A recent bottleneck of Y chromosome diversity coincides with a global change in culture
Monika KarminEstonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia; [email protected] [email protected]Lauri SaagEstonian Biocentre, Tartu, 51010, Estonia; Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51010, Estonia;Mário VicenteDivision of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;Melissa A. Wilson SayresDepartment of Integrative Biology, University of California Berkeley, Berkeley, California 94720, USA; School of Life Sciences and The Biodesign Institute, Tempe, Arizona 85287-5001, USA;Mari JärveEstonian Biocentre, Tartu, 51010, Estonia;Ulvi Gerst TalasDepartment of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;Siiri RootsiEstonian Biocentre, Tartu, 51010, Estonia;Anne-Mai IlumäEEstonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;Reedik MägiEstonian Genome Center, University of Tartu, Tartu, 51010, Estonia;Mario MittEstonian Genome Center, University of Tartu, Tartu, 51010, Estonia; Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;Luca PaganiDivision of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;Tarmo PuurandDepartment of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;Zuzana FaltyskovaDivision of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;Florian ClementeDivision of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;Alexia CardonaDivision of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;Ene MetspaluEstonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;Hovhannes SahakyanEstonian Biocentre, Tartu, 51010, Estonia; Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, 0014, Armenia;Bayazit YunusbayevEstonian Biocentre, Tartu, 51010, Estonia; Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia;Georgi HudjashovEstonian Biocentre, Tartu, 51010, Estonia; Department of Psychology, University of Auckland, Auckland, 1142, New Zealand;Michael DeGiorgioDepartment of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA;Eva‐Liis LoogväliEstonian Biocentre, Tartu, 51010, Estonia;Christina EichstaedtDivision of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;Mikk EelmetsEstonian Biocentre, Tartu, 51010, Estonia; Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;Gyaneshwer ChaubeyEstonian Biocentre, Tartu, 51010, Estonia;Kristiina TambetsEstonian Biocentre, Tartu, 51010, Estonia;Sergei LitvinovEstonian Biocentre, Tartu, 51010, Estonia; Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia;Maru MorminaDepartment of Applied Social Sciences, University of Winchester, Winchester, SO22 4NR, United Kingdom;Yali XueThe Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom;Qasim AyubThe Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom;G. ZoraqiCenter of Molecular Diagnosis and Genetic Research, University Hospital of Obstetrics and Gynecology, Tirana, ALB1005, Albania;Thorfinn Sand KorneliussenDepartment of Integrative Biology, University of California Berkeley, Berkeley, California 94720, USA; Center for GeoGenetics, University of Copenhagen, Copenhagen, DK-1350, Denmark;Farida AkhatovaDepartment of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russia;Joseph LachanceDepartment of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6145, USA; School of Biology, Georgia Institute of Technology, Atlanta, 30332, Georgia, USA;Sarah A. TishkoffDepartment of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6145, USA; Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6313, USA;К. Т. МомыналиевDNcode Laboratories, Moscow, 119992, Russia;François‐Xavier RicautEvolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France;Pradiptajati KusumaEvolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France; Eijkman Institute for Molecular Biology, Jakarta, 10430, Indonesia;Harilanto RazafindrazakaEvolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France;Denis PierronEvolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France;Murray P. CoxStatistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand;Gazi Nurun Nahar SultanaCentre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka, Dhaka-1000, Bangladesh;Rane WillerslevArctic Research Centre, Aarhus University, Aarhus, DK-8000, Denmark;Craig MullerCenter for GeoGenetics, University of Copenhagen, Copenhagen, DK-1350, Denmark;Michael WestawayEnvironmental Futures Research Institute, Griffith University, Nathan, 4111, Australia;David M. LambertEnvironmental Futures Research Institute, Griffith University, Nathan, 4111, Australia;Vedrana ŠkaroGenos, DNA Laboratory, Zagreb, 10000, Croatia; University of Osijek, Medical School, Osijek, 31000, Croatia;Lejla KovačevićCentogene AG, Rostock, 18057, Germany;Shahlo ТurdikulovaInstitute of Bioorganic Chemistry, Academy of Science, Tashkent, 100143, Uzbekistan;Dilbar DalimovaInstitute of Bioorganic Chemistry, Academy of Science, Tashkent, 100143, Uzbekistan;Р. И. ХусаиноваInstitute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia;Natalya TrofimovaEstonian Biocentre, Tartu, 51010, Estonia; Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia;В. Р. АхметоваInstitute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia;I. M. KhidiyatovaInstitute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia;Daria