title: Genomic analyses inform on migration events during the peopling of Eurasia.
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.
authors.affiliation: Estonian Biocentre, Tartu, Estonia.|Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.|Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Pagani
authors.affiliation: Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK.
authors.forename: Daniel John
authors.initials: DJ
authors.lastname: Lawson
authors.affiliation: Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.|Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Evelyn
authors.initials: E
authors.lastname: Jagoda
authors.affiliation: Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Alexander
authors.initials: A
authors.lastname: Mörseburg
authors.affiliation: Integrative Systems Biology Lab, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.|Department of Zoology, University of Cambridge, Cambridge, UK.
authors.forename: Anders
authors.initials: A
authors.lastname: Eriksson
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu, Estonia.|Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
authors.forename: Mario
authors.initials: M
authors.lastname: Mitt
authors.affiliation: Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.|Institut de Biologie Computationnelle, Université Montpellier 2, Montpellier, France.
authors.forename: Florian
authors.initials: F
authors.lastname: Clemente
authors.affiliation: Estonian Biocentre, Tartu, Estonia.|Department of Psychology, University of Auckland, Auckland, 1142, New Zealand.|Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
authors.forename: Georgi
authors.initials: G
authors.lastname: Hudjashov
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: DeGiorgio
authors.affiliation: Estonian Biocentre, Tartu, Estonia.
authors.forename: Lauri
authors.initials: L
authors.lastname: Saag
authors.affiliation: Institute for Human Genetics, University of California, San Francisco, California 94143, USA.
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Wall
authors.affiliation: Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.|MRC Epidemiology Unit, University of Cambridge, Institute of Metabolic Science, Box 285, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ.
authors.forename: Alexia
authors.initials: A
authors.lastname: Cardona
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu, Estonia.
authors.forename: Reedik
authors.initials: R
authors.lastname: Mägi
authors.affiliation: School of Life Sciences, Tempe, AZ, 85287 USA.|Center for Evolution and Medicine, The Biodesign Institute, Tempe, AZ, 85287 USA.
authors.forename: Melissa A
authors.initials: MA
authors.lastname: Wilson Sayres
authors.affiliation: Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Sarah
authors.initials: S
authors.lastname: Kaewert
authors.affiliation: Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Inchley
authors.affiliation: Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Christiana L
authors.initials: CL
authors.lastname: Scheib
authors.affiliation: Estonian Biocentre, Tartu, Estonia.
authors.forename: Mari
authors.initials: M
authors.lastname: Järve
authors.affiliation: Estonian Biocentre, Tartu, Estonia.|Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
authors.forename: Monika
authors.initials: M
authors.lastname: Karmin
authors.affiliation: Mathematical Sciences, University of Southampton, Southampton SO17 1BJ, UK.|Institute for Complex Systems Simulation, University of Southampton, Southampton SO17 1BJ, UK.
authors.forename: Guy S
authors.initials: GS
authors.lastname: Jacobs
authors.affiliation: Division of Biological Sciences, University of Montana, Missoula, MT, USA.
authors.forename: Tiago
authors.initials: T
authors.lastname: Antao
authors.affiliation: Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Florin Mircea
authors.initials: FM
authors.lastname: Iliescu
authors.affiliation: Estonian Biocentre, Tartu, Estonia.|Institute of Genetics and Cytology, National Academy of Sciences, Minsk, Belarus.
authors.forename: Alena
authors.initials: A
authors.lastname: Kushniarevich
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom.
authors.forename: Qasim
authors.initials: Q
authors.lastname: Ayub
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom.
authors.forename: Chris
authors.initials: C
authors.lastname: Tyler-Smith
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom.
authors.forename: Yali
authors.initials: Y
authors.lastname: Xue
authors.affiliation: Estonian Biocentre, Tartu, Estonia.|Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.
authors.forename: Bayazit
authors.initials: B
authors.lastname: Yunusbayev
authors.affiliation: Estonian Biocentre, Tartu, Estonia.
authors.forename: Kristiina
authors.initials: K
authors.lastname: Tambets
authors.affiliation: Estonian Biocentre, Tartu, Estonia.
authors.forename: Chandana Basu
authors.initials: CB
authors.lastname: Mallick
authors.affiliation: Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
authors.forename: Lehti
authors.initials: L
authors.lastname: Saag
authors.affiliation: Kuban State Medical University, Krasnodar, Russia.
authors.forename: Elvira
authors.initials: E
authors.lastname: Pocheshkhova
authors.affiliation: Scientific-Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Georgia.
authors.forename: George
authors.initials: G
authors.lastname: Andriadze
authors.affiliation: Center for GeoGenetics, University of Copenhagen, Denmark.
authors.forename: Craig
authors.initials: C
authors.lastname: Muller
authors.affiliation: Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Australia.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Westaway
authors.affiliation: Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Australia.
authors.forename: David M
authors.initials: DM
authors.lastname: Lambert
authors.affiliation: Center of Molecular Diagnosis and Genetic Research, University Hospital of Obstetrics and Gynecology, Tirana, Albania.
authors.forename: Grigor
authors.initials: G
authors.lastname: Zoraqi
authors.affiliation: Center of High Technology, Academy of Sciences, Republic of Uzbekistan.
