Reconstructing Eastern Indonesian Population History: Insights from a Genetic Perspective

Gludhug Ariyo Purnomo1,2*, Shimona Kealy3, Sue O’Connor3, Antoinette Schapper4,5, Ben Shaw3,6, Bastien Llamas7,8,9, João C. Teixeira7,8,6,10, Herawati Sudoyo11, and Raymond Tobler3,6,7

1Adelaide University, Australia; 2Mochtar Riady Institute for Nanotechnology, Indonesia; 3Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Australia; 4Vrije Universiteit Amsterdam, the Netherlands; 5Lacito‑CNRS, France; 6Evolution of Cultural Diversity Initiative, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Australia; 7Australian Centre for Ancient DNA, The Environment Institute, School of Biological Sciences, The University of Adelaide, Australia; 8Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, School of Biological Sciences, University of Adelaide, Australia; 9National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Australia; 10Centre for Interdisciplinary Studies, University of Coimbra, Portugal; 11Genome Diversity and Disease Laboratory, Mochtar Riady Institute for Nanotechnology, Indonesia; *gludhug.purnomo@adelaide.edu.au

The Wallacean Archipelago in the eastern part of Indonesia was first settled by anatomically modern humans (AMH) around 50 thousand years ago (kya). While present‑day populations in Wallacea exhibit a longitudinal counter‑gradient of Papuan‑ and Asian‑related ancestry, typically attributed to Austronesian seafarers ~3.5 kya, recent multidisciplinary evidence suggests a more complex history. Integrating genetic data alongside linguistic and archaeological evidence, primarily from previously undocumented populations, we present a comprehensive study of the genetic history of Wallacea and West Papua. Here, we demonstrate that Wallacean societies were transformed by the spread of Papuan genes and languages over the past 3,500 years—coinciding with interactions between Austronesian seafarers and Wallacean‑Papuan groups. The vast majority (~75–100%) of Papuan‑related ancestry in Wallacea derives from New Guinea back‑migrations, with only a minor fraction tracing back to early AMH settlers. Papuan and Wallacean genetic lineages mixed primarily in the western and central regions of the archipelago, coinciding with the widespread introduction of Austronesian ancestry (~40–85% of modern Wallacean genomes). However, continuous genetic exchange into the Historical Period complicates precise dating of these admixture events. Our findings reveal a dynamic Wallacean population history, shaped by Papuan migrations and Austronesian expansion. This study refines our understanding of human movement and genetic diversity in the region, challenging traditional models of Wallacea’s population history.