Genomic Insights into the Population History of Northern Sahul from West New Guinea

ISSHIKI Mariko1*, Augustinus Soemantri2, OHTSUKA Ryutaro3, NAKAZAWA Minato4, ISHIDA Takafumi1,5, and OHASHI Jun1

1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan; 2Department of Pediatrics, Faculty of Medicine, Diponegoro University, Indonesia; 3Japan Wildlife Research Center, Japan; 4Department of Public Health, Graduate School of Health Sciences, Kobe University, Japan; 5Graduate School of Asian and African Area Studies, Kyoto University, Japan; *m-isshiki@g.ecc.u-tokyo.ac.jp

Migration into the Sahul continent is one of the earliest migrations that required open‑sea voyages. Despite its importance for understanding early human dispersals, the migration routes and the subsequent population history remain incompletely understood. In particular, genomic data from western New Guinea are still scarce, limiting our ability to reconstruct population history in this key region. Here, we analysed whole‑genome sequences from 163 unrelated individuals sampled across New Guinea Island and surrounding islands, including 80 individuals newly sequenced in this study. Genome‑wide analyses reveal clear population differentiation between eastern highland populations (e.g., Enga and Jiwaka) and populations from the lowlands and western highlands (e.g., Abun, Asmat, Sepik, and Dani). Gene flow across the Central Range of New Guinea appears limited, indicating that this mountain chain has long acted as a major geographic barrier shaping genetic variation across the island. Approximately 4% of the genomes of all groups derive from Denisovan ancestry, consistent with previous studies, and no significant differences in Denisovan contribution were detected among populations. Analyses of mitochondrial DNA (mtDNA) and the non‑recombining region of the Y chromosome (NRY) reveal contrasting patterns: Y‑chromosome lineages show stronger population structure than mtDNA, consistent with long‑standing patrilocal residence practices. Phylogenetic analyses further identify a west–east population split around ~20–30 kya, suggesting that key aspects of regional population structure were already emerging during the Late Pleistocene. Together, these findings highlight a complex demographic history in northern Sahul, shaped by geographic barriers and social practices that have influenced human mobility and interaction.