Patrick Reilly, Stephen Rong, Daniela Tejada-Martínez, Samantha L. Miller, Audrey Tjahjadi, Chang Liu, Jared F. Akers, Alysa Pomer, Margaret E. Prentice, D. Andrew Merriwether, Françoise R. Friedlaender, George Koki, JONATHAN S. FRIEDLAENDER, Steven K. Reilly, Serena Tucci
Near Oceanic populations harbor substantial 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 1284 worldwide genomes, revealing major distinctions among and within islands, including long-term isolation and strong population bottlenecks. We reconstructed 1.897 billion base pairs of the archaic genome, including 831.9 million base pairs of Denisovan sequence, and 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 3127 high-frequency introgressed expression-modulating variants, finding an enrichment of functional impacts on genes in the interferon-γ signaling pathway including JAK1 , GBP2 , and OAS1 .