Modern and Ancient Genomes Reveal Neolithic Paternal Expansions of Millet and Rice Farmers and Demic Diffusion from China into Mainland Southeast Asia

Overview

This study reconstructs paternal demographic history across East and Southeast Asia through analysis of 14435 ancient and present-day individuals, including 584 newly sequenced complete Y-chromosome genomes. The research establishes the highest-resolution Y-chromosome phylogeny for ancient East and Southeast Asian populations and identifies 138 paternal lineages with origins during the Neolithic period. The investigation specifically examines the genetic signature of millet farming expansion from northern China into southern regions and Mainland Southeast Asia, with emphasis on demic diffusion patterns and population structure differentiation among Han and minority ethnolinguistic groups.

Methods and approach

The study employs a comprehensive paternal genomic dataset incorporating both ancient and contemporary samples across Eurasian populations. A maximum-likelihood phylogenetic framework was constructed for eastern Eurasian Y-chromosome diversity, incorporating 584 newly sequenced whole Y-chromosome genomes. Time-calibrated phylogenetic analysis was applied to identify and date paternal lineage diversification events. The temporal reconstruction focuses on the Neolithic period and subsequent expansions. Population structure analysis differentiated northern and southern Han populations alongside ethnolinguistic minority groups classified by geographic region and linguistic affiliation (Tai-Kadai, Hmong-Mien, Tibeto-Burman speakers).

Results

Analysis identified 138 paternal lineages with Neolithic diversification origins, of which 17 dominant lineages are shared between China and Mainland Southeast Asia. A marked paternal expansion originates approximately 5000 years ago, with peak expansion between 3500 and 3000 years ago. Northern and southern Han populations exhibit minimal paternal differentiation, whereas southern ethnolinguistic minorities display distinct substructures: coastal populations align genetically with Tai-Kadai speakers, southwestern populations with Hmong-Mien speakers, and highland populations with Tibeto-Burman speakers. The reconstruction reveals substantial paternal contributions from ancient millet farmers and their Han descendants to the genetic composition of southern China and Mainland Southeast Asia, with secondary enrichment from rice farmer-mediated population movements.

Implications

The findings provide empirical support for a demic diffusion model of Neolithic farming expansion and Han cultural dissemination into southern China and Mainland Southeast Asia. The paternal lineage data demonstrate that agricultural transition in these regions involved substantial human migration and gene flow rather than cultural transmission alone. The genetic architecture reflects historical population movements associated with millet and rice farming economies during the mid-to-late Neolithic period. The study establishes that ethnolinguistic diversity in southern China and Mainland Southeast Asia is substantially explained by spatially structured paternal contributions from successive farming populations, with geographic clustering of lineages corresponding to linguistic and cultural boundaries. These results provide a genomic framework for understanding Holocene demic processes in East and Southeast Asia and their relationship to subsistence economy transitions and ethnolinguistic development.