Research

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

    • 1Estonian Biocentre, Tartu, 51010, Estonia;
    • 2Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
    • 3Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51010, Estonia;
    • 4Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;
    • 5Department of Integrative Biology, University of California Berkeley, Berkeley, California 94720, USA;
    • 6School of Life Sciences and The Biodesign Institute, Tempe, Arizona 85287-5001, USA;
    • 7Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
    • 8Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia;
    • 9Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
    • 10Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, 0014, Armenia;
    • 11Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia;
    • 12Department of Psychology, University of Auckland, Auckland, 1142, New Zealand;
    • 13Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA;
    • 14Department of Applied Social Sciences, University of Winchester, Winchester, SO22 4NR, United Kingdom;
    • 15The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom;
    • 16Center of Molecular Diagnosis and Genetic Research, University Hospital of Obstetrics and Gynecology, Tirana, ALB1005, Albania;
    • 17Center for GeoGenetics, University of Copenhagen, Copenhagen, DK-1350, Denmark;
    • 18Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia;
    • 19Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russia;
    • 20Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6145, USA;
    • 21School of Biology, Georgia Institute of Technology, Atlanta, 30332, Georgia, USA;
    • 22Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6313, USA;
    • 23DNcode Laboratories, Moscow, 119992, Russia;
    • 24Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France;
    • 25Eijkman Institute for Molecular Biology, Jakarta, 10430, Indonesia;
    • 26Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand;
    • 27Centre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka, Dhaka-1000, Bangladesh;
    • 28Arctic Research Centre, Aarhus University, Aarhus, DK-8000, Denmark;
    • 29Environmental Futures Research Institute, Griffith University, Nathan, 4111, Australia;
    • 30Genos, DNA Laboratory, Zagreb, 10000, Croatia;
    • 31University of Osijek, Medical School, Osijek, 31000, Croatia;
    • 32Centogene AG, Rostock, 18057, Germany;
    • 33Institute of Bioorganic Chemistry, Academy of Science, Tashkent, 100143, Uzbekistan;
    • 34Institute of Cytology and Genetics, Novosibirsk, 630090, Russia;
    • 35Institute of Molecular Biology and Medicine, Bishkek, 720040, Kyrgyzstan;
    • 36Kuban State Medical University, Krasnodar, 350063, Russia;
    • 37L.N. Gumilyov Eurasian National University, Astana, 010008, Kazakhstan;
    • 38Center for Life Sciences, Nazarbayev University, Astana, 010000, Kazakhstan;
    • 39Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, 677010, Russia;
    • 40Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, 677000, Russia;
    • 41Mongolian Academy of Medical Sciences, Ulaanbaatar, 210620, Mongolia;
    • 42National Cancer Centre Singapore, 169610, Singapore;
    • 43Northern State Medical University, Arkhangelsk, 163000, Russia;
    • 44Anthony Nolan, London, NW3 2NU, United Kingdom;
    • 45Department of Anthropology, University College London, London, WC1E 6BT, United Kingdom;
    • 46RIPAS Hospital, Bandar Seri Begawan, BE1518, Brunei;
    • 47Scientific-Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Tbilisi, 0162, Georgia;
    • 48St. Catherine Specialty Hospital, Zabok, 49210, Croatia;
    • 49Eberly College of Science, Pennsylvania State University, University Park, Pennsylvania 16802, USA;
    • 50University of Split, Medical School, Split, 21000, Croatia;
    • 51V.N. Karazin Kharkiv National University, Kharkiv, 61022, Ukraine;
    • 52Department of Genetics and Bioengineering, Faculty of Engineering and Information Technologies, International Burch University, Sarajevo, 71000, Bosnia and Herzegovina;
    • 53Institute of Genetics and Cytology, National Academy of Sciences, Minsk, 220072, Belarus;
    • 54Department of Human Genetics, Radboud University Medical Center, Nijmegen, 106525 GA, The Netherlands;
    • 55Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, 115478, Russia;
    • 56Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, 685000, Russia;
    • 57Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom;
    • 58Integrative Systems Biology Lab, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia;
    • 59Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA;
    • 60ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA;
    • 61Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA;
    • 62The Henry Stewart Group, London, WC1A 2HN, United Kingdom;
    • 63Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia;
    • 64University Hospital of North Norway, Tromsøe, N-9038, Norway;
    • 65Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom;
    • 66Estonian Academy of Sciences, Tallinn, 10130, Estonia
    • 67 These authors contributed equally to this work.
Published March 13, 2015. Vol 25 Issue 4, pp. 459-466. https://doi.org/10.1101/gr.186684.114
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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.

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