Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA1. So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939–7751 calibrated years before present (yr cal bp; present taken as ad 1950), and Gua Cha in Malaysia (4.4–4.2 kyr cal bp)1. Here we report, to our knowledge, the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (comprising mainland southeast Asia and the continental islands of western Indonesia) and Pleistocene Sahul (Australia–New Guinea). We extracted DNA from the petrous bone of a young female hunter-gatherer buried 7.3–7.2 kyr cal bp at the limestone cave of Leang Panninge2 in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic forager, who is associated with the ‘Toalean’ technocomplex3,4, shares most genetic drift and morphological similarities with present-day Papuan and Indigenous Australian groups, yet represents a previously unknown divergent human lineage that branched off around the time of the split between these populations approximately 37,000 years ago5. We also describe Denisovan and deep Asian-related ancestries in the Leang Panninge genome, and infer their large-scale displacement from the region today.

The rock art of Southeast Asia has been less thoroughly studied than that of Europe or Australia, and it has generally been considered to be more recent in origin. New dating evidence from Mainland and Island Southeast Asia, however, demonstrates that the earliest motifs (hand stencils and naturalistic animals) are of late Pleistocene age and as early as those of Europe. The similar form of the earliest painted motifs in Europe, Africa and Southeast Asia suggests that they are the product of a shared underlying behaviour, but the difference in context (rockshelters) indicates that experiences in deep caves cannot have been their inspiration.

Long-distance trade in obsidian from sources in the southwest Pacific has been well-docwnented for the Lapita culture complex, beginning about 1600 BC Analyses of obsidian artifacts from recent excavations at Bukit Tengkorak in southeastern Sabah (Borneo, Malaysia) indicate the use of obsidian from multiple sources in Melanesia as early as the 5th millenniwn BC The archaeological presence of obsidian, up to more than 3500 Ian from its source, is the surviving evidence of what was almost certainly the longest Neolithic trade route in the world. In addition, these results indicate that long-distance trade networks existed in Indonesia at least 2500 years prior to the Lapita culture, and strengthen hypotheses of its origins in southeast Asia.

Hanging Coffin is a unique and ancient burial custom that has been practiced in southern China, Southeast Asia, and near Oceania regions for more than 3,000 years. Here, we conducted mitochondrial whole-genome analyses of 41 human remains sampled from 13 Hanging Coffin sites in southern China and northern Thailand, which were dated between 2,500 and 660 years before present. We found that there were genetic connections between the Hanging Coffin people living in different geographic regions. Notably, the matrilineal genetic diversity of the Hanging Coffin people from southern China is much higher than those from northern Thailand, consistent with the hypothesized single origin of the Hanging Coffin custom in southern China about 3,600 years ago, followed by its dispersal in southern China through demic diffusion, whereas the major dispersal pattern in Southeast Asia is cultural assimilation in the past 2,000 years.

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