Whole-genome sequencing reveals Yunnan as the crossroads of east and Southeast Asia for human gene flow

Yunnan Province has long served as a key nexus facilitating economic and cultural exchanges between East Asia, Southeast Asia, and Qinghai-Tibet Plateau. However, previous genetic studies were largely limited by sparse marker density, low sequencing depth, or single-population designs, leaving the population genetic structure and demographic history insufficiently resolved. Here, we conduct a high-resolution population genetic study based on 366 high-depth whole-genome sequencing samples from six ethnic groups, including Bai, Dai, Hani, Miao, Tibetan, and Han. We identify approximately 3.51 million novel variants and reveal fine-scale population structure and complex demographic histories among Yunnan ethnic groups. Beyond the three ancestries proposed by the tri-genealogy hypothesis, we detect a Han Chinese-related lineage, Yan-Huang, within multiple Yunnan populations. We further demonstrate that Yunnan represents a major gene-flow hotspot across East and Southeast Asia despite geographic barriers. Finally, we identify genomic loci under positive selection with candidate genes enriched in immune regulation, energy metabolism, cardiac development, and dietary adaptation, highlighting the role of local environmental pressures in shaping the genetic diversity of Yunnan populations.