Genomic analyses inform on migration events during the peopling of Eurasia

Luca Pagani; Daniel John Lawson; Evelyn Jagoda; Alexander Mörseburg; Anders Eriksson; Mario Mitt; Florian Clemente; Georgi Hudjashov; Michael DeGiorgio; Lauri Saag; Jeffrey D. Wall; Alexia Cardona; Reedik Mägi; Melissa A. Wilson Sayres; Sarah Kaewert; Charlotte Inchley; Christiana L. Scheib; Mari Järve; Monika Karmin; Guy S. Jacobs; Tiago Antao; Florin Mircea Iliescu; Alena Kushniarevich; Qasim Ayub; Chris Tyler-Smith; Yali Xue; Bayazit Yunusbayev; Kristiina Tambets; Chandana Basu Mallick; Lehti Saag; Elvira Pocheshkhova; George Andriadze; Craig Muller; Michael C. Westaway; David M. Lambert; Grigor Zoraqi; Shahlo Turdikulova; Dilbar Dalimova; Zhaxylyk Sabitov; Gazi Nurun Nahar Sultana; Joseph Lachance; Sarah Tishkoff; Kuvat Momynaliev; Jainagul Isakova; Larisa D. Damba; Marina Gubina; Pagbajabyn Nymadawa; Irina Evseeva; Lubov Atramentova; Olga Utevska; François-Xavier Ricaut; Nicolas Brucato; Herawati Sudoyo; Thierry Letellier; Murray P. Cox; Nikolay A. Barashkov; Vedrana Škaro; Lejla Mulahasanovic´; Dragan Primorac; Hovhannes Sahakyan; Maru Mormina; Christina A. Eichstaedt; Daria V. Lichman; Syafiq Abdullah; Gyaneshwer Chaubey; Joseph T. S. Wee; Evelin Mihailov; Alexandra Karunas; Sergei Litvinov; Rita Khusainova; Natalya Ekomasova; Vita Akhmetova; Irina Khidiyatova; Damir Marjanović; Levon Yepiskoposyan; Doron M. Behar; Elena Balanovska; Andres Metspalu; Miroslava Derenko; Boris Malyarchuk; Mikhail Voevoda; Sardana A. Fedorova; Ludmila P. Osipova; Marta Mirazón Lahr; Pascale Gerbault; Matthew Leavesley; Andrea Bamberg Migliano; Michael Petraglia; Oleg Balanovsky; Elza K. Khusnutdinova; Ene Metspalu; Mark G. Thomas; Andrea Manica; Rasmus Nielsen; Richard Villems; Eske Willerslev; Toomas Kivisild; Mait Metspalu

doi:10.1038/nature19792

Genomic analyses inform on migration events during the peopling of Eurasia

Luca Pagani, Daniel John Lawson, Evelyn Jagoda, Alexander Mörseburg, Anders Eriksson, Mario Mitt, Florian Clemente, Georgi Hudjashov, Michael DeGiorgio, Lauri Saag, Jeffrey D. Wall, Alexia Cardona, Reedik Mägi, Melissa A. Wilson Sayres, Sarah Kaewert, Charlotte Inchley, Christiana L. Scheib, Mari Järve, Monika Karmin, Guy S. JacobsTiago Antao, Florin Mircea Iliescu, Alena Kushniarevich, Qasim Ayub, Chris Tyler-Smith, Yali Xue, Bayazit Yunusbayev, Kristiina Tambets, Chandana Basu Mallick, Lehti Saag, Elvira Pocheshkhova, George Andriadze, Craig Muller, Michael C. Westaway, David M. Lambert, Grigor Zoraqi, Shahlo Turdikulova, Dilbar Dalimova, Zhaxylyk Sabitov, Gazi Nurun Nahar Sultana, Joseph Lachance, Sarah Tishkoff, Kuvat Momynaliev, Jainagul Isakova, Larisa D. Damba, Marina Gubina, Pagbajabyn Nymadawa, Irina Evseeva, Lubov Atramentova, Olga Utevska, François-Xavier Ricaut, Nicolas Brucato, Herawati Sudoyo, Thierry Letellier, Murray P. Cox, Nikolay A. Barashkov, Vedrana Škaro, Lejla Mulahasanovic´, Dragan Primorac, Hovhannes Sahakyan, Maru Mormina, Christina A. Eichstaedt, Daria V. Lichman, Syafiq Abdullah, Gyaneshwer Chaubey, Joseph T. S. Wee, Evelin Mihailov, Alexandra Karunas, Sergei Litvinov, Rita Khusainova, Natalya Ekomasova, Vita Akhmetova, Irina Khidiyatova, Damir Marjanović, Levon Yepiskoposyan, Doron M. Behar, Elena Balanovska, Andres Metspalu, Miroslava Derenko, Boris Malyarchuk, Mikhail Voevoda, Sardana A. Fedorova, Ludmila P. Osipova, Marta Mirazón Lahr, Pascale Gerbault, Matthew Leavesley, Andrea Bamberg Migliano, Michael Petraglia, Oleg Balanovsky, Elza K. Khusnutdinova, Ene Metspalu, Mark G. Thomas, Andrea Manica, Rasmus Nielsen, Richard Villems, Eske Willerslev, Toomas Kivisild, Mait Metspalu

