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Genome Res. 2015 Apr;25(4):459-66. doi: 10.1101/gr.186684.114. Epub 2015 Mar 13.

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

Author information

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

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.

PMID:
25770088
PMCID:
PMC4381518
DOI:
10.1101/gr.186684.114
[Indexed for MEDLINE]
Free PMC Article

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