Species delimitation within a taxonomically complex group: An example from the genus Apodemus (Rodentia: Muridae)

Species delimitation based on genetic data plays a critical role in taxonomy research, particularly for resolving taxonomically complex groups and detecting cryptic diversity. However, few studies have assessed the consistency and reliability of the various species delimitation approaches using the real dataset. In this study, we compared the most widely used approaches for species delimitation within the complex group of the Apodemus genus from China. Multiple species delimitation approaches were applied, including the multispecies coalescent model- and machine learning-based approaches. Unexpectedly, we observed considerable discrepancies across methods, with some results lacking taxonomic validity. To resolve the taxonomic puzzle of this taxon, we integrated phylogenetic and population analyses with morphological and ecological assessments, ultimately recognizing nine valid species and identifying one cryptic species. Phylogeographic analyses of endemic lineages in east Himalayan Mountains of Southwest China indicated that orogