Molecular Systematics and Distribution Pattern Evolution of Triplophysa Species in China: A Comparison of Widespread and Narrow-Range Taxa

The genus Triplophysa (Nemacheilidae), a dominant component of the Qinghai–Tibet Plateau (QTP) fish fauna, remains poorly understood in its evolutionary relationships and phylogeography. We integrated mitochondrial phylogenomics and population genetics (COI and cytb) with MaxEnt modeling across four time periods—the present, the Last Interglacial (LIG), the Last Glacial Maximum (LGM), and the Mid-Holocene Optimum (MHO)—to examine 12 Triplophysa species, ranging from widely distributed to narrowly endemic taxa. Phylogenetic analyses recovered a monophyletic Triplophysa with a clear split between cave- and non-cave-dwelling lineages. Six range-restricted species (T. stenura, T. dalaica, T. siluroides, T. obscura, T. hsutschouensis, and T. minxianensis) formed reciprocally monophyletic clades, whereas widespread species (T. leptosoma, T. stoliczkae, T. brevicauda, T. orientalis, and T. bleekeri) exhibited non-monophyletic patterns in mitochondrial gene trees, likely reflecting incomplete lineage sorting or mitochondrial capture, though distinguishing these processes requires nuclear data. A positive association between genetic diversity and range size was observed for COI nucleotide diversity when two bottleneck-affected species were excluded. Paleoclimatic reconstructions revealed that suitable habitats expanded to their maximum during the LGM and contracted during interglacials, highlighting two climatically stable refugia in the central Loess Plateau–northern Qinling foothills and the eastern QTP margin–northern Hengduan Mountains. Our results demonstrate a tight coupling between phylogenetic patterns and range dynamics, with narrowly distributed endemics exhibiting both monophyly and reduced genetic diversity. These findings identify genetically vulnerable species as conservation priorities and provide a scientific framework for safeguarding Triplophysa diversity in a warming world.