Biological, Environmental Sciences and Engineering

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

287 Scopus citations

Abstract

High-Coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long-and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago. © 2016 Macmillan Publishers Limited, part of Springer Nature.

Original language	English (US)
Pages (from-to)	238-242
Number of pages	5
Journal	Nature
Volume	538
Issue number	7624
DOIs	https://doi.org/10.1038/nature19792
State	Published - Sep 21 2016

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: Support was provided by: Estonian Research Infrastructure Roadmap grant no 3.2.0304.11-0312; Australian Research Council Discovery grants (DP110102635 and DP140101405) (D.M.L., M.W. and E.W.); Danish National Research Foundation; the Lundbeck Foundation and KU2016 (E.W.); ERC Starting Investigator grant (FP7 - 261213) (T.K.); Estonian Research Council grant PUT766 (G.C. and M.K.); EU European Regional Development Fund through the Centre of Excellence in Genomics to Estonian Biocentre (R.V.; M.Me. and A.Me.), and Centre of Excellence for Genomics and Translational Medicine Project No. 2014-2020.4.01.15-0012 to EGC of UT (A.Me.) and EBC (M.Me.); Estonian Institutional Research grant IUT24-1 (L.S., M.J., A.K., B.Y., K.T., C.B.M., Le.S., H.Sa., S.L., D.M.B., E.M., R.V., G.H., M.K., G.C., T.K. and M.Me.) and IUT20-60 (A.Me.); French Ministry of Foreign and European Affairs and French ANR grant number ANR-14-CE31-0013-01 (F.-X.R.); Gates Cambridge Trust Funding (E.J.); ICG SB RAS (No. VI.58.1.1) (D.V.L.); Leverhulme Programme grant no. RP2011-R-045 (A.B.M., P.G. and M.G.T.); Ministry of Education and Science of Russia; Project 6.656.2014/K (S.A.F.); NEFREX grant funded by the European Union (People Marie Curie Actions; International Research Staff Exchange Scheme; call FP7-PEOPLE-2012-IRSES-number 318979) (M.Me., G.H. and M.K.); NIH grants 5DP1ES022577 05, 1R01DK104339-01, and 1R01GM113657-01 (S.Tis.); Russian Foundation for Basic Research (grant N 14-06-00180a) (M.G.); Russian Foundation for Basic Research; grant 16-04-00890 (O.B. and E.B); Russian Science Foundation grant 14-14-00827 (O.B.); The Russian Foundation for Basic Research (14-04-00725-a), The Russian Humanitarian Scientific Foundation (13-11-02014) and the Program of the Basic Research of the RAS Presidium “Biological diversity” (E.K.K.); Wellcome Trust and Royal Society grant WT104125AIA & the Bristol Advanced Computing Research Centre (http://www.bris.ac.uk/acrc/) (D.J.L.); Wellcome Trust grant 098051 (Q.A.; C.T.-S. and Y.X.); Wellcome Trust Senior Research Fellowship grant 100719/Z/12/Z (M.G.T.); Young Explorers Grant from the National Geographic Society (8900-11) (C.A.E.); ERC Consolidator Grant 647787 ‘LocalAdaptatio’ (A.Ma.); Program of the RAS Presidium “Basic research for the development of the Russian Arctic” (B.M.); Russian Foundation for Basic Research grant 16-06-00303 (E.B.); a Rutherford Fellowship (RDF-10-MAU-001) from the Royal Society of New Zealand (M.P.C.).

