Multiple southward migrations of Neolithic Chinese farmers into Southeast Asia revealed from large-scale Y-chromosome sequences

The scale and timing of genetic contributions from ancient millet- and rice-farming populations in China to Southeast Asian populations remain incompletely understood, particularly concerning Y-chromosome diversity. Here, a comprehensive dataset of Chinese Y-chromosome variations, including 1507 high-coverage sequences from ethnolinguistically diverse groups, was analyzed alongside 780 ancient genomes from eastern Eurasia and 1748 low-coverage sequences from Southeast Asia. We reconstructed a high-resolution, time-calibrated Y-chromosome phylogeny, revealing multiple male-biased expansions associated with Neolithic cultural innovations in South China. These expansions markedly shaped the paternal ancestry of both South China and mainland Southeast Asia. Founding lineages linked to Hmong-Mien and Tai-Kadai speakers were traced, revealing notable growth during the Middle Neolithic. Phylogeographic structure, network analyses, and haplogroup distributions indicate complex demographic interactions that established the genetic legacy of Neolithic farmers in Southeast Asia. These findings highlight recurrent southward migrations of Chinese farmer-related groups and their enduring influence on the paternal genetic landscape of ancient and present-day Southeast Asians.