Phylogeomics Reveals Ancestral Introgression and Paleogeoclimate Co‐Facilitated Speciation and Diversification of Chinese Endemic Cavefishes

values) are enriched for Gene Ontology terms related to circadian behaviour, phenotypic plasticity, lipid metabolism, oxygen transport and reproduction. Demographic simulations further suggest that geoclimatic factors, together with the unique genetic attributes of the group, likely promoted founder effects, inbreeding, and subsequent declines in effective population size, resulting in two distinct demographic trajectories. Additionally, our results indicate that the origin and speciation of the TCG were closely synchronised with the rapid uplift of the Qinghai-Tibet Plateau and associated climatic transitions. We further identify three distinct stages of lineage diversification, characterised by alternating accelerations and declines driven by tectonic-climate interactions that were synchronised with major Asian orogenic events and monsoon cycles.