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10.1038/nature19792

Cite this

Pagani, L., Lawson, D. J., Jagoda, E., Mörseburg, A., Eriksson, A., Mitt, M., Clemente, F., Hudjashov, G., DeGiorgio, M., Saag, L., Wall, J. D., Cardona, A., Mägi, R., Sayres, M. A. W., Kaewert, S., Inchley, C., Scheib, C. L., Järve, M., Karmin, M., ... Metspalu, M. (2016). Genomic analyses inform on migration events during the peopling of Eurasia. Nature, 538(7624), 238-242. https://doi.org/10.1038/nature19792

@article{c31a7cdaac274b70b7ff28f5e34d873f,

title = "Genomic analyses inform on migration events during the peopling of Eurasia",

abstract = "High-Coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long-and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago. {\textcopyright} 2016 Macmillan Publishers Limited, part of Springer Nature.",

author = "Luca Pagani and Lawson, {Daniel John} and Evelyn Jagoda and Alexander M{\"o}rseburg and Anders Eriksson and Mario Mitt and Florian Clemente and Georgi Hudjashov and Michael DeGiorgio and Lauri Saag and Wall, {Jeffrey D.} and Alexia Cardona and Reedik M{\"a}gi and Sayres, {Melissa A. Wilson} and Sarah Kaewert and Charlotte Inchley and Scheib, {Christiana L.} and Mari J{\"a}rve and Monika Karmin and Jacobs, {Guy S.} and Tiago Antao and Iliescu, {Florin Mircea} and Alena Kushniarevich and Qasim Ayub and Chris Tyler-Smith and Yali Xue and Bayazit Yunusbayev and Kristiina Tambets and Mallick, {Chandana Basu} and Lehti Saag and Elvira Pocheshkhova and George Andriadze and Craig Muller and Westaway, {Michael C.} and Lambert, {David M.} and Grigor Zoraqi and Shahlo Turdikulova and Dilbar Dalimova and Zhaxylyk Sabitov and Sultana, {Gazi Nurun Nahar} and Joseph Lachance and Sarah Tishkoff and Kuvat Momynaliev and Jainagul Isakova and Damba, {Larisa D.} and Marina Gubina and Pagbajabyn Nymadawa and Irina Evseeva and Lubov Atramentova and Olga Utevska and Fran{\c c}ois-Xavier Ricaut and Nicolas Brucato and Herawati Sudoyo and Thierry Letellier and Cox, {Murray P.} and Barashkov, {Nikolay A.} and Vedrana {\v S}karo and Lejla Mulahasanovic´ and Dragan Primorac and Hovhannes Sahakyan and Maru Mormina and Eichstaedt, {Christina A.} and Lichman, {Daria V.} and Syafiq Abdullah and Gyaneshwer Chaubey and Wee, {Joseph T. S.} and Evelin Mihailov and Alexandra Karunas and Sergei Litvinov and Rita Khusainova and Natalya Ekomasova and Vita Akhmetova and Irina Khidiyatova and Damir Marjanovi{\'c} and Levon Yepiskoposyan and Behar, {Doron M.} and Elena Balanovska and Andres Metspalu and Miroslava Derenko and Boris Malyarchuk and Mikhail Voevoda and Fedorova, {Sardana A.} and Osipova, {Ludmila P.} and Lahr, {Marta Miraz{\'o}n} and Pascale Gerbault and Matthew Leavesley and Migliano, {Andrea Bamberg} and Michael Petraglia and Oleg Balanovsky and Khusnutdinova, {Elza K.} and Ene Metspalu and Thomas, {Mark G.} and Andrea Manica and Rasmus Nielsen and Richard Villems and Eske Willerslev and Toomas Kivisild and Mait Metspalu",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: Support was provided by: Estonian Research Infrastructure Roadmap grant no 3.2.0304.11-0312; Australian Research Council Discovery grants (DP110102635 and DP140101405) (D.M.L., M.W. and E.W.); Danish National Research Foundation; the Lundbeck Foundation and KU2016 (E.W.); ERC Starting Investigator grant (FP7 - 261213) (T.K.); Estonian Research Council grant PUT766 (G.C. and M.K.); EU European Regional Development Fund through the Centre of Excellence in Genomics to Estonian Biocentre (R.V.; M.Me. and A.Me.), and Centre of Excellence for Genomics and Translational Medicine Project No. 2014-2020.4.01.15-0012 to EGC of UT (A.Me.) and EBC (M.Me.); Estonian Institutional Research grant IUT24-1 (L.S., M.J., A.K., B.Y., K.T., C.B.M., Le.S., H.Sa., S.L., D.M.B., E.M., R.V., G.H., M.K., G.C., T.K. and M.Me.) and IUT20-60 (A.Me.); French Ministry of Foreign and European Affairs and French ANR grant number ANR-14-CE31-0013-01 (F.-X.R.); Gates Cambridge Trust Funding (E.J.); ICG SB RAS (No. VI.58.1.1) (D.V.L.); Leverhulme Programme grant no. RP2011-R-045 (A.B.M., P.G. and M.G.T.); Ministry of Education and Science of Russia; Project 6.656.2014/K (S.A.F.); NEFREX grant funded by the European Union (People Marie Curie Actions; International Research Staff Exchange Scheme; call FP7-PEOPLE-2012-IRSES-number 318979) (M.Me., G.H. and M.K.); NIH grants 5DP1ES022577 05, 1R01DK104339-01, and 1R01GM113657-01 (S.Tis.); Russian Foundation for Basic Research (grant N 14-06-00180a) (M.G.); Russian Foundation for Basic Research; grant 16-04-00890 (O.B. and E.B); Russian Science Foundation grant 14-14-00827 (O.B.); The Russian Foundation for Basic Research (14-04-00725-a), The Russian Humanitarian Scientific Foundation (13-11-02014) and the Program of the Basic Research of the RAS Presidium “Biological diversity” (E.K.K.); Wellcome Trust and Royal Society grant WT104125AIA & the Bristol Advanced Computing Research Centre (http://www.bris.ac.uk/acrc/) (D.J.L.); Wellcome Trust grant 098051 (Q.A.; C.T.-S. and Y.X.); Wellcome Trust Senior Research Fellowship grant 100719/Z/12/Z (M.G.T.); Young Explorers Grant from the National Geographic Society (8900-11) (C.A.E.); ERC Consolidator Grant 647787 {\textquoteleft}LocalAdaptatio{\textquoteright} (A.Ma.); Program of the RAS Presidium “Basic research for the development of the Russian Arctic” (B.M.); Russian Foundation for Basic Research grant 16-06-00303 (E.B.); a Rutherford Fellowship (RDF-10-MAU-001) from the Royal Society of New Zealand (M.P.C.).",

