title: A recent bottleneck of Y chromosome diversity coincides with a global change in culture.
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.
authors.affiliation: Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia; tk331@cam.ac.uk monika.karmin@gmail.com.
authors.forename: Monika
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authors.lastname: Karmin
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authors.forename: Lauri
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authors.affiliation: Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;
authors.forename: Mário
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authors.affiliation: Department of Integrative Biology, University of California Berkeley, Berkeley, California 94720, USA; School of Life Sciences and The Biodesign Institute, Tempe, Arizona 85287-5001, USA;
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authors.affiliation: Estonian Biocentre, Tartu, 51010, Estonia;
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authors.affiliation: Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
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authors.affiliation: Estonian Biocentre, Tartu, 51010, Estonia;
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authors.affiliation: Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
authors.forename: Anne-Mai
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authors.affiliation: Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia;
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authors.affiliation: Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia; Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
authors.forename: Mario
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authors.affiliation: Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;
authors.forename: Luca
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authors.affiliation: Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
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authors.affiliation: Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;
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authors.affiliation: Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;
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authors.affiliation: Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
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authors.affiliation: Estonian Biocentre, Tartu, 51010, Estonia; Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia;
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authors.affiliation: Department 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;
authors.forename: Nikolay A
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authors.affiliation: Northern State Medical University, Arkhangelsk, 163000, Russia; Anthony Nolan, London, NW3 2NU, United Kingdom;
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authors.affiliation: RIPAS Hospital, Bandar Seri Begawan, BE1518, Brunei;
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authors.affiliation: Scientific-Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Tbilisi, 0162, Georgia;
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authors.affiliation: University 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;
authors.forename: Dragan
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authors.affiliation: V.N. Karazin Kharkiv National University, Kharkiv, 61022, Ukraine;
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authors.affiliation: V.N. Karazin Kharkiv National University, Kharkiv, 61022, Ukraine;
authors.forename: Olga
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authors.affiliation: Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, 0014, Armenia;
authors.forename: Levon
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authors.affiliation: Genos, DNA Laboratory, Zagreb, 10000, Croatia; Department of Genetics and Bioengineering, Faculty of Engineering and Information Technologies, International Burch University, Sarajevo, 71000, Bosnia and Herzegovina;
authors.forename: Damir
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authors.affiliation: Estonian Biocentre, Tartu, 51010, Estonia; Institute of Genetics and Cytology, National Academy of Sciences, Minsk, 220072, Belarus;
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authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, 106525 GA, The Netherlands;
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authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, 106525 GA, The Netherlands;
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authors.affiliation: Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, 115478, Russia;
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authors.affiliation: Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, 685000, Russia;
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authors.affiliation: Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia;
authors.forename: Andres
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authors.affiliation: Department 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;
authors.forename: Sardana
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authors.lastname: Fedorova
authors.affiliation: Department 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;
authors.forename: Anders
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authors.affiliation: Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom;
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authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA;
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authors.affiliation: ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA;
authors.forename: Tatiana M
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authors.affiliation: Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA;
authors.forename: Krishna R
authors.initials: KR
authors.lastname: Veeramah
authors.affiliation: The Henry Stewart Group, London, WC1A 2HN, United Kingdom;
authors.forename: Neil
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authors.affiliation: ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA;
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authors.affiliation: Institute of Cytology and Genetics, Novosibirsk, 630090, Russia;
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authors.affiliation: Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, 115478, Russia; Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia;
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authors.affiliation: Institute 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;
authors.forename: Elza K
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authors.affiliation: University Hospital of North Norway, Tromsøe, N-9038, Norway;
authors.forename: Knut
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authors.affiliation: Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
authors.forename: Maido
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authors.affiliation: Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom;
authors.forename: Mark G
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authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom;
authors.forename: Chris
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authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA;
authors.forename: Peter A
authors.initials: PA
authors.lastname: Underhill
authors.affiliation: Center for GeoGenetics, University of Copenhagen, Copenhagen, DK-1350, Denmark;
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
authors.affiliation: Department of Integrative Biology, University of California Berkeley, Berkeley, California 94720, USA;
authors.forename: Rasmus
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authors.lastname: Nielsen
authors.affiliation: Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
authors.forename: Mait
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authors.lastname: Metspalu
authors.affiliation: Estonian 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, Estonia.
authors.forename: Richard
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authors.lastname: Villems
authors.affiliation: Estonian Biocentre, Tartu, 51010, Estonia; Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom; tk331@cam.ac.uk monika.karmin@gmail.com.
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mesh_terms: D001483:Base Sequence; D041322:Chromosomes, Human, Y / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics; D005828:Genetics, Population; D006239:Haplotypes / Q000235:genetics; D006801:Humans; D008297:Male; D008957:Models, Genetic; D010802:Phylogeny; D044469:Racial Groups / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial