Abstract: Cavefishes display pronounced troglomorphic adaptations, such as visual degeneration, depigmentation, and scale reduction, as specialized responses to subterranean environments. Among these, the cave loaches (CLS) of the family Nemacheilidae represent China’s second-most diverse cavefish group; however, their evolutionary history remains poorly understood. To bridge this knowledge gap, we conducted whole-genome resequencing of 62 CLS species and two closely related taxa, complementing these data with published genomic resources. The reconstructed phylogeny identified ancient introgression as the primary driving force behind phylogenetic discordance, with incomplete lineage sorting as a secondary contributor. Pleistocene climatic fluctuations, coupled with species-specific genetic architectures, generated four distinct demographic trajectories across populations. Additionally, we delineated four distinct phases of lineage diversification in CLS, shaped by tectonic–climatic interactions, with alternating periods of acceleration and decline synchronized with the Asian orogenic and monsoonal cycles. This study provides the first integrated genomic perspective on the evolution of the CLS, demonstrating how biotic and abiotic factors have collectively shaped subterranean biodiversity.

Key words: cavefish, demographics, diversification, introgression, Phylogenomics