Science. 2026 Jun 11; 392(6803): eadr6749

Roland Heynkes 23.6.2026, CC BY-SA-4.0 DE

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Gliederung

NR BACX

AU Patrick F. Reilly, Stephen Rong, Daniela Tejada-Martinez, Samantha L. Miller, Audrey Tjahjadi, Chang Liu, Jared Akers, Alysa Pomer, Margaret E. Prentice, D. Andrew Merriwether, Françoise R. Friedlaender, George Koki, Jonathan S. Friedlaender, Steven K. Reilly, Serena Tucci

TI Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania

QU Science. 2026 Jun 11; 392(6803): eadr6749. doi: 10.1126/science.adr6749. Epub 2026 Jun 11.

AB 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-? signaling pathway including JAK1, GBP2, and OAS1.

SP englisch

VT Editor’s summary Between 2 and 5% of modern Eurasian genomes are derived from admixture with Neanderthals and Denisovans, with Papua New Guineans bearing the largest fractions. However, Oceanian populations remain underrepresented in genetic studies, resulting in questions about the landscape of archaic introgression, including difficult-to-identify features such as structural variants. Hsieh et al. used long-read sequencing to identify archaic-derived structural variants in two Papua New Guinean individuals, finding many unique insertions and deletions, as well as 11 centromeres potentially inherited from archaic hominins. Reilly et al. examined whole-genome sequences from 177 Near Oceanian individuals, revealing many potentially adaptively introgressed regions. The authors tested some of these for their gene-regulatory potential using massively parallel reporter assays. Together, these studies give us greater insight into how archaic introgression has shaped these historically underrepresented populations. - Corinne Simonti

Structured Abstract
INTRODUCTION
Because of their different settlement histories, the Pacific Islands have been divided into Near and Remote Oceania. Near Oceania—the region consisting of New Guinea, the Bismarck Archipelago, and the main Solomon Islands—was settled ~42,000 years ago and thereafter remained largely isolated at the edge of human settlement. Not until ~5000 years ago, with the advent of new migration pressures from Asia, were the rest of the Pacific Islands inhabited—Remote Oceania, encompassing Vanuatu, New Caledonia, Fiji, Polynesia, and Micronesia. Near Oceanic populations harbor substantial cultural, phenotypic, and genetic diversity, including the largest amounts of archaic introgression inherited from Neanderthals and Denisovans. However, they have been substantially underrepresented in whole-genome sequencing and functional genomic consortia to date.

RATIONALE
We sequenced 177 high-coverage genomes from 12 diverse Near Oceanic populations and analyzed them alongside 1284 genomes from worldwide populations. We investigated the demographic history of groups descended from early settlers of the Pacific and the extent and distribution of Neanderthal and Denisovan introgression in Near Oceanic genomes, including adaptive archaic variation, and performed a massively parallel reporter assay to identify the functional consequences of adaptive archaic introgressed variants.

RESULTS
Near Oceanians in our study fall along a gradient of genetic similarity from Papuan-speaking groups of New Guinea and the Baining of New Britain to the Polynesian outlier groups of the Solomon Islands, although we also observed signals of long-term isolation in Papuan-speaking groups. Furthermore, both the Baining and Polynesian outlier groups showed evidence of major population bottlenecks, emphasizing complex population structure and demographic history in this region. We reconstructed archaic introgressed sequence covering 70.7% of the callable archaic genome (1.897 billion base pairs) including 505 million base pairs (Mbp) of previously unidentified archaic sequence and three times more Denisovan sequence than previous studies (831.9 Mbp). We uncovered evidence for introgression from three Denisovan-like groups into the ancestors of Near Oceanians, revealing a new twist on our interactions with archaic hominins. We refined maps of archaic “deserts” and identified a strong novel signal of adaptive Denisovan introgression at TRPS1, a skeletal development gene previously found under selection in central African rainforest hunter-gatherers and highland Ecuadorians. Using a massively parallel reporter assay, we discovered 3127 high-frequency introgressed expression-modulating variants targeting 1422 genes and found an enrichment of high-frequency introgressed variants with protein-coding, splicing, and regulatory impacts on immune pathways. These include adaptive archaic variants affecting genes in the interferon-? pathway, including JAK1, GBP2, and the COVID-19–associated OAS1 locus, where we functionally characterized a Denisovan haplotype unique to Oceanic populations. Although some of these adaptive introgression signals, such as TNFAIP3 and HLA-DRA, may be related to malaria susceptibility, few are widely shared across Near Oceania, suggesting multiple independent instances of local adaptation. Many of these immune-related genes are also pleiotropic, including TRPS1 and TANK.

CONCLUSION
We characterized the evolutionary, phenotypic, and functional consequences of archaic introgressed variants in Near Oceanians and identified putatively causal archaic variants contributing to parallel local adaptation of both the immune system and skeletal development.

ZF Menschen erreichten die Inseln im nahen Ozeanien anscheinend schon vor etwa 42.000 Jahren. Seitdem lebten dort viele kleine Völker, die aufgrund ihrer zigtausend Jahre anhaltenden Isolation viele Sprachen und andere kulturelle Eigenheiten entwickelten. Sie unterscheiden sich aber auch phänotypisch und genetisch. Um die genetische Vielfalt zu berücksichtigen, wurden 177 Vollgenome aus dem nahen Ozeanien mit hoher Abdeckung sequenziert und mit 1.284 Genomen aus aller Welt verglichen. wodurch sich erhebliche Unterschiede zwischen und innerhalb der Inseln zeigten, darunter langfristige Isolation und starke Populationsengpässe. Wir rekonstruierten 1,897 Milliarden Basenpaare des archaischen Genoms, darunter 831,9 Millionen Basenpaare der Denisova-Sequenz, und fanden Hinweise auf Introgression von drei Denisova-ähnlichen Gruppen bei den Near-Oceanianern sowie auf adaptive Denisova-Introgression bei TRPS1, einem Gen für die Skelettentwicklung, das auch bei zentralafrikanischen Regenwald-Jäger-Sammlern und Hochlandbewohnern Ecuadors unter Selektion steht. Anschließend führten wir einen massiv-parallelen Reporter-Assay durch und entdeckten 3.127 hochfrequente, introgressierte, die Expression modulierende Varianten, wobei wir eine Häufung funktioneller Auswirkungen auf Gene im Interferon-ß-Signalweg feststellten, darunter JAK1, GBP2 und OAS1. Übersetzt mit DeepL.com (kostenlose Version)

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