Genomic analyses inform on migration events during the peopling of Eurasia

Luca Pagani, Daniel John Lawson, Evelyn Jagoda, Alexander Morseburg, Anders Eriksson, Mario Mitt, Florian Clemente, Georgi Hudjashov, Michael DeGiorgio, Lauri Saag, Jeffrey D. Wall, Alexia Cardona, Reedik Magi, Melissa A. Wilson Sayres, Sarah Kaewert, Charlotte Inchley, Christina L. Scheib, Mari Jarve, Monika Karmin, Guy S. Jacobs & 6 others Tiago Antao, Florin Mircea Iliescu, Alena Kushniarevich, Qasim Ayub, Chris Tyler-Smith, Maru Mormina

Research output: Other contributionResearchpeer-review

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Abstract

High-coverage whole-genome sequence studies have so far focused on a limited number1 of geographically restricted populations2–5, or been targeted at specific diseases, such as cancer6. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history7–9 and refuelled the debate on the mutation rate in humans10. 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 record11, and admixture between AMHs and Neanderthals predating the main Eurasian expansion12, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.
Original languageEnglish
Publication statusPublished - 21 Sep 2016

Keywords

  • genomic data
  • genomic analyses
  • population history

Cite this

Pagani, L., Lawson, D. J., Jagoda, E., Morseburg, A., Eriksson, A., Mitt, M., ... Mormina, M. (2016, Sep 21). Genomic analyses inform on migration events during the peopling of Eurasia.
Pagani, Luca ; Lawson, Daniel John ; Jagoda, Evelyn ; Morseburg, Alexander ; Eriksson, Anders ; Mitt, Mario ; Clemente, Florian ; Hudjashov, Georgi ; DeGiorgio, Michael ; Saag, Lauri ; Wall, Jeffrey D. ; Cardona, Alexia ; Magi, Reedik ; Sayres, Melissa A. Wilson ; Kaewert, Sarah ; Inchley, Charlotte ; Scheib, Christina L. ; Jarve, Mari ; Karmin, Monika ; Jacobs, Guy S. ; Antao, Tiago ; Iliescu, Florin Mircea ; Kushniarevich, Alena ; Ayub, Qasim ; Tyler-Smith, Chris ; Mormina, Maru. / Genomic analyses inform on migration events during the peopling of Eurasia. 2016.
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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 number1 of geographically restricted populations2–5, or been targeted at specific diseases, such as cancer6. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history7–9 and refuelled the debate on the mutation rate in humans10. 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 record11, and admixture between AMHs and Neanderthals predating the main Eurasian expansion12, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.",
keywords = "genomic data, genomic analyses, population history",
author = "Luca Pagani and Lawson, {Daniel John} and Evelyn Jagoda and Alexander Morseburg 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 Magi and Sayres, {Melissa A. Wilson} and Sarah Kaewert and Charlotte Inchley and Scheib, {Christina L.} and Mari Jarve 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 Maru Mormina",
year = "2016",
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Pagani, L, Lawson, DJ, Jagoda, E, Morseburg, A, Eriksson, A, Mitt, M, Clemente, F, Hudjashov, G, DeGiorgio, M, Saag, L, Wall, JD, Cardona, A, Magi, R, Sayres, MAW, Kaewert, S, Inchley, C, Scheib, CL, Jarve, M, Karmin, M, Jacobs, GS, Antao, T, Iliescu, FM, Kushniarevich, A, Ayub, Q, Tyler-Smith, C & Mormina, M 2016, Genomic analyses inform on migration events during the peopling of Eurasia..

Genomic analyses inform on migration events during the peopling of Eurasia. / Pagani, Luca; Lawson, Daniel John; Jagoda, Evelyn; Morseburg, Alexander; Eriksson, Anders; Mitt, Mario; Clemente, Florian; Hudjashov, Georgi; DeGiorgio, Michael; Saag, Lauri; Wall, Jeffrey D.; Cardona, Alexia; Magi, Reedik; Sayres, Melissa A. Wilson; Kaewert, Sarah; Inchley, Charlotte; Scheib, Christina L.; Jarve, Mari; Karmin, Monika; Jacobs, Guy S.; Antao, Tiago; Iliescu, Florin Mircea; Kushniarevich, Alena; Ayub, Qasim; Tyler-Smith, Chris; Mormina, Maru.

2016, .

Research output: Other contributionResearchpeer-review

TY - GEN

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

AU - Pagani, Luca

AU - Lawson, Daniel John

AU - Jagoda, Evelyn

AU - Morseburg, 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 - Magi, Reedik

AU - Sayres, Melissa A. Wilson

AU - Kaewert, Sarah

AU - Inchley, Charlotte

AU - Scheib, Christina L.

AU - Jarve, 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 - Mormina, Maru

PY - 2016/9/21

Y1 - 2016/9/21

N2 - High-coverage whole-genome sequence studies have so far focused on a limited number1 of geographically restricted populations2–5, or been targeted at specific diseases, such as cancer6. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history7–9 and refuelled the debate on the mutation rate in humans10. 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 record11, and admixture between AMHs and Neanderthals predating the main Eurasian expansion12, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.

AB - High-coverage whole-genome sequence studies have so far focused on a limited number1 of geographically restricted populations2–5, or been targeted at specific diseases, such as cancer6. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history7–9 and refuelled the debate on the mutation rate in humans10. 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 record11, and admixture between AMHs and Neanderthals predating the main Eurasian expansion12, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.

KW - genomic data

KW - genomic analyses

KW - population history

M3 - Other contribution

ER -

Pagani L, Lawson DJ, Jagoda E, Morseburg A, Eriksson A, Mitt M et al. Genomic analyses inform on migration events during the peopling of Eurasia. 2016.