year = "2016",

month = sep,

day = "21",

doi = "10.1038/nature19792",

language = "English (US)",

volume = "538",

pages = "238--242",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

number = "7624",

}

Pagani, L, Lawson, DJ, Jagoda, E, Mörseburg, A, Eriksson, A, Mitt, M, Clemente, F, Hudjashov, G, DeGiorgio, M, Saag, L, Wall, JD, Cardona, A, Mägi, R, Sayres, MAW, Kaewert, S, Inchley, C, Scheib, CL, Järve, M, Karmin, M, Jacobs, GS, Antao, T, Iliescu, FM, Kushniarevich, A, Ayub, Q, Tyler-Smith, C, Xue, Y, Yunusbayev, B, Tambets, K, Mallick, CB, Saag, L, Pocheshkhova, E, Andriadze, G, Muller, C, Westaway, MC, Lambert, DM, Zoraqi, G, Turdikulova, S, Dalimova, D, Sabitov, Z, Sultana, GNN, Lachance, J, Tishkoff, S, Momynaliev, K, Isakova, J, Damba, LD, Gubina, M, Nymadawa, P, Evseeva, I, Atramentova, L, Utevska, O, Ricaut, F-X, Brucato, N, Sudoyo, H, Letellier, T, Cox, MP, Barashkov, NA, Škaro, V, Mulahasanovic´, L, Primorac, D, Sahakyan, H, Mormina, M, Eichstaedt, CA, Lichman, DV, Abdullah, S, Chaubey, G, Wee, JTS, Mihailov, E, Karunas, A, Litvinov, S, Khusainova, R, Ekomasova, N, Akhmetova, V, Khidiyatova, I, Marjanović, D, Yepiskoposyan, L, Behar, DM, Balanovska, E, Metspalu, A, Derenko, M, Malyarchuk, B, Voevoda, M, Fedorova, SA, Osipova, LP, Lahr, MM, Gerbault, P, Leavesley, M, Migliano, AB, Petraglia, M, Balanovsky, O, Khusnutdinova, EK, Metspalu, E, Thomas, MG, Manica, A, Nielsen, R, Villems, R, Willerslev, E, Kivisild, T & Metspalu, M 2016, 'Genomic analyses inform on migration events during the peopling of Eurasia', Nature, vol. 538, no. 7624, pp. 238-242. https://doi.org/10.1038/nature19792

