It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

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. 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 number1 of geographically restricted populations2,3,4,5, 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 history7,8,9 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.

The origin of the Andaman "Negrito" and Nicobar "Mongoloid" populations has been ambiguous. Our analyses of complete mitochondrial DNA sequences from Onges and Great Andaman populations revealed two deeply branching clades that share their most recent common ancestor in founder haplogroup M, with lineages spread among India, Africa, East Asia, New Guinea, and Australia. This distribution suggests that these two clades have likely survived in genetic isolation since the initial settlement of the islands during an out-of-Africa migration by anatomically modern humans. In contrast, Nicobarese sequences illustrate a close genetic relationship with populations from Southeast Asia.