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 Wilson Sayres, Sarah Kaewert, Charlotte Inchley, Christiana L. Scheib, Mari Järve, Monika Karmin, Guy S. Jacobs & 77 others Tiago Antao, Florin Mircea Iliescu, Alena Kushniarevich, Qasim Ayub, Chris Tyler-Smith, Yali Xue, Bayazit Yunusbayev, Kristiina Tambets, Chandana Basu Mallick, 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, Murray P. Cox, Nikolay A. Barashkov, Lejla Mulahasanović, Lejla Mulahasanović, Dragan Primorac, Maru Mormina, Christina A. Eichstaedt, Christina A. Eichstaedt, Daria V. Lichman, Gyaneshwer Chaubey, Joseph T.S. Wee, Evelin Mihailov, Alexandra Karunas, Sergei Litvinov, Sergei Litvinov, Natalya Ekomasova, Vita Akhmetova, Irina Khidiyatova, Irina Khidiyatova, Levon Yepiskoposyan, Doron M. Behar, Elena Balanovska, Andres Metspalu, Miroslava Derenko, Boris Malyarchuk, Mikhail Voevoda, Mikhail Voevoda, 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

Research output: Contribution to journalArticle

113 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)238-242
Number of pages5
JournalNature
Volume538
Issue number7624
DOIs
StatePublished - Jul 1 2016

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Genome
Human Genome
Neanderthals
Population
Fossils
Gene Flow
Mutation Rate
Population Density
Population Groups
Neoplasms
Datasets

ASJC Scopus subject areas

  • Medicine(all)
  • General

Cite this

Pagani, L., Lawson, D. J., Jagoda, E., Mörseburg, A., Eriksson, A., Mitt, 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

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

In: Nature, Vol. 538, No. 7624, 01.07.2016, p. 238-242.

Research output: Contribution to journalArticle

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, Wilson Sayres, M, 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, 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, FX, Brucato, N, Sudoyo, H, Letellier, T, Cox, MP, Cox, MP, Barashkov, NA, Mulahasanović, L, Mulahasanović, L, Primorac, D, Mormina, M, Eichstaedt, CA, Eichstaedt, CA, Lichman, DV, Chaubey, G, Wee, JTS, Mihailov, E, Karunas, A, Litvinov, S, Litvinov, S, Ekomasova, N, Akhmetova, V, Khidiyatova, I, Khidiyatova, I, Yepiskoposyan, L, Behar, DM, Balanovska, E, Metspalu, A, Derenko, M, Malyarchuk, B, Voevoda, M, Voevoda, M, 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
Pagani L, Lawson DJ, Jagoda E, Mörseburg A, Eriksson A, Mitt M et al. Genomic analyses inform on migration events during the peopling of Eurasia. Nature. 2016 Jul 1;538(7624):238-242. https://doi.org/10.1038/nature19792
Pagani, Luca ; Lawson, Daniel John ; Jagoda, Evelyn ; Mörseburg, Alexander ; Eriksson, Anders ; Mitt, Mario ; Clemente, Florian ; Hudjashov, Georgi ; Degiorgio, Michael ; Saag, Lauri ; Wall, Jeffrey D. ; Cardona, Alexia ; Mägi, Reedik ; Wilson Sayres, Melissa ; Kaewert, Sarah ; Inchley, Charlotte ; Scheib, Christiana L. ; Järve, Mari ; Karmin, Monika ; Jacobs, Guy S. ; Antao, Tiago ; Iliescu, Florin Mircea ; Kushniarevich, Alena ; Ayub, Qasim ; Tyler-Smith, Chris ; Xue, Yali ; Yunusbayev, Bayazit ; Tambets, Kristiina ; Mallick, Chandana Basu ; Pocheshkhova, Elvira ; Andriadze, George ; Muller, Craig ; Westaway, Michael C. ; Lambert, David M. ; Zoraqi, Grigor ; Turdikulova, Shahlo ; Dalimova, Dilbar ; Sabitov, Zhaxylyk ; Sultana, Gazi Nurun Nahar ; Lachance, Joseph ; Tishkoff, Sarah ; Momynaliev, Kuvat ; Isakova, Jainagul ; Damba, Larisa D. ; Gubina, Marina ; Nymadawa, Pagbajabyn ; Evseeva, Irina ; Atramentova, Lubov ; Utevska, Olga ; Ricaut, François Xavier ; Brucato, Nicolas ; Sudoyo, Herawati ; Letellier, Thierry ; Cox, Murray P. ; Cox, Murray P. ; Barashkov, Nikolay A. ; Mulahasanović, Lejla ; Mulahasanović, Lejla ; Primorac, Dragan ; Mormina, Maru ; Eichstaedt, Christina A. ; Eichstaedt, Christina A. ; Lichman, Daria V. ; Chaubey, Gyaneshwer ; Wee, Joseph T.S. ; Mihailov, Evelin ; Karunas, Alexandra ; Litvinov, Sergei ; Litvinov, Sergei ; Ekomasova, Natalya ; Akhmetova, Vita ; Khidiyatova, Irina ; Khidiyatova, Irina ; Yepiskoposyan, Levon ; Behar, Doron M. ; Balanovska, Elena ; Metspalu, Andres ; Derenko, Miroslava ; Malyarchuk, Boris ; Voevoda, Mikhail ; Voevoda, Mikhail ; Osipova, Ludmila P. ; Lahr, Marta Mirazón ; Gerbault, Pascale ; Leavesley, Matthew ; Migliano, Andrea Bamberg ; Petraglia, Michael ; Balanovsky, Oleg ; Khusnutdinova, Elza K. ; Metspalu, Ene ; Thomas, Mark G. ; Manica, Andrea ; Nielsen, Rasmus ; Villems, Richard ; Willerslev, Eske ; Kivisild, Toomas ; Metspalu, Mait. / Genomic analyses inform on migration events during the peopling of Eurasia. In: Nature. 2016 ; Vol. 538, No. 7624. pp. 238-242.
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AU - Lawson, Daniel John

AU - Jagoda, Evelyn

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AU - Mitt, Mario

AU - Clemente, Florian

AU - Hudjashov, Georgi

AU - Degiorgio, Michael

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AU - Ayub, Qasim

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AU - Yunusbayev, Bayazit

AU - Tambets, Kristiina

AU - Mallick, Chandana Basu

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 - Cox, Murray P.

AU - Barashkov, Nikolay A.

AU - Mulahasanović, Lejla

AU - Mulahasanović, Lejla

AU - Primorac, Dragan

AU - Mormina, Maru

AU - Eichstaedt, Christina A.

AU - Eichstaedt, Christina A.

AU - Lichman, Daria V.

AU - Chaubey, Gyaneshwer

AU - Wee, Joseph T.S.

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AU - Karunas, Alexandra

AU - Litvinov, Sergei

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AU - Yepiskoposyan, Levon

AU - Behar, Doron M.

AU - Balanovska, Elena

AU - Metspalu, Andres

AU - Derenko, Miroslava

AU - Malyarchuk, Boris

AU - Voevoda, Mikhail

AU - Voevoda, Mikhail

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

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