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. 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

Monika Karmin  1 , Lauri Saag  2 , Mário Vicente  3 , Melissa A Wilson Sayres  4 , Mari Järve  5 , Ulvi Gerst Talas  6 , Siiri Rootsi  5 , Anne-Mai Ilumäe  7 , Reedik Mägi  8 , Mario Mitt  9 , Luca Pagani  3 , Tarmo Puurand  6 , Zuzana Faltyskova  3 , Florian Clemente  3 , Alexia Cardona  3 , Ene Metspalu  7 , Hovhannes Sahakyan  10 , Bayazit Yunusbayev  11 , Georgi Hudjashov  12 , Michael DeGiorgio  13 , Eva-Liis Loogväli  5 , Christina Eichstaedt  3 , Mikk Eelmets  14 , Gyaneshwer Chaubey  5 , Kristiina Tambets  5 , Sergei Litvinov  11 , Maru Mormina  15 , Yali Xue  16 , Qasim Ayub  16 , Grigor Zoraqi  17 , Thorfinn Sand Korneliussen  18 , Farida Akhatova  19 , Joseph Lachance  20 , Sarah Tishkoff  21 , Kuvat Momynaliev  22 , François-Xavier Ricaut  23 , Pradiptajati Kusuma  24 , Harilanto Razafindrazaka  23 , Denis Pierron  23 , Murray P Cox  25 , Gazi Nurun Nahar Sultana  26 , Rane Willerslev  27 , Craig Muller  28 , Michael Westaway  29 , David Lambert  29 , Vedrana Skaro  30 , Lejla Kovačevic  31 , Shahlo Turdikulova  32 , Dilbar Dalimova  32 , Rita Khusainova  33 , Natalya Trofimova  11 , Vita Akhmetova  34 , Irina Khidiyatova  33 , Daria V Lichman  35 , Jainagul Isakova  36 , Elvira Pocheshkhova  37 , Zhaxylyk Sabitov  38 , Nikolay A Barashkov  39 , Pagbajabyn Nymadawa  40 , Evelin Mihailov  8 , Joseph Wee Tien Seng  41 , Irina Evseeva  42 , Andrea Bamberg Migliano  43 , Syafiq Abdullah  44 , George Andriadze  45 , Dragan Primorac  46 , Lubov Atramentova  47 , Olga Utevska  47 , Levon Yepiskoposyan  48 , Damir Marjanovic  49 , Alena Kushniarevich  50 , Doron M Behar  5 , Christian Gilissen  51 , Lisenka Vissers  51 , Joris A Veltman  51 , Elena Balanovska  52 , Miroslava Derenko  53 , Boris Malyarchuk  53 , Andres Metspalu  8 , Sardana Fedorova  39 , Anders Eriksson  54 , Andrea Manica  55 , Fernando L Mendez  56 , Tatiana M Karafet  57 , Krishna R Veeramah  58 , Neil Bradman  59 , Michael F Hammer  57 , Ludmila P Osipova  35 , Oleg Balanovsky  60 , Elza K Khusnutdinova  33 , Knut Johnsen  61 , Maido Remm  6 , Mark G Thomas  62 , Chris Tyler-Smith  16 , Peter A Underhill  56 , Eske Willerslev  28 , Rasmus Nielsen  63 , Mait Metspalu  7 , Richard Villems  64 , Toomas Kivisild  65
Affiliations

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

Monika Karmin et al. Genome Res. 2015 Apr.

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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Figures

Figure 1.
Figure 1.
The phylogenetic tree of 456 whole Y chromosome sequences and a map of sampling locations. The phylogenetic tree is reconstructed using BEAST. Clades coalescing within 10% of the overall depth of the tree have been collapsed. Only main haplogroup labels are shown (details are provided in Supplemental Information 6). Colors indicate geographic origin of samples (Supplemental Table S1), and fill proportions of the collapsed clades represent the proportion of samples from a given region. Asterisk (*) marks the inclusion of samples from Caucasus area. Personal Genomes Project (http://www.personalgenomes.org) samples of unknown and mixed geographic/ethnic origin are shown in black. The proposed structure of Y chromosome haplogroup naming (Supplemental Table S5) is given in Roman numbers on the y-axis.
Figure 2.
Figure 2.
Cumulative Bayesian skyline plots of Y chromosome and mtDNA diversity by world regions. The red dashed lines highlight the horizons of 10 kya and 50 kya. Individual plots for each region are presented in Supplemental Figure S4A.
See this image and copyright information in PMC

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