TY - JOUR

T1 - Genomic analyses inform on migration events during the peopling of Eurasia

AU - Pagani, Luca

AU - Lawson, Daniel John

AU - Jagoda, Evelyn

AU - Mörseburg, Alexander

AU - Eriksson, Anders

AU - Mitt, Mario

AU - Clemente, Florian

AU - Hudjashov, Georgi

AU - DeGiorgio, Michael

AU - Saag, Lauri

AU - Wall, Jeffrey D.

AU - Cardona, Alexia

AU - Mägi, Reedik

AU - Sayres, Melissa A. Wilson

AU - Kaewert, Sarah

AU - Inchley, Charlotte

AU - Scheib, Christiana L.

AU - Järve, Mari

AU - Karmin, Monika

AU - Jacobs, Guy S.

AU - Antao, Tiago

AU - Iliescu, Florin Mircea

AU - Kushniarevich, Alena

AU - Ayub, Qasim

AU - Tyler-Smith, Chris

AU - Xue, Yali

AU - Yunusbayev, Bayazit

AU - Tambets, Kristiina

AU - Mallick, Chandana Basu

AU - Saag, Lehti

AU - Pocheshkhova, Elvira

AU - Andriadze, George

AU - Muller, Craig

AU - Westaway, Michael C.

AU - Lambert, David M.

AU - Zoraqi, Grigor

AU - Turdikulova, Shahlo

AU - Dalimova, Dilbar

AU - Sabitov, Zhaxylyk

AU - Sultana, Gazi Nurun Nahar

AU - Lachance, Joseph

AU - Tishkoff, Sarah

AU - Momynaliev, Kuvat

AU - Isakova, Jainagul

AU - Damba, Larisa D.

AU - Gubina, Marina

AU - Nymadawa, Pagbajabyn

AU - Evseeva, Irina

AU - Atramentova, Lubov

AU - Utevska, Olga

AU - Ricaut, François-Xavier

AU - Brucato, Nicolas

AU - Sudoyo, Herawati

AU - Letellier, Thierry

AU - Cox, Murray P.

AU - Barashkov, Nikolay A.

AU - Škaro, Vedrana

AU - Mulahasanovic´, Lejla

AU - Primorac, Dragan

AU - Sahakyan, Hovhannes

AU - Mormina, Maru

AU - Eichstaedt, Christina A.

AU - Lichman, Daria V.

AU - Abdullah, Syafiq

AU - Chaubey, Gyaneshwer

AU - Wee, Joseph T. S.

AU - Mihailov, Evelin

AU - Karunas, Alexandra

AU - Litvinov, Sergei

AU - Khusainova, Rita

AU - Ekomasova, Natalya

AU - Akhmetova, Vita

AU - Khidiyatova, Irina

AU - Marjanović, Damir

AU - Yepiskoposyan, Levon

AU - Behar, Doron M.

AU - Balanovska, Elena

AU - Metspalu, Andres

AU - Derenko, Miroslava

AU - Malyarchuk, Boris

AU - Voevoda, Mikhail

AU - Fedorova, Sardana A.

AU - Osipova, Ludmila P.

AU - Lahr, Marta Mirazón

AU - Gerbault, Pascale

AU - Leavesley, Matthew

AU - Migliano, Andrea Bamberg

AU - Petraglia, Michael

AU - Balanovsky, Oleg

AU - Khusnutdinova, Elza K.

