A recent bottleneck of Y chromosome diversity coincides with a global change in culture
- Monika Karmin1,2,67,
- Lauri Saag1,3,67,
- Mário Vicente4,67,
- Melissa A. Wilson Sayres5,6,67,
- Mari Järve1,
- Ulvi Gerst Talas7,
- Siiri Rootsi1,
- Anne-Mai Ilumäe1,2,
- Reedik Mägi8,
- Mario Mitt8,9,
- Luca Pagani4,
- Tarmo Puurand7,
- Zuzana Faltyskova4,
- Florian Clemente4,
- Alexia Cardona4,
- Ene Metspalu1,2,
- Hovhannes Sahakyan1,10,
- Bayazit Yunusbayev1,11,
- Georgi Hudjashov1,12,
- Michael DeGiorgio13,
- Eva-Liis Loogväli1,
- Christina Eichstaedt4,
- Mikk Eelmets1,7,
- Gyaneshwer Chaubey1,
- Kristiina Tambets1,
- Sergei Litvinov1,11,
- Maru Mormina14,
- Yali Xue15,
- Qasim Ayub15,
- Grigor Zoraqi16,
- Thorfinn Sand Korneliussen5,17,
- Farida Akhatova18,19,
- Joseph Lachance20,21,
- Sarah Tishkoff20,22,
- Kuvat Momynaliev23,
- François-Xavier Ricaut24,
- Pradiptajati Kusuma24,25,
- Harilanto Razafindrazaka24,
- Denis Pierron24,
- Murray P. Cox26,
- Gazi Nurun Nahar Sultana27,
- Rane Willerslev28,
- Craig Muller17,
- Michael Westaway29,
- David Lambert29,
- Vedrana Skaro30,31,
- Lejla Kovačević32,
- Shahlo Turdikulova33,
- Dilbar Dalimova33,
- Rita Khusainova11,18,
- Natalya Trofimova1,11,
- Vita Akhmetova11,
- Irina Khidiyatova11,18,
- Daria V. Lichman34,
- Jainagul Isakova35,
- Elvira Pocheshkhova36,
- Zhaxylyk Sabitov37,38,
- Nikolay A. Barashkov39,40,
- Pagbajabyn Nymadawa41,
- Evelin Mihailov8,
- Joseph Wee Tien Seng42,
- Irina Evseeva43,44,
- Andrea Bamberg Migliano45,
- Syafiq Abdullah46,
- George Andriadze47,
- Dragan Primorac31,48,49,50,
- Lubov Atramentova51,
- Olga Utevska51,
- Levon Yepiskoposyan10,
- Damir Marjanović30,52,
- Alena Kushniarevich1,53,
- Doron M. Behar1,
- Christian Gilissen54,
- Lisenka Vissers54,
- Joris A. Veltman54,
- Elena Balanovska55,
- Miroslava Derenko56,
- Boris Malyarchuk56,
- Andres Metspalu8,
- Sardana Fedorova39,40,
- Anders Eriksson57,58,
- Andrea Manica57,
- Fernando L. Mendez59,
- Tatiana M. Karafet60,
- Krishna R. Veeramah61,
- Neil Bradman62,
- Michael F. Hammer60,
- Ludmila P. Osipova34,
- Oleg Balanovsky55,63,
- Elza K. Khusnutdinova11,18,
- Knut Johnsen64,
- Maido Remm7,
- Mark G. Thomas65,
- Chris Tyler-Smith15,
- Peter A. Underhill59,
- Eske Willerslev17,
- Rasmus Nielsen5,
- Mait Metspalu1,2,67,
- Richard Villems1,2,66,67 and
- Toomas Kivisild4,1,67
- 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, United Kingdom;
- 5Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA;
- 6School of Life Sciences and The Biodesign Institute, Tempe, Arizona, 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, Armenia;
- 11Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, Russia;
- 12Department of Psychology, University of Auckland, Auckland, 1142, New Zealand;
- 13Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA;
- 14Department of Applied Social Sciences, University of Winchester, Winchester, United Kingdom;
- 15The Wellcome Trust Sanger Institute, Hinxton, United Kingdom;
- 16Center of Molecular Diagnosis and Genetic Research, University Hospital of Obstetrics and Gynecology, Tirana, Albania;
- 17Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark;
- 18Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia;
- 19Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia;
- 20Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
- 21School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA;
- 22Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
- 23DNcode Laboratories, Moscow, Russia;
- 24Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France;
- 25Eijkman Institute for Molecular Biology, Jakarta, Indonesia;
- 26Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand;
- 27Centre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka, Bangladesh;
- 28Arctic Research Centre, Aarhus University, Aarhus, DK-8000, Denmark;
- 29Environmental Futures Research Institute, Griffith University, Nathan, Australia;
- 30Genos, DNA Laboratory, Zagreb, Croatia;
- 31University of Osijek, Medical School, Osijek, Croatia;
- 32Centogene AG, Rostock, Germany;
- 33Institute of Bioorganic Chemistry, Academy of Science, Tashkent, 100143, Uzbekistan;
- 34Institute of Cytology and Genetics, Novosibirsk, Russia;
- 35Institute of Molecular Biology and Medicine, Bishkek, Kyrgyzstan;
- 36Kuban State Medical University, Krasnodar, Russia;
- 37L. N. Gumilyov Eurasian National University, Astana, Kazakhstan;
- 38Center for Life Sciences, Nazarbayev University, Astana, Kazakhstan;
- 39Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russia;
- 40Laboratory of Molecular Biology, Institute of Natural Sciences, M. K. Ammosov North-Eastern Federal University, Yakutsk, Russia;
- 41Mongolian Academy of Medical Sciences, Ulaanbaatar, Mongolia;
- 42National Cancer Centre Singapore, Singapore;
- 43Northern State Medical University, Arkhangelsk, Russia;
- 44Anthony Nolan, London, UK;
- 45Department of Anthropology, University College London, London, United Kingdom;
- 46RIPAS Hospital, Bandar Seri Begawan, Brunei;
- 47Scientific-Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Tbilisi, Georgia;
- 48St. Catherine Specialty Hospital, Zabok, Croatia;
- 49Eberly College of Science, Pennsylvania State University, University Park, Pennsylvania, USA;
- 50University of Split, Medical School, Split, Croatia;
- 51V. N. Karazin Kharkiv National University, Kharkiv, Ukraine;
- 52Department of Genetics and Bioengineering, Faculty of Engineering and Information Technologies, International Burch University, Sarajevo, Bosnia and Herzegovina;
- 53Institute of Genetics and Cytology, National Academy of Sciences, Minsk, Belarus;
- 54Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands;
- 55Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, Russia;
- 56Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia;
- 57Department of Zoology, University of Cambridge, Cambridge, United Kingdom;
- 58Integrative Systems Biology Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia;
- 59Department of Genetics, Stanford University School of Medicine, Stanford, California, USA;
- 60ARL Division of Biotechnology, University of Arizona, Tucson, Arizona, USA;
- 61Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA;
- 62The Henry Stewart Group, London, United Kingdom;
- 63Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia;
- 64University Hospital of North Norway, Tromsøe, Norway;
- 65Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom;
- 66Estonian Academy of Sciences, Tallinn, Estonia
- Corresponding authors: tk331{at}cam.ac.uk, monika.karmin{at}gmail.com
-
↵67 These authors contributed equally to this work.
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.186684.114.
- Received November 6, 2014.
- Accepted February 13, 2015.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
