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

Monika Karmin; Lauri Saag; Mário Vicente; Melissa 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 S. 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; Toomas Kivisild

doi:10.1101/gr.186684.114

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

Monika Karmin, Lauri Saag, Mário Vicente, Melissa 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 DeGiorgioEva Liis Loogväli, Christina Eichstaedt, Mikk Eelmets, Gyaneshwer Chaubey, Kristiina Tambets, Sergei Litvinov, Maru Mormina, Yali Xue, Qasim Ayub, Grigor Zoraqi, Thorfinn S. 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, Toomas Kivisild

Life Sciences, School of (SOLS)

Research output: Contribution to journal › Article › peer-review

264 Scopus citations

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.

Original language	English (US)
Pages (from-to)	459-466
Number of pages	8
Journal	Genome research
Volume	25
Issue number	4
DOIs	https://doi.org/10.1101/gr.186684.114
State	Published - Apr 1 2015

ASJC Scopus subject areas

Genetics
Genetics(clinical)

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Karmin, M., Saag, L., Vicente, M., Wilson Sayres, M., Järve, M., Talas, U. G., Rootsi, S., Ilumäe, A. M., Mägi, R., Mitt, M., Pagani, L., Puurand, T., Faltyskova, Z., Clemente, F., Cardona, A., Metspalu, E., Sahakyan, H., Yunusbayev, B., Hudjashov, G., ... Kivisild, T. (2015). A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome research, 25(4), 459-466. https://doi.org/10.1101/gr.186684.114

Karmin, M, Saag, L, Vicente, M, Wilson Sayres, M, Järve, M, Talas, UG, Rootsi, S, Ilumäe, AM, Mägi, R, Mitt, M, Pagani, L, Puurand, T, Faltyskova, Z, Clemente, F, Cardona, A, Metspalu, E, Sahakyan, H, Yunusbayev, B, Hudjashov, G, DeGiorgio, M, Loogväli, EL, Eichstaedt, C, Eelmets, M, Chaubey, G, Tambets, K, Litvinov, S, Mormina, M, Xue, Y, Ayub, Q, Zoraqi, G, Korneliussen, TS, Akhatova, F, Lachance, J, Tishkoff, S, Momynaliev, K, Ricaut, FX, Kusuma, P, Razafindrazaka, H, Pierron, D, Cox, MP, Sultana, GNN, Willerslev, R, Muller, C, Westaway, M, Lambert, D, Skaro, V, Kovačević, L, Turdikulova, S, Dalimova, D, Khusainova, R, Trofimova, N, Akhmetova, V, Khidiyatova, I, Lichman, DV, Isakova, J, Pocheshkhova, E, Sabitov, Z, Barashkov, NA, Nymadawa, P, Mihailov, E, Seng, JWT, Evseeva, I, Migliano, AB, Abdullah, S, Andriadze, G, Primorac, D, Atramentova, L, Utevska, O, Yepiskoposyan, L, Marjanović, D, Kushniarevich, A, Behar, DM, Gilissen, C, Vissers, L, Veltman, JA, Balanovska, E, Derenko, M, Malyarchuk, B, Metspalu, A, Fedorova, S, Eriksson, A, Manica, A, Mendez, FL, Karafet, TM, Veeramah, KR, Bradman, N, Hammer, MF, Osipova, LP, Balanovsky, O, Khusnutdinova, EK, Johnsen, K, Remm, M, Thomas, MG, Tyler-Smith, C, Underhill, PA, Willerslev, E, Nielsen, R, Metspalu, M, Villems, R & Kivisild, T 2015, 'A recent bottleneck of Y chromosome diversity coincides with a global change in culture', Genome research, vol. 25, no. 4, pp. 459-466. https://doi.org/10.1101/gr.186684.114

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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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note = "Publisher Copyright: {\textcopyright} 2015 Karmin et al.",

year = "2015",

month = apr,

day = "1",

doi = "10.1101/gr.186684.114",

language = "English (US)",

volume = "25",

pages = "459--466",

journal = "Genome research",

issn = "1088-9051",

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TY - JOUR

T1 - A recent bottleneck of Y chromosome diversity coincides with a global change in culture

