Five Southward Waves: A Large-Scale Y-Chromosome Phylogeny Reveals Neolithic Farmer Expansions from China into Southeast Asia

How did Neolithic farming populations from China move south into Southeast Asia? The process has long been debated across linguistics, archaeology, and genetics. A team led by He Guanglin of Sichuan University, writing in Science Advances, uses the largest integrated Y-chromosome dataset to date to reconstruct a high-resolution, time-calibrated history of paternal expansion.

The study combines three data types: 1,507 high-coverage Y-chromosome sequences, 780 ancient East Asian genomes, and 1,748 low-coverage Southeast Asian sequences. The resulting Y phylogeny has fine temporal resolution, and it identifies at least five male-driven waves of Neolithic farmer expansion from China into Southeast Asia.

On the paternal side, O1 and O2 are the main contributing haplogroups. Five lineages—O1a-M119, O1-F1252, O1-F789, O2-M7, and O2-Z25921—form the core paternal founders, with expansion windows roughly 4,000 to 6,000 years ago. Geographically and linguistically, the five waves correspond respectively to the spread of Austroasiatic, Austronesian, and Kra-Dai speakers.

Unlike earlier work that relied mainly on single modern-population snapshots, this study folds in ancient East Asian genomes, letting lineage divergence times be cross-referenced with archaeological cultural sequences. The 780 ancient genomes provide direct temporal anchors for questions about which lineage appeared where, and when.

At the paternal level, the results support a demic-diffusion model for the southward spread of farming: people moved with their crops rather than ideas traveling alone. The thousand-scale Y data let researchers separate expansion events in distinct time windows rather than treating the southward movement as one undifferentiated migration. The authors caution that the Y chromosome records only the paternal line, and that the full population history still needs autosomal and mitochondrial evidence—but the linguistic-geographic consistency of the five waves already provides a clear paternal skeleton for future integrated work.

Overall, the paper offers one of the highest-resolution paternal-genetic frameworks yet for understanding the coupled spread of people, agriculture, and languages between East and Southeast Asia in the Neolithic.

Source: Mengge Wang, Yunhui Liu, Lintao Luo et al.; corresponding Guanglin He. Science Advances, 2026-02-18.