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

I'm super excited to share our new paper, out in Advanced Access in Genome Research, A recent bottleneck of Y chromosome diversity coincides with a global change in culture!

Update: you can listen to a local NPR interview with Mark Brodie about this work here: http://kjzz.org/content/116152/does-evolution-favor-rich-and-powerful

In a nutshell:

Graphic designed by Sabine Deviche.

To help explain the paper, check out this ASUnews article by Sandra Leander: https://asunews.asu.edu/20150316-y-chromosome-bottleneck

And, for a longer, visual, explanation, check out this *awesome* infographic made for us by Sabine Deviche.

Graphic designed by Sabine Deviche.

One on the methods we use to study the Y chromosome and mtDNA is the coalescent. Here is a short video explaining the coalescent, and highlighting the difference between census population size (all the people in the population, and the effective population size (those people who left genetic relics in our DNA that we can study today):

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

• Monika Karmin*, 
• Lauri Saag*, 
• Mário Vicente*, 
• Melissa A. Wilson Sayres*, 
• Mari Järve, 
• Ulvi Gerst Talas, 
• Siiri Rootsi, 
• Anne-Mai Ilumäe, 
• Reedik Mägi, 
• Mario Mitt, 
• Luca Pagani, 
• Tarmo Puurand, 
• Zuzana Faltyskova, 
• Florian Clemente, 
• Alexia Cardona, 
• Ene Metspalu, 
• Hovhannes Sahakyan, 
• Bayazit Yunusbayev, 
• Georgi Hudjashov, 
• Michael DeGiorgio, 
• Eva-Liis Loogväli, 
• Christina Eichstaedt, 
• Mikk Eelmets, 
• Gyaneshwer Chaubey, 
• Kristiina Tambets, 
• Sergei Litvinov, 
• Maru Mormina, 
• Yali Xue, 
• Qasim Ayub, 
• Grigor Zoraqi, 
• Thorfinn Sand Korneliussen, 
• Farida Akhatova, 
• Joseph Lachance, 
• Sarah Tishkoff, 
• Kuvat Momynaliev, 
• François-Xavier Ricaut, 
• Pradiptajati Kusuma, 
• Harilanto Razafindrazaka, 
• Denis Pierron, 
• Murray P. Cox, 
• Gazi Nurun Nahar Sultana, 
• Rane Willerslev, 
• Craig Muller, 
• Michael Westaway, 
• David Lambert, 
• Vedrana Skaro, 
• Lejla Kovačević, 
• Shahlo Turdikulova, 
• Dilbar Dalimova, 
• Rita Khusainova, 
• Natalya Trofimova, 
• Vita Akhmetova, 
• Irina Khidiyatova, 
• Daria V. Lichman, 
• Jainagul Isakova, 
• Elvira Pocheshkhova, 
• Zhaxylyk Sabitov, 
• Nikolay A. Barashkov, 
• Pagbajabyn Nymadawa, 
• Evelin Mihailov, 
• Joseph Wee Tien Seng, 
• Irina Evseeva, 
• Andrea Bamberg Migliano, 
• Syafiq Abdullah, 
• George Andriadze, 
• Dragan Primorac, 
• Lubov Atramentova, 
• Olga Utevska, 
• Levon Yepiskoposyan, 
• Damir Marjanović, 
• Alena Kushniarevich, 
• Doron M. Behar, 
• Christian Gilissen, 
• Lisenka Vissers, 
• Joris A. Veltman, 
• Elena Balanovska, 
• Miroslava Derenko, 
• Boris Malyarchuk, 
• Andres Metspalu, 
• Sardana Fedorova, 
• Anders Eriksson, 
• Andrea Manica, 
• Fernando L. Mendez, 
• Tatiana M. Karafet, 
• Krishna R. Veeramah, 
• Neil Bradman, 
• Michael F. Hammer, 
• Ludmila P. Osipova, 
• Oleg Balanovsky, 
• Elza K. Khusnutdinova, 
• Knut Johnsen, 
• Maido Remm, 
• Mark G. Thomas, 
• Chris Tyler-Smith, 
• Peter A. Underhill, 
• Eske Willerslev, 
• Rasmus Nielsen, 
• Mait Metspalu*, 
• Richard Villems*, 
• and Toomas Kivisild*

