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

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.