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Supplemental data from: Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania

Tucci, Serena1

Published Mar 31, 2026 on Dryad. https://doi.org/10.5061/dryad.2fqz612z6

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Mar 31, 2026 version files 145.94 MB

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Abstract

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.