The Estonian Biocentre Human Genome Diversity Panel (EGDP)

Previous human genetic studies, based on sampling small numbers of populations, have supported a recent out-of-Africa dispersal model with minor additional input from archaic humans. Here, we present a novel dataset of 377 (two additional genomes are accessible through EGA through managed access program) high-coverage human genomes from 125 populations worldwide. The combination of high spatial and genomic coverage enabled us to refine current knowledge of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size. The examined Papuan genomes (hereafter taken as representative of the broader Sahul region) show an excess of haplotype sharing with Africans. This is compatible with traces of an early and otherwise extinct non-African lineage in the Papuan genome, evidence of which was so far only available in the Western Asian fossil record. Our tests of positive and balancing selection highlight a number of new metabolism- and immunity-related loci as candidates for local adaptation.