The prehistoric peopling of Southeast Asia

TLDR

Southeast Asia’s human occupation history is debated, with evidence of Hòabìnhian hunter‑gatherers until ~4000 yr BCE, followed by farming expansion and competing theories of indigenous agriculture versus a southward farmer migration shaping current genetic diversity. Sequencing 26 ancient genomes reveals that both Hòabìnhian hunter‑gatherers and East Asian farmers contributed to present Southeast Asian genetic diversity, with additional migrations shaping island SEA and Vietnam, thereby resolving a long‑standing debate.

Abstract

The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the “two-layer” hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.