Journal Article

Genomic analyses inform on migration events during the peopling of Eurasia

Kushniarevich, Alena, Marjanović, Damir, Sayres, Melissa A. Wilson, Saag, Lehti, Mihailov, Evelin, Thomas, Mark G., Jagoda, Evelyn, Škaro, Vedrana, Cardona, Alexia, Pocheshkhova, Elvira, Eriksson, Anders, Evseeva, Irina, Dalimova, Dilbar, Saag, Lauri, Eichstaedt, Christina A., Scheib, Christiana L., Westaway, Michael C., Primorac, Dragan, Yepiskoposyan, Levon, Sultana, Gazi Nurun Nahar, Wall, Jeffrey D., Kaewert, Sarah, Karunas, Alexandra, Järve, Mari, Ayub, Qasim, Tishkoff, Sarah, Malyarchuk, Boris, Litvinov, Sergei, Andriadze, George, Mägi, Reedik, Xue, Yali, Villems, Richard, Leavesley, Matthew, Osipova, Ludmila P., Turdikulova, Shahlo, Karmin, Monika, Wee, Joseph T. S., Tambets, Kristiina, Khusainova, Rita, Barashkov, Nikolay A., Lachance, Joseph, Yunusbayev, Bayazit, Fedorova, Sardana A., Khidiyatova, Irina, Mulahasanovic´, Lejla, Lichman, Daria V., Metspalu, Mait, Cox, Murray P., Atramentova, Lubov, Damba, Larisa D., Ekomasova, Natalya, Nymadawa, Pagbajabyn, Sudoyo, Herawati, Gerbault, Pascale, Inchley, Charlotte, Gubina, Marina, Migliano, Andrea Bamberg, Manica, Andrea, Utevska, Olga, Voevoda,

2016

Overview

Whole-genome sequencing of individuals from 125 populations provides insight into patterns of genetic diversity, natural selection and human demographic history during the peopling of Eurasia and finds evidence for genetic vestiges of an early expansion of modern humans out of Africa in Papuans. The DNA of early human migrations Three international collaborations reporting in this issue of Nature describe 787 high-quality genomes from individuals from geographically diverse populations. David Reich and colleagues analysed whole-genome sequences of 300 individuals from 142 populations. Their findings include an accelerated estimated rate of accumulation of mutations in non-Africans compared to Africans since divergence, and that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans but from the same source as that of other non-Africans. Eske Willerlsev and colleagues obtained whole-genome data for 83 Aboriginal Australians and 25 Papuans from the New Guinea Highlands. They estimate that Aboriginal Australians and Papuans diverged from Eurasian populations 51,000–72,000 years ago, following a single out-of-Africa dispersal. Luca Pagani et al . report on a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations. Their analyses support the model by which all non-African populations derive most of their genetic ancestry from a single recent migration out of Africa, although a Papuan contribution suggests a trace of an earlier human expansion. High-coverage whole-genome sequence studies have so far focused on a limited number 1 of geographically restricted populations 2 , 3 , 4 , 5 , or been targeted at specific diseases, such as cancer 6 . Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history 7 , 8 , 9 and refuelled the debate on the mutation rate in humans 10 . 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 11 , and admixture between AMHs and Neanderthals predating the main Eurasian expansion 12 , our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 45/22 / 45/23 / 631/181/19/2471 / 631/181/2474 / 631/208/182 / 631/208/212/2304 / 704/158/1745 / Africa - ethnology / Animals / Asia / Biological anthropology / Datasets as Topic / DNA sequencing / Estonia / Europe / Fossils / Gene Flow / Genes / Genetics, Population / Genome, Human - genetics / Genomes / Genomics / Haplotypes / Heterozygote / History, Ancient / Hominids / Human Migration - history / Humanities and Social Sciences / Humans / letter / Methods / Migration / multidisciplinary / Neanderthals - genetics / New Guinea / Population / Population Dynamics / Population number / Racial Groups - genetics / Science / Studies