Large-Scale Genomics Reveals Three-Source Ancestry and Layered Adaptation to High Altitude in Tibetan Chickens.

Tibetan chickens exhibit adaptive traits for the hypoxic Tibetan Plateau, yet how distinct ancestral inputs, their timing, and their functional consequences jointly shape this adaptation remains poorly understood. To address this, we integrated admixture modeling with ancestry tract-length dating across 1054 whole genomes, resolving three distinct ancestral sources-Northwest China (NWC), the Sichuan-Yunnan adjacent region (SYA), and the Southern Himalayan Foothills (SHF)-whose contributions are temporally stratified: NWC forms the deepest founding layer (>928 generations), SHF records an ancient but low-intensity signal (∼928 generations; 95% CI: 875-1024), and SYA reflects a major recent expansion (∼514 generations; 95% CI: 493-541) with stepwise diffusion across the plateau. Selection scans calibrated against a demographic null model indicated that these sources are enriched for distinct functional categories: NWC for vascular homeostasis and coagulation (e.g., VWF, TSPAN9), SYA for calcium signaling and metabolic regulation (e.g., CACNA2D1, AMY2A), and SHF for pulmonary vascular remodeling (e.g., AGTR1). These findings indicate that high-altitude adaptation in Tibetan chickens involves temporally layered contributions from multiple ancestral sources, each associated with distinct candidate functional pathways-a pattern consistent with human-mediated dispersal shaping the genetic architecture of highland populations.