A recent bottleneck of Y chromosome diversity coincides with a global change in culture - PubMed (original) (raw)

doi: 10.1101/gr.186684.114. Epub 2015 Mar 13.

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

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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.

© 2015 Karmin et al.; Published by Cold Spring Harbor Laboratory Press.

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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.

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