AU - Metspalu, Ene

AU - Thomas, Mark G.

AU - Manica, Andrea

AU - Nielsen, Rasmus

AU - Villems, Richard

AU - Willerslev, Eske

AU - Kivisild, Toomas

AU - Metspalu, Mait

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: Support was provided by: Estonian Research Infrastructure Roadmap grant no 3.2.0304.11-0312; Australian Research Council Discovery grants (DP110102635 and DP140101405) (D.M.L., M.W. and E.W.); Danish National Research Foundation; the Lundbeck Foundation and KU2016 (E.W.); ERC Starting Investigator grant (FP7 - 261213) (T.K.); Estonian Research Council grant PUT766 (G.C. and M.K.); EU European Regional Development Fund through the Centre of Excellence in Genomics to Estonian Biocentre (R.V.; M.Me. and A.Me.), and Centre of Excellence for Genomics and Translational Medicine Project No. 2014-2020.4.01.15-0012 to EGC of UT (A.Me.) and EBC (M.Me.); Estonian Institutional Research grant IUT24-1 (L.S., M.J., A.K., B.Y., K.T., C.B.M., Le.S., H.Sa., S.L., D.M.B., E.M., R.V., G.H., M.K., G.C., T.K. and M.Me.) and IUT20-60 (A.Me.); French Ministry of Foreign and European Affairs and French ANR grant number ANR-14-CE31-0013-01 (F.-X.R.); Gates Cambridge Trust Funding (E.J.); ICG SB RAS (No. VI.58.1.1) (D.V.L.); Leverhulme Programme grant no. RP2011-R-045 (A.B.M., P.G. and M.G.T.); Ministry of Education and Science of Russia; Project 6.656.2014/K (S.A.F.); NEFREX grant funded by the European Union (People Marie Curie Actions; International Research Staff Exchange Scheme; call FP7-PEOPLE-2012-IRSES-number 318979) (M.Me., G.H. and M.K.); NIH grants 5DP1ES022577 05, 1R01DK104339-01, and 1R01GM113657-01 (S.Tis.); Russian Foundation for Basic Research (grant N 14-06-00180a) (M.G.); Russian Foundation for Basic Research; grant 16-04-00890 (O.B. and E.B); Russian Science Foundation grant 14-14-00827 (O.B.); The Russian Foundation for Basic Research (14-04-00725-a), The Russian Humanitarian Scientific Foundation (13-11-02014) and the Program of the Basic Research of the RAS Presidium “Biological diversity” (E.K.K.); Wellcome Trust and Royal Society grant WT104125AIA & the Bristol Advanced Computing Research Centre (http://www.bris.ac.uk/acrc/) (D.J.L.); Wellcome Trust grant 098051 (Q.A.; C.T.-S. and Y.X.); Wellcome Trust Senior Research Fellowship grant 100719/Z/12/Z (M.G.T.); Young Explorers Grant from the National Geographic Society (8900-11) (C.A.E.); ERC Consolidator Grant 647787 ‘LocalAdaptatio’ (A.Ma.); Program of the RAS Presidium “Basic research for the development of the Russian Arctic” (B.M.); Russian Foundation for Basic Research grant 16-06-00303 (E.B.); a Rutherford Fellowship (RDF-10-MAU-001) from the Royal Society of New Zealand (M.P.C.).

PY - 2016/9/21

Y1 - 2016/9/21

N2 - High-Coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long-and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago. © 2016 Macmillan Publishers Limited, part of Springer Nature.

AB - High-Coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long-and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago. © 2016 Macmillan Publishers Limited, part of Springer Nature.

UR - http://hdl.handle.net/10754/622409

UR - http://www.nature.com/nature/journal/v538/n7624/full/nature19792.html

UR - http://www.scopus.com/inward/record.url?scp=84981502573&partnerID=8YFLogxK

U2 - 10.1038/nature19792

DO - 10.1038/nature19792

M3 - Article

C2 - 27654910

SN - 0028-0836

VL - 538

SP - 238

EP - 242

JO - Nature

JF - Nature

IS - 7624

ER -

Genomic analyses inform on migration events during the peopling of Eurasia

Abstract

Bibliographical note

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