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Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local Euro-pean wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process. domestication | evolution | gene flow | Neolithic International audience

How early human groups were organized Sequencing ancient hominid remains has provided insights into the relatedness between individuals. However, it is not clear whether ancient humans bred among close relatives, as is common in some modern human cultures. Sikora et al. report genome sequences from four early humans buried close together in western Russia about 34,000 years ago (see the Perspective by Bergström and Tyler-Smith). The individuals clustered together genetically and came from a population with a small effective size, but they were not very closely related. Thus, these people may represent a single social group that was part of a larger mating network, similar to contemporary hunter-gatherers. The lack of close inbreeding might help to explain the survival advantage of anatomically modern humans. Science , this issue p. 659 ; see also p. 586

The sequencing was funded by the Simons Foundation (SFARI 280376) and the US National Science Foundation (BCS-1032255). I.M. was supported by a Long Term Fellowship grant LT001095/2014 from the Human Frontier Science program. P.S. was supported by the Wenner-Gren foundation and the Swedish Research Council (VR grant 2014-453). T.W. and M.G. were supported by an NIJ grant 2014-DN-BX-K089. Y.E. was supported by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund and by NIJ grant 2014-DN-BX-K089. D.L. was supported by the Natural Sciences and Engineering Research Council of Canada. T.K. was supported by ERC Starting Investigator grant FP7 - 261213. R.S. received support from Russian Foundation for Basic Research (#15-04-02543). S.D. received support from the Russian Foundation for Basic Research (#16-34-00599). R.K., E.K. and S.L. were supported by the Russian Foundation for Basic Research (11-04-00725-a). E.B. was supported by the Russian Foundation for Basic Research (16-06-00303). O.B. was supported by the Russian Scientific Fund (14-04-00827) and by the Russian Foundation for Basic Research (16-04-00890). D.M.B., H.S., E.M., R.V. and M.M. were supported by Institutional Research Funding from the Estonian Research Council IUT24-1 and by the European Regional Development Fund (European Union) through the Centre of Excellence in Genomics to Estonian Biocentre and University of Tartu. D.C. was supported by the Spanish MINECO grant CGL-44351-P. L.B.J. and W.S.W. were supported by NIH grant GM59290. S.A.T. was supported by NIH grants 5DP1ES022577 05, 1R01DK104339-01, and 1R01GM113657-01. C.T.-S. and Y.X. were supported by The Wellcome Trust grant 098051. C.M.B. was supported by NSF grants 0924726 and 1153911. K.T. was supported by CSIR Network Project grant (GENESIS: BSC0121). J.P.S. and Y.S.S. were supported in part by an NIH grant R01-GM094402, and a Packard Fellowship for Science and Engineering. G.R., J.K and S.P. were funded by the Max Planck Society. N.P. and D.R. were supported by NIH grant GM100233 and D.R. is a Howard Hughes Medical Institute investigator Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

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.