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 Kovačevic´; 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 Marjanovic´; 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 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 DeGiorgioEva-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 Kovačevic´, 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 Marjanovic´, 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

Biological, Environmental Sciences and Engineering

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

280 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 - Mar 13 2015

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01

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10.1101/gr.186684.114

https://repository.kaust.edu.sa/bitstream/10754/550413/1/Genome%20Res.-2015-Karmin-gr.186684.114.pdf

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Karmin, M., Saag, L., Vicente, M., Sayres, M. A. W., 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

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title = "A recent bottleneck of Y chromosome diversity coincides with a global change in culture",

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.",

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

note = "KAUST Repository Item: Exported on 2020-10-01",

year = "2015",

month = mar,

day = "13",

doi = "10.1101/gr.186684.114",

language = "English (US)",

volume = "25",

pages = "459--466",

journal = "Genome Research",

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publisher = "Cold Spring Harbor Laboratory Press",

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Karmin, M, Saag, L, Vicente, M, Sayres, MAW, Järve, M, Talas, UG, 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, DeGiorgio, M, Loogväli, E-L, 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, F-X, Kusuma, P, Razafindrazaka, H, Pierron, D, Cox, MP, Sultana, GNN, Willerslev, R, Muller, C, Westaway, M, Lambert, D, Skaro, V, Kovačevic´, 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, Marjanovic´, 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

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 - Sayres, Melissa A. Wilson

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 Sand

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 - Kovačevic´, 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 - Marjanovic´, 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

N1 - KAUST Repository Item: Exported on 2020-10-01

PY - 2015/3/13

Y1 - 2015/3/13

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.

UR - http://hdl.handle.net/10754/550413

UR - http://genome.cshlp.org/lookup/doi/10.1101/gr.186684.114

UR - http://www.scopus.com/inward/record.url?scp=84927713385&partnerID=8YFLogxK

U2 - 10.1101/gr.186684.114

DO - 10.1101/gr.186684.114

M3 - Article

C2 - 25770088

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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