authors.forename: Shahlo
authors.initials: S
authors.lastname: Turdikulova
authors.affiliation: Institute of Bioorganic Chemistry Academy of Science, Republic of Uzbekistan.
authors.forename: Dilbar
authors.initials: D
authors.lastname: Dalimova
authors.affiliation: L.N. Gumilyov Eurasian National University, Astana, Kazakhstan.
authors.forename: Zhaxylyk
authors.initials: Z
authors.lastname: Sabitov
authors.affiliation: Centre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka-1000, Bangladesh.
authors.forename: Gazi Nurun Nahar
authors.initials: GNN
authors.lastname: Sultana
authors.affiliation: Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104-6145, USA.|School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Lachance
authors.affiliation: Departments of Genetics and Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Sarah
authors.initials: S
authors.lastname: Tishkoff
authors.affiliation: DNcode laboratories, Moscow, Russia.
authors.forename: Kuvat
authors.initials: K
authors.lastname: Momynaliev
authors.affiliation: Institute of Molecular Biology and Medicine, Bishkek, Kyrgyz Republic.
authors.forename: Jainagul
authors.initials: J
authors.lastname: Isakova
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
authors.forename: Larisa D
authors.initials: LD
authors.lastname: Damba
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
authors.forename: Marina
authors.initials: M
authors.lastname: Gubina
authors.affiliation: Mongolian Academy of Medical Sciences, Ulaanbaatar, Mongolia.
authors.forename: Pagbajabyn
authors.initials: P
authors.lastname: Nymadawa
authors.affiliation: Northern State Medical University, Arkhangelsk, Russia.|Anthony Nolan, London, United Kingdom.
authors.forename: Irina
authors.initials: I
authors.lastname: Evseeva
authors.affiliation: V. N. Karazin Kharkiv National University, Kharkiv, Ukraine.
authors.forename: Lubov
authors.initials: L
authors.lastname: Atramentova
authors.affiliation: V. N. Karazin Kharkiv National University, Kharkiv, Ukraine.
authors.forename: Olga
authors.initials: O
authors.lastname: Utevska
authors.affiliation: 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.
authors.forename: François-Xavier
authors.initials: FX
authors.lastname: Ricaut
authors.affiliation: 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.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Brucato
authors.affiliation: Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
authors.forename: Herawati
authors.initials: H
authors.lastname: Sudoyo
authors.affiliation: 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.
authors.forename: Thierry
authors.initials: T
authors.lastname: Letellier
authors.affiliation: Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
authors.forename: Murray P
authors.initials: MP
authors.lastname: Cox
authors.affiliation: Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russia.|Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russia.
authors.forename: Nikolay A
authors.initials: NA
authors.lastname: Barashkov
authors.affiliation: Genos, DNA laboratory, Zagreb, Croatia.|University of Osijek, Medical School, Osijek, Croatia.
authors.forename: Vedrana
authors.initials: V
authors.lastname: Skaro
authors.affiliation: Center for Genomics and Transcriptomics, CeGaT, GmbH, Tübingen, Germany.
authors.forename: Lejla
authors.initials: L
authors.lastname: Mulahasanovic
authors.affiliation: St. Catherine Speciality Hospital, Zabok, Croatia.|Eberly College of Science, The Pennsylvania State University, University Park, PA, USA.|University of Split, Medical School, Split, Croatia.|University of Osijek, Medical School, Osijek, Croatia.
authors.forename: Dragan
authors.initials: D
authors.lastname: Primorac
authors.affiliation: Estonian Biocentre, Tartu, Estonia.|Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Republic of Armenia, 7 Hasratyan Street, 0014, Yerevan, Armenia.
authors.forename: Hovhannes
authors.initials: H
authors.lastname: Sahakyan
authors.affiliation: Department of Applied Social Sciences, University of Winchester, Sparkford Road, Winchester SO22 4NR, UK.
authors.forename: Maru
authors.initials: M
authors.lastname: Mormina
authors.affiliation: Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.|Thoraxclinic at the University Hospital Heidelberg, Heidelberg, Germany.
authors.forename: Christina A
authors.initials: CA
authors.lastname: Eichstaedt
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.|Novosibirsk State University, Novosibirsk, Russia.
authors.forename: Daria V
authors.initials: DV
authors.lastname: Lichman
authors.affiliation: RIPAS Hospital, Bandar Seri Begawan, Brunei Darussalam.
authors.forename: Syafiq
authors.initials: S
authors.lastname: Abdullah
authors.affiliation: Estonian Biocentre, Tartu, Estonia.
authors.forename: Gyaneshwer
authors.initials: G
authors.lastname: Chaubey
authors.affiliation: National Cancer Centre Singapore, Singapore.
authors.forename: Joseph T S
authors.initials: JTS
authors.lastname: Wee
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu, Estonia.
authors.forename: Evelin
authors.initials: E
authors.lastname: Mihailov
authors.affiliation: Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.|Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Karunas
authors.affiliation: Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.|Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia.|Estonian Biocentre, Tartu, Estonia.
