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

  1. Toomas Kivisild1,4,67
  1. 1Estonian Biocentre, Tartu, 51010, Estonia;
  2. 2Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
  3. 3Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51010, Estonia;
  4. 4Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;
  5. 5Department of Integrative Biology, University of California Berkeley, Berkeley, California 94720, USA;
  6. 6School of Life Sciences and The Biodesign Institute, Tempe, Arizona 85287-5001, USA;
  7. 7Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
  8. 8Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia;
  9. 9Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
  10. 10Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, 0014, Armenia;
  11. 11Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia;
  12. 12Department of Psychology, University of Auckland, Auckland, 1142, New Zealand;
  13. 13Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA;
  14. 14Department of Applied Social Sciences, University of Winchester, Winchester, SO22 4NR, United Kingdom;
  15. 15The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom;
  16. 16Center of Molecular Diagnosis and Genetic Research, University Hospital of Obstetrics and Gynecology, Tirana, ALB1005, Albania;
  17. 17Center for GeoGenetics, University of Copenhagen, Copenhagen, DK-1350, Denmark;
  18. 18Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia;
  19. 19Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russia;
  20. 20Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6145, USA;
  21. 21School of Biology, Georgia Institute of Technology, Atlanta, 30332, Georgia, USA;
  22. 22Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6313, USA;
  23. 23DNcode Laboratories, Moscow, 119992, Russia;
  24. 24Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France;
  25. 25Eijkman Institute for Molecular Biology, Jakarta, 10430, Indonesia;
  26. 26Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand;
  27. 27Centre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka, Dhaka-1000, Bangladesh;
  28. 28Arctic Research Centre, Aarhus University, Aarhus, DK-8000, Denmark;
  29. 29Environmental Futures Research Institute, Griffith University, Nathan, 4111, Australia;
  30. 30Genos, DNA Laboratory, Zagreb, 10000, Croatia;
  31. 31University of Osijek, Medical School, Osijek, 31000, Croatia;
  32. 32Centogene AG, Rostock, 18057, Germany;
  33. 33Institute of Bioorganic Chemistry, Academy of Science, Tashkent, 100143, Uzbekistan;
  34. 34Institute of Cytology and Genetics, Novosibirsk, 630090, Russia;
  35. 35Institute of Molecular Biology and Medicine, Bishkek, 720040, Kyrgyzstan;
  36. 36Kuban State Medical University, Krasnodar, 350063, Russia;
  37. 37L.N. Gumilyov Eurasian National University, Astana, 010008, Kazakhstan;
  38. 38Center for Life Sciences, Nazarbayev University, Astana, 010000, Kazakhstan;
  39. 39Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, 677010, Russia;
  40. 40Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, 677000, Russia;
  41. 41Mongolian Academy of Medical Sciences, Ulaanbaatar, 210620, Mongolia;
  42. 42National Cancer Centre Singapore, 169610, Singapore;
  43. 43Northern State Medical University, Arkhangelsk, 163000, Russia;
  44. 44Anthony Nolan, London, NW3 2NU, United Kingdom;
  45. 45Department of Anthropology, University College London, London, WC1E 6BT, United Kingdom;
  46. 46RIPAS Hospital, Bandar Seri Begawan, BE1518, Brunei;
  47. 47Scientific-Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Tbilisi, 0162, Georgia;
  48. 48St. Catherine Specialty Hospital, Zabok, 49210, Croatia;
  49. 49Eberly College of Science, Pennsylvania State University, University Park, Pennsylvania 16802, USA;
  50. 50University of Split, Medical School, Split, 21000, Croatia;
  51. 51V.N. Karazin Kharkiv National University, Kharkiv, 61022, Ukraine;
  52. 52Department of Genetics and Bioengineering, Faculty of Engineering and Information Technologies, International Burch University, Sarajevo, 71000, Bosnia and Herzegovina;
  53. 53Institute of Genetics and Cytology, National Academy of Sciences, Minsk, 220072, Belarus;
  54. 54Department of Human Genetics, Radboud University Medical Center, Nijmegen, 106525 GA, The Netherlands;
  55. 55Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, 115478, Russia;
  56. 56Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, 685000, Russia;
  57. 57Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom;
  58. 58Integrative Systems Biology Lab, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia;
  59. 59Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA;
  60. 60ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA;
  61. 61Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA;
  62. 62The Henry Stewart Group, London, WC1A 2HN, United Kingdom;
  63. 63Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia;
  64. 64University Hospital of North Norway, Tromsøe, N-9038, Norway;
  65. 65Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom;
  66. 66Estonian Academy of Sciences, Tallinn, 10130, Estonia
  1. Corresponding authors: tk331{at}cam.ac.uk, monika.karmin{at}gmail.com

  1. ↵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

  • 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/.

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  1. Published in Advance March 13, 2015, doi: 10.1101/gr.186684.114 Genome Res. 25: 459-466 © 2015 Karmin et al.; Published by Cold Spring Harbor Laboratory Press

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