Phylogenetic relationships of Nemacheilidae cavefish (Heminoemacheilus, Oreonectes, Yunnanilus, Paranemachilus, and Troglonectes) revealed by analysis of mitochondrial genome and seven nuclear genes

Phylogenetic relationships of Nemacheilidae cavefish (Heminoemacheilus, Oreonectes, Yunnanilus, Paranemachilus, and Troglonectes) revealed by analysis of mitochondrial genome and seven nuclear genes DEAR EDITOR,Cave loaches within the family Nemacheilidae are among the most diverse group of cavefish in southwestern China.Although certain species have been included in previous phylogenetic studies, the intergeneric and interspecific relationships of Chinese cave loaches in Nemacheilidae remain poorly investigated due to insufficient sampling.In this study, a total of 45 samples from 37 recognized species and two unidentified species of cave loaches were collected, accounting for 87.5% of the eight recognized genera of cave loaches within the family Nemacheilidae in China.The complete mitochondrial genome (mitogenome) and seven nuclear genes were sequenced, and the phylogenetic tree of Chinese cave loaches was reconstructed.Both Bayesian inference and maximum-likelihood analyses resolved the phylogenetic relationships at the generic and species levels, suggesting the effectiveness of this multilocus marker system in determining phylogenetic relationships in Chinese cave loaches.Phylogenetic analysis not only confirmed previous taxonomic hypotheses based on morphological data but also provided new insights into the relationships of many cave loaches at the genus and species levels as well as suggestions for the current taxonomy of cave loaches within the family Nemacheilidae.The karst regions of southwestern China are considered the center of Chinese cavefish biodiversity, boasting the most concentrated distribution of cavefish in the world.However, many cavefish species in the region remain poorly known and highly threatened (IUCN, 2022).Nemacheilidae, which contains approximately 22 genera and 269 species, constitutes one of the largest and most diverse families, second only to Cyprinidae in terms of diversity (Zhang et al., 2020).These cave loaches, which include both stygophilic and stygobitic species, are restricted in their distribution to the karst regions of southwestern China and exhibit highly specialized morphologies (Lan et al., 2013;Li, 2018).This has led to inadequately resolved taxonomies and enigmatic phylogenetic relationships among cave groups.The presence of both subterranean and surface-dwelling phenotypes among