Reconstructing the west-east genetic division in Indonesia using ancient genomes

The deep-water Wallace's line marks a major biogeographic boundary separating western and eastern Indonesia, yet the origin of this genetic divide remains unresolved due to limited ancient genomic data from western Indonesia. In this study, we report two Late Neolithic genomic data from western Indonesia, integrated with 19 published ancient genomes from Island Southeast Asia (7,000 to 200 BP). Our analyses suggest a dual-phase formation of the west-east genetic structure: an Early Holocene west-east divergence, with western forager-related ancestry closer to Hòabìnhian-associated groups and eastern forager-related ancestry closer to Papuan-related groups; and later Neolithic and post-Neolithic demographic processes, including the Austronesian expansion, additional Mainland Southeast Asian gene flow into western Wallacea, and Papuan-associated back-migration into eastern Wallacea, reinforced and reshaped this earlier structure. We therefore propose a revised demographic model in which repeated Holocene migrations acted on pre-existing regional differences to generate the genetic landscape of present-day Indonesian populations.