authors.forename: Sergei
authors.initials: S
authors.lastname: Litvinov
authors.affiliation: Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.|Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia.
authors.forename: Rita
authors.initials: R
authors.lastname: Khusainova
authors.affiliation: Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia.
authors.forename: Natalya
authors.initials: N
authors.lastname: Ekomasova
authors.affiliation: Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.
authors.forename: Vita
authors.initials: V
authors.lastname: Akhmetova
authors.affiliation: Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.|Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia.
authors.forename: Irina
authors.initials: I
authors.lastname: Khidiyatova
authors.affiliation: Department of Genetics and Bioengineering. Faculty of Engineering and Information Technologies, International Burch University, Sarajevo, Bosnia and Herzegovina.|Institute for Anthropological Researches, Zagreb, Croatia.
authors.forename: Damir
authors.initials: D
authors.lastname: Marjanović
authors.affiliation: Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Republic of Armenia, 7 Hasratyan Street, 0014, Yerevan, Armenia.
authors.forename: Levon
authors.initials: L
authors.lastname: Yepiskoposyan
authors.affiliation: Estonian Biocentre, Tartu, Estonia.
authors.forename: Doron M
authors.initials: DM
authors.lastname: Behar
authors.affiliation: Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow 115478, Russia.
authors.forename: Elena
authors.initials: E
authors.lastname: Balanovska
authors.affiliation: Department of Zoology, University of Cambridge, Cambridge, UK.|Estonian Genome Center, University of Tartu, Tartu, Estonia.
authors.forename: Andres
authors.initials: A
authors.lastname: Metspalu
authors.affiliation: Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
authors.forename: Miroslava
authors.initials: M
authors.lastname: Derenko
authors.affiliation: Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
authors.forename: Boris
authors.initials: B
authors.lastname: Malyarchuk
authors.affiliation: Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, Russia.|Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.|Novosibirsk State University, Novosibirsk, Russia.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Voevoda
authors.affiliation: Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russia.|Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russia.
authors.forename: Sardana A
authors.initials: SA
authors.lastname: Fedorova
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.|Novosibirsk State University, Novosibirsk, Russia.
authors.forename: Ludmila P
authors.initials: LP
authors.lastname: Osipova
authors.affiliation: Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Marta Mirazón
authors.initials: MM
authors.lastname: Lahr
authors.affiliation: Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.
authors.forename: Pascale
authors.initials: P
authors.lastname: Gerbault
authors.affiliation: Department of Archaeology, University of Papua New Guinea, University PO Box 320, NCD, Papua New Guinea.|College of Arts, Society and Education, James Cook University, PO Box 6811, Cairns QLD 4870, Australia.
authors.forename: Matthew
authors.initials: M
authors.lastname: Leavesley
authors.affiliation: Department of Anthropology, University College London, London, United Kingdom.
authors.forename: Andrea Bamberg
authors.initials: AB
authors.lastname: Migliano
authors.affiliation: Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, D-07743 Jena, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Petraglia
authors.affiliation: Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia.|Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow 115478, Russia.
authors.forename: Oleg
authors.initials: O
authors.lastname: Balanovsky
authors.affiliation: Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.|Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia.
authors.forename: Elza K
authors.initials: EK
authors.lastname: Khusnutdinova
authors.affiliation: Estonian Biocentre, Tartu, Estonia.|Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
authors.forename: Ene
authors.initials: E
authors.lastname: Metspalu
authors.affiliation: Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.
authors.forename: Mark G
authors.initials: MG
authors.lastname: Thomas
authors.affiliation: Department of Zoology, University of Cambridge, Cambridge, UK.
authors.forename: Andrea
authors.initials: A
authors.lastname: Manica
authors.affiliation: Department of Integrative Biology, University of California Berkeley, Berkeley 94720, CA, USA.
authors.forename: Rasmus
authors.initials: R
authors.lastname: Nielsen
authors.affiliation: Estonian Biocentre, Tartu, Estonia.|Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.|Estonian Academy of Sciences, 6 Kohtu Street, Tallinn 10130, Estonia.
authors.forename: Richard
authors.initials: R
authors.lastname: Villems
authors.affiliation: Center for GeoGenetics, University of Copenhagen, Denmark.
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
authors.affiliation: Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.|Estonian Biocentre, Tartu, Estonia.
authors.forename: Toomas
authors.initials: T
authors.lastname: Kivisild
authors.affiliation: Estonian Biocentre, Tartu, Estonia.
authors.forename: Mait
authors.initials: M
authors.lastname: Metspalu
mesh_terms: D000818:Animals; D006801:Humans; D000349:Africa / Q000208:ethnology; D001208:Asia; D066264:Datasets as Topic; D004957:Estonia; D005060:Europe; D005580:Fossils; D051456:Gene Flow; D005828:Genetics, Population; D015894:Genome, Human / Q000235:genetics; D023281:Genomics; D006579:Heterozygote; D049690:History, Ancient; D063426:Human Migration / Q000266:history; D059125:Neanderthals / Q000235:genetics; D009512:New Guinea; D011157:Population Dynamics; D044469:Racial Groups / Q000235:genetics