Reconstructing the West-East Genetic Division in Indonesia Using Ancient Genomes

AI interpretationAI-generated

Ancient DNA reveals how Indonesia's east-west genetic divide formed in two phases.

Wallace's line is a deep-water boundary between western and eastern Indonesia, and this study asks when and how the human genetic divide across it arose. The authors sequenced two Late Neolithic genomes from western Indonesia and combined them with 19 published ancient genomes from Island Southeast Asia spanning 7,000 to 200 years ago. Their model shows the divide is not a single event but a layered process built over the Holocene.

• The west-east genetic structure formed in two phases, starting with an Early Holocene divergence between western and eastern forager-related ancestries.
• Western forager-related ancestry is closer to Hoabinhian-associated groups, while eastern forager-related ancestry is closer to Papuan-related groups.
• Later Neolithic and post-Neolithic migrations, including the Austronesian expansion, mainland Southeast Asian gene flow into western Wallacea, and Papuan-associated back-migration into eastern Wallacea, reinforced and reshaped this earlier structure.

Sample interpretation

The study adds two new Late Neolithic genomes from western Indonesia, a region previously poor in ancient DNA. Both male samples carry Y haplogroups O-F3288 and O-FT131196, and both carry mitochondrial haplogroup Y2a1. Combined with 19 published ancient genomes from Island Southeast Asia dated 7,000 to 200 BP, these samples help anchor the western side of the east-west genetic boundary.

For genealogy enthusiasts

For ancestry enthusiasts, this means Indonesian genetic history is not simply 'Austronesian vs Papuan'. Deep Holocene forager differences came first, and later migrations layered onto them. Modern Indonesian profiles should be read as mixtures shaped by repeated migration, not a single origin story.