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Reconstructing the west-east genetic division in Indonesia using ancient genomes
Yu Xu1,2,3, Ketut Wiradnyana4, Hui Zhou1,5,6
1State Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Iscience
|May 25, 2026
Summary
Ancient Indonesian genomes reveal a dual-phase origin for the Wallace's line genetic divide. Early Holocene migrations established distinct western and eastern ancestries, later reshaped by Neolithic expansions and back-migrations.
Area of Science:
- Population Genetics
- Ancient Genomics
- Biogeography
Background:
- The Wallace's line is a significant biogeographic boundary in Indonesia.
- The genetic origins of this divide are unclear due to scarce ancient DNA from western Indonesia.
Purpose of the Study:
- To investigate the genetic history of western Indonesia using ancient genomic data.
- To understand the formation of the genetic structure across Wallace's line.
Main Methods:
- Analysis of two Late Neolithic genomes from western Indonesia.
- Integration with 19 published ancient genomes from Island Southeast Asia.
- Comparative genomic analyses to infer population histories.
Main Results:
- Identified an Early Holocene divergence between western (Hòabìnhian-related) and eastern (Papuan-related) forager ancestries.
- Documented later Neolithic and post-Neolithic gene flow, including Austronesian expansion and Papuan back-migration.
- Revealed that these later events reinforced and reshaped the initial genetic structure.
Conclusions:
- Propose a revised demographic model for Indonesian population history.
- Emphasize the role of repeated Holocene migrations acting on pre-existing regional differences.
- Highlight the complex interplay of ancient migrations in shaping present-day genetic diversity.
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