Genomic footprints of ancient multi-species introgression events among allopatric cave-adapted Triplophysa species

The South-Central China (SCC) region is a global biodiversity hotspot that harbors considerable aquatic endemism; however, the evolutionary history of its cave-adapted Triplophysa (Cypriniformes: Nemacheilidae) species remains unresolved to date because of limited genetic markers and sampling. Here, we employed low-coverage whole-genome sequencing (lcWGS) and a newly designed Nemacheilidae-specific ultraconserved element (UCE) probe set to generate multiple markers and investigated the phylogenomics of 89 individuals of genus Triplophysa, spanning both cave- and riverine-adapted lineages. (1) Our phylogenetic reconstruction revealed a well-supported backbone phylogeny for cave-adapted Triplophysa, subdividing them into four main clades. (2) Divergence dating suggested that cave-adapted Triplophysa originated in the early Miocene (∼21 MYA), sharing a common ancestor with Triplophysa wulongensis. (3) Genome-wide tests (QuIBL, f-branch) demonstrated extensive incomplete lineage sorting and ancient introgression among ancestral lineages, suggesting that reticulate evolution may have driven the radiation of these cave fishes by providing a reservoir of genetic variation. Based on our results, we propose a scenario in which the early colonization of cave-adapted Triplophysa species was catalyzed by tectonic activity along the Ailao Shan-Red River shear zone (ARSZ). Our findings provide the first genome-scale evidence linking Miocene tectonics to the origin and diversification of subterranean ichthyofauna in SCC.