7624):238-242. doi: 10.1038/nature19792. Epub 2016 Sep 21.

Genomic analyses inform on migration events during the peopling of Eurasia.

Author information

1
Estonian Biocentre, Tartu, Estonia.
2
Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.
3
Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy.
4
Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK.
5
Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
6
Integrative Systems Biology Lab, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
7
Department of Zoology, University of Cambridge, Cambridge, UK.
8
Estonian Genome Center, University of Tartu, Tartu, Estonia.
9
Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
10
Institut de Biologie Computationnelle, Université Montpellier 2, Montpellier, France.
11
Department of Psychology, University of Auckland, Auckland, 1142, New Zealand.
12
Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
13
Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
14
Institute for Human Genetics, University of California, San Francisco, California 94143, USA.
15
MRC Epidemiology Unit, University of Cambridge, Institute of Metabolic Science, Box 285, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ.
16
School of Life Sciences, Tempe, AZ, 85287 USA.
17
Center for Evolution and Medicine, The Biodesign Institute, Tempe, AZ, 85287 USA.
18
Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
19
Mathematical Sciences, University of Southampton, Southampton SO17 1BJ, UK.
20
Institute for Complex Systems Simulation, University of Southampton, Southampton SO17 1BJ, UK.
21
Division of Biological Sciences, University of Montana, Missoula, MT, USA.
22
Institute of Genetics and Cytology, National Academy of Sciences, Minsk, Belarus.
23
The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom.
24
Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.
25
Kuban State Medical University, Krasnodar, Russia.
26
Scientific-Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Georgia.
27
Center for GeoGenetics, University of Copenhagen, Denmark.
28
Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Australia.
29
Center of Molecular Diagnosis and Genetic Research, University Hospital of Obstetrics and Gynecology, Tirana, Albania.
30
Center of High Technology, Academy of Sciences, Republic of Uzbekistan.
31
Institute of Bioorganic Chemistry Academy of Science, Republic of Uzbekistan.
32
L.N. Gumilyov Eurasian National University, Astana, Kazakhstan.
33
Centre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka-1000, Bangladesh.
34
Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104-6145, USA.
35
School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA.
36
Departments of Genetics and Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
37
DNcode laboratories, Moscow, Russia.
38
Institute of Molecular Biology and Medicine, Bishkek, Kyrgyz Republic.
39
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
40
Mongolian Academy of Medical Sciences, Ulaanbaatar, Mongolia.
41
Northern State Medical University, Arkhangelsk, Russia.
42
Anthony Nolan, London, United Kingdom.
43
V. N. Karazin Kharkiv National University, Kharkiv, Ukraine.
44
Evolutionary Medicine group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France.
45
Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
46
Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russia.
47
Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russia.
48
Genos, DNA laboratory, Zagreb, Croatia.
49
University of Osijek, Medical School, Osijek, Croatia.
50
Center for Genomics and Transcriptomics, CeGaT, GmbH, Tübingen, Germany.
51
St. Catherine Speciality Hospital, Zabok, Croatia.
52
Eberly College of Science, The Pennsylvania State University, University Park, PA, USA.
53
University of Split, Medical School, Split, Croatia.
54
Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Republic of Armenia, 7 Hasratyan Street, 0014, Yerevan, Armenia.
55
Department of Applied Social Sciences, University of Winchester, Sparkford Road, Winchester SO22 4NR, UK.
56
Thoraxclinic at the University Hospital Heidelberg, Heidelberg, Germany.
57
Novosibirsk State University, Novosibirsk, Russia.
58
RIPAS Hospital, Bandar Seri Begawan, Brunei Darussalam.
59
National Cancer Centre Singapore, Singapore.
60
Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia.
61
Department of Genetics and Bioengineering. Faculty of Engineering and Information Technologies, International Burch University, Sarajevo, Bosnia and Herzegovina.
62
Institute for Anthropological Researches, Zagreb, Croatia.
63
Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow 115478, Russia.
64
Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
65
Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, Russia.
66
Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom.
67
Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.
68
Department of Archaeology, University of Papua New Guinea, University PO Box 320, NCD, Papua New Guinea.
69
College of Arts, Society and Education, James Cook University, PO Box 6811, Cairns QLD 4870, Australia.
70
Department of Anthropology, University College London, London, United Kingdom.
71
Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, D-07743 Jena, Germany.
72
Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia.
73
Department of Integrative Biology, University of California Berkeley, Berkeley 94720, CA, USA.
74
Estonian Academy of Sciences, 6 Kohtu Street, Tallinn 10130, Estonia.
#
Contributed equally

Abstract

High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.

PMID:
27654910
PMCID:
PMC5164938
DOI:
10.1038/nature19792
[Indexed for MEDLINE]
Free PMC Article

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