V. LichmanInstitute of Cytology and Genetics, Novosibirsk, 630090, Russia;Jainagul IsakovaInstitute of Molecular Biology and Medicine, Bishkek, 720040, Kyrgyzstan;Elvira PocheshkhovaKuban State Medical University, Krasnodar, 350063, Russia;Zhaxylyk SabitovL.N. Gumilyov Eurasian National University, Astana, 010008, Kazakhstan; Center for Life Sciences, Nazarbayev University, Astana, 010000, Kazakhstan;Nikolay A. BarashkovDepartment of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, 677010, Russia; Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, 677000, Russia;Pagbajabyn NymadawaMongolian Academy of Medical Sciences, Ulaanbaatar, 210620, Mongolia;Evelin MihailovEstonian Genome Center, University of Tartu, Tartu, 51010, Estonia;Joseph Wee Tien SengNational Cancer Centre Singapore, 169610, Singapore;Irina EvseevaNorthern State Medical University, Arkhangelsk, 163000, Russia; Anthony Nolan, London, NW3 2NU, United Kingdom;Andrea Bamberg MiglianoDepartment of Anthropology, University College London, London, WC1E 6BT, United Kingdom;Syafiq AbdullahRIPAS Hospital, Bandar Seri Begawan, BE1518, Brunei;George AndriadzeScientific-Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Tbilisi, 0162, Georgia;Dragan PrimoracUniversity of Osijek, Medical School, Osijek, 31000, Croatia; St. Catherine Specialty Hospital, Zabok, 49210, Croatia; Eberly College of Science, Pennsylvania State University, University Park, Pennsylvania 16802, USA; University of Split, Medical School, Split, 21000, Croatia;Л. А. АтраментоваV.N. Karazin Kharkiv National University, Kharkiv, 61022, Ukraine;Olga UtevskaV.N. Karazin Kharkiv National University, Kharkiv, 61022, Ukraine;Levon YepiskoposyanLaboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, 0014, Armenia;Damir MarjanovićGenos, DNA Laboratory, Zagreb, 10000, Croatia; Department of Genetics and Bioengineering, Faculty of Engineering and Information Technologies, International Burch University, Sarajevo, 71000, Bosnia and Herzegovina;Alena KushniarevichEstonian Biocentre, Tartu, 51010, Estonia; Institute of Genetics and Cytology, National Academy of Sciences, Minsk, 220072, Belarus;Doron M. BeharEstonian Biocentre, Tartu, 51010, Estonia;Christian GilissenDepartment of Human Genetics, Radboud University Medical Center, Nijmegen, 106525 GA, The Netherlands;Lisenka E.L.M. VissersDepartment of Human Genetics, Radboud University Medical Center, Nijmegen, 106525 GA, The Netherlands;Joris A. VeltmanDepartment of Human Genetics, Radboud University Medical Center, Nijmegen, 106525 GA, The Netherlands;Elena BalanovskaResearch Centre for Medical Genetics, Russian Academy of Sciences, Moscow, 115478, Russia;М. В. ДеренкоGenetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, 685000, Russia;B. А. MalyarchukGenetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, 685000, Russia;Andres MetspaluEstonian Genome Center, University of Tartu, Tartu, 51010, Estonia;С.А. ФедороваDepartment of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, 677010, Russia; Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, 677000, Russia;Anders ErikssonDepartment of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom; Integrative Systems Biology Lab, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia;Andrea ManicaDepartment of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom;Fernando L. MéndezDepartment of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA;Tatiana M. KarafetARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA;Krishna R. VeeramahDepartment of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA;Neil BradmanThe Henry Stewart Group, London, WC1A 2HN, United Kingdom;Michael F. HammerARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA;L. P. OsipovaInstitute of Cytology and Genetics, Novosibirsk, 630090, Russia;Oleg BalanovskyResearch Centre for Medical Genetics, Russian Academy of Sciences, Moscow, 115478, Russia; Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia;Э. К. ХуснутдиноваInstitute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia;Knut JohnsenUniversity Hospital of North Norway, Tromsøe, N-9038, Norway;Maido RemmDepartment of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;Mark ThomasResearch Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom;Chris Tyler‐SmithThe Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom;Peter A. UnderhillDepartment of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA;Eske WillerslevCenter for GeoGenetics, University of Copenhagen, Copenhagen, DK-1350, Denmark;Rasmus NielsenDepartment of Integrative Biology, University of California Berkeley, Berkeley, California 94720, USA;Mait MetspaluEstonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;Richard VillemsEstonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia; Estonian Academy of Sciences, Tallinn, 10130, EstoniaToomas KivisildEstonian Biocentre, Tartu, 51010, Estonia; Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom; [email protected] [email protected]
ABI
Abstract
It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.