AU - Karmin, Monika

AU - Saag, Lauri

AU - Vicente, Mário

AU - Wilson Sayres, Melissa

AU - Järve, Mari

AU - Talas, Ulvi Gerst

AU - Rootsi, Siiri

AU - Ilumäe, Anne Mai

AU - Mägi, Reedik

AU - Mitt, Mario

AU - Pagani, Luca

AU - Puurand, Tarmo

AU - Faltyskova, Zuzana

AU - Clemente, Florian

AU - Cardona, Alexia

AU - Metspalu, Ene

AU - Sahakyan, Hovhannes

AU - Yunusbayev, Bayazit

AU - Hudjashov, Georgi

AU - DeGiorgio, Michael

AU - Loogväli, Eva Liis

AU - Eichstaedt, Christina

AU - Eelmets, Mikk

AU - Chaubey, Gyaneshwer

AU - Tambets, Kristiina

AU - Litvinov, Sergei

AU - Mormina, Maru

AU - Xue, Yali

AU - Ayub, Qasim

AU - Zoraqi, Grigor

AU - Korneliussen, Thorfinn S.

AU - Akhatova, Farida

AU - Lachance, Joseph

AU - Tishkoff, Sarah

AU - Momynaliev, Kuvat

AU - Ricaut, François Xavier

AU - Kusuma, Pradiptajati

AU - Razafindrazaka, Harilanto

AU - Pierron, Denis

AU - Cox, Murray P.

AU - Sultana, Gazi Nurun Nahar

AU - Willerslev, Rane

AU - Muller, Craig

AU - Westaway, Michael

AU - Lambert, David

AU - Skaro, Vedrana

AU - Kovačević, Lejla

AU - Turdikulova, Shahlo

AU - Dalimova, Dilbar

AU - Khusainova, Rita

AU - Trofimova, Natalya

AU - Akhmetova, Vita

AU - Khidiyatova, Irina

AU - Lichman, Daria V.

AU - Isakova, Jainagul

AU - Pocheshkhova, Elvira

AU - Sabitov, Zhaxylyk

AU - Barashkov, Nikolay A.

AU - Nymadawa, Pagbajabyn

AU - Mihailov, Evelin

AU - Seng, Joseph Wee Tien

AU - Evseeva, Irina

AU - Migliano, Andrea Bamberg

AU - Abdullah, Syafiq

AU - Andriadze, George

AU - Primorac, Dragan

AU - Atramentova, Lubov

AU - Utevska, Olga

AU - Yepiskoposyan, Levon

AU - Marjanović, Damir

AU - Kushniarevich, Alena

AU - Behar, Doron M.

AU - Gilissen, Christian

AU - Vissers, Lisenka

AU - Veltman, Joris A.

AU - Balanovska, Elena

AU - Derenko, Miroslava

AU - Malyarchuk, Boris

AU - Metspalu, Andres

AU - Fedorova, Sardana

AU - Eriksson, Anders

AU - Manica, Andrea

AU - Mendez, Fernando L.

AU - Karafet, Tatiana M.

AU - Veeramah, Krishna R.

AU - Bradman, Neil

AU - Hammer, Michael F.

AU - Osipova, Ludmila P.

AU - Balanovsky, Oleg

AU - Khusnutdinova, Elza K.

AU - Johnsen, Knut

AU - Remm, Maido

AU - Thomas, Mark G.

AU - Tyler-Smith, Chris

AU - Underhill, Peter A.

AU - Willerslev, Eske

AU - Nielsen, Rasmus

AU - Metspalu, Mait

AU - Villems, Richard

AU - Kivisild, Toomas

PY - 2015/4/1

Y1 - 2015/4/1

N2 - 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.

AB - 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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U2 - 10.1101/gr.186684.114

DO - 10.1101/gr.186684.114

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AN - SCOPUS:84927713385

SN - 1088-9051

VL - 25

SP - 459

EP - 466

JO - Genome research

JF - Genome research

IS - 4

ER -

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

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