Previous research indicates that human genetic diversity in Wallacea—islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves—has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter–gatherer communities. Yet, inferences based on present-day groups proved insufficient to disentangle this region’s demographic movements and admixture timings. Here, we investigate the spatio-temporal patterns of variation in Wallacea based on genome-wide data from 16 ancient individuals (2600–250 years BP) from the North Moluccas, Sulawesi and East Nusa Tenggara. While ancestry in the northern islands primarily reflects contact between Austronesian- and Papuan-related groups, ancestry in the southern islands reveals additional contributions from Mainland Southeast Asia that seem to predate the arrival of Austronesians. Admixture time estimates further support multiple and/or continuous admixture involving Papuan- and Asian-related groups throughout Wallacea. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.

先前的研究表明，华莱士岛——现今印度尼西亚东部和东帝汶的岛屿，从未属于巽他或萨胡尔大陆架的一部分——的人类遗传多样性是由南岛移民农民和土著狩猎采集社区之间复杂的相互作用形成的。然而，事实证明，基于当今群体的推论不足以解开该地区的人口流动和混合时间。在这里，我们根据来自北摩鹿加群岛、苏拉威西岛和东努沙登加拉岛的 16 个古代个体（2600-250 年 BP）的全基因组数据研究了华莱士的时空变异模式。虽然北部岛屿的血统主要反映了南岛和巴布亚相关群体之间的联系，南部岛屿的血统揭示了来自东南亚大陆的额外贡献，这些贡献似乎早于南岛人的到来。混合时间估计进一步支持涉及整个华莱士的巴布亚和亚洲相关群体的多重和/或连续混合。我们的研究结果澄清了先前争论的混合时代，并表明新石器时代向东南亚岛屿的扩散与多个遗传祖先的传播有关。