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, United Kingdom;
5. ⁵Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA;
6. ⁶School of Life Sciences and The Biodesign Institute, Tempe, Arizona, 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, Armenia;
11. ¹¹Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, Russia;
12. ¹²Department of Psychology, University of Auckland, Auckland, 1142, New Zealand;
13. ¹³Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA;
14. ¹⁴Department of Applied Social Sciences, University of Winchester, Winchester, United Kingdom;
15. ¹⁵The Wellcome Trust Sanger Institute, Hinxton, United Kingdom;
16. ¹⁶Center of Molecular Diagnosis and Genetic Research, University Hospital of Obstetrics and Gynecology, Tirana, Albania;
17. ¹⁷Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark;
18. ¹⁸Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia;
19. ¹⁹Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia;
20. ²⁰Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
21. ²¹School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA;
22. ²²Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
23. ²³DNcode Laboratories, Moscow, Russia;
24. ²⁴Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France;
25. ²⁵Eijkman Institute for Molecular Biology, Jakarta, Indonesia;
26. ²⁶Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand;
27. ²⁷Centre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka, Bangladesh;
28. ²⁸Arctic Research Centre, Aarhus University, Aarhus, DK-8000, Denmark;
29. ²⁹Environmental Futures Research Institute, Griffith University, Nathan, Australia;
30. ³⁰Genos, DNA Laboratory, Zagreb, Croatia;
31. ³¹University of Osijek, Medical School, Osijek, Croatia;
32. ³²Centogene AG, Rostock, Germany;
33. ³³Institute of Bioorganic Chemistry, Academy of Science, Tashkent, 100143, Uzbekistan;
34. ³⁴Institute of Cytology and Genetics, Novosibirsk, Russia;
35. ³⁵Institute of Molecular Biology and Medicine, Bishkek, Kyrgyzstan;
36. ³⁶Kuban State Medical University, Krasnodar, Russia;
37. ³⁷L. N. Gumilyov Eurasian National University, Astana, Kazakhstan;
38. ³⁸Center for Life Sciences, Nazarbayev University, Astana, Kazakhstan;
39. ³⁹Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russia;
40. ⁴⁰Laboratory of Molecular Biology, Institute of Natural Sciences, M. K. Ammosov North-Eastern Federal University, Yakutsk, Russia;
41. ⁴¹Mongolian Academy of Medical Sciences, Ulaanbaatar, Mongolia;
42. ⁴²National Cancer Centre Singapore, Singapore;
43. ⁴³Northern State Medical University, Arkhangelsk, Russia;
44. ⁴⁴Anthony Nolan, London, UK;
45. ⁴⁵Department of Anthropology, University College London, London, United Kingdom;
46. ⁴⁶RIPAS Hospital, Bandar Seri Begawan, Brunei;
47. ⁴⁷Scientific-Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Tbilisi, Georgia;
48. ⁴⁸St. Catherine Specialty Hospital, Zabok, Croatia;
49. ⁴⁹Eberly College of Science, Pennsylvania State University, University Park, Pennsylvania, USA;
50. ⁵⁰University of Split, Medical School, Split, Croatia;
51. ⁵¹V. N. Karazin Kharkiv National University, Kharkiv, Ukraine;
52. ⁵²Department of Genetics and Bioengineering, Faculty of Engineering and Information Technologies, International Burch University, Sarajevo, Bosnia and Herzegovina;
53. ⁵³Institute of Genetics and Cytology, National Academy of Sciences, Minsk, Belarus;
54. ⁵⁴Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands;
55. ⁵⁵Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, Russia;
56. ⁵⁶Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia;
57. ⁵⁷Department of Zoology, University of Cambridge, Cambridge, United Kingdom;
58. ⁵⁸Integrative Systems Biology Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia;
59. ⁵⁹Department of Genetics, Stanford University School of Medicine, Stanford, California, USA;
60. ⁶⁰ARL Division of Biotechnology, University of Arizona, Tucson, Arizona, USA;
61. ⁶¹Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA;
62. ⁶²The Henry Stewart Group, London, United Kingdom;
63. ⁶³Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia;
64. ⁶⁴University Hospital of North Norway, Tromsøe, Norway;
65. ⁶⁵Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom;
66. ⁶⁶Estonian Academy of Sciences, Tallinn, Estonia

1. Corresponding authors: tk331@cam.ac.uk, monika.karmin@gmail.com

1. * 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.

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Update: Popular Science articles about this research:

Francie Diep, science journalist, Pacific Stand
http://www.psmag.com/nature-and-technology/17-to-1-reproductive-success

Danielle Paquette, Washington Post
http://www.washingtonpost.com/blogs/wonkblog/wp/2015/03/18/how-wealth-trumped-natural-selection-and-changed-our-ancestors-sex-lives/?hpid=z4

Mark Brodie, KJZZ, NPR radio
http://kjzz.org/content/116152/does-evolution-favor-rich-and-powerful

Estonian paper
http://pluss.postimees.ee/3131333/geenid-naitavad-urgmeeste-voimu

Amanda Marcotte, Slate:
http://www.slate.com/blogs/xx_factor/2015/03/20/the_brutality_of_the_stone_age_only_1_man_had_children_for_every_17_women.html?wpsrc=fol_fb

Janet Feng, IFLS
http://www.iflscience.com/health-and-medicine/women-were-out-reproducing-men-4000-years-ago

reddit
http://www.reddit.com/r/science/comments/2zcudp/wealth_and_power_may_have_played_a_stronger_role/

Genetic Engineering and Biotechnology News
http://www.genengnews.com/gen-news-highlights/male-genes-preserve-survival-of-the-wealthiest-legacy/81251045/

Sarah Kaplan, Washington Post
http://www.washingtonpost.com/news/morning-mix/wp/2015/03/18/how-survival-of-the-fittest-became-survival-of-the-richest/

IANS, The Economic Times
http://economictimes.indiatimes.com/magazines/panache/wealth-behind-decline-in-number-of-reproducing-males-study/articleshow/46609782.cms

Will Parker, Science GoGo
http://www.scienceagogo.com/news/20150216195902.shtml

ANI, ZeeNewsIndia
http://zeenews.india.com/news/sci-tech/male-genetic-diversity-declined-due-to-wealth-power-rather-than-survival-of-fittest_1563084.html

News Staff, Science2.0
http://www.science20.com/news_articles/social_fitness_did_a_genetic_bottleneck_occur_because_of_wealth_and_power-154047

Anthony Rivas, Medical Daily
http://www.medicaldaily.com/did-cultural-shift-influence-human-evolution-how-farming-might-have-changed-genetic-326094