Near Oceanic populations harbor remarkable cultural, phenotypic, and genetic diversity, yet are drastically underrepresented in human genomics. We generated 177 high-coverage Near Oceanian whole genomes and analyzed them alongside 1,284 worldwide genomes, revealing major distinctions among and within islands including long-term isolation and strong population bottlenecks. We reconstructed 1.897 Gbp of the archaic genome including 831.9 Mbp of Denisovan sequence, found evidence for introgression from three Denisovan-like groups in Near Oceanians, and adaptive Denisovan introgression at TRPS1, a skeletal development gene also under selection in central African rainforest hunter-gatherers and highland Ecuadorians. We then performed a massively parallel reporter assay and discovered 3,127 high-frequency introgressed expression-modulating variants, finding an enrichment of functional impacts on genes in the IFNγ signalling pathway including JAK1, GBP2, and OAS1.

Funding provided by: National Institute of General Medical SciencesROR ID: https://ror.org/04q48ey07Award Number: 1R35GM147565-01 Funding provided by: National Human Genome Research InstituteROR ID: https://ror.org/00baak391Award Number: R00HG010669 Funding provided by: National Human Genome Research InstituteROR ID: https://ror.org/00baak391Award Number: R01HG012872 Funding provided by: Office of the DirectorROR ID: https://ror.org/00fj8a872Award Number: 1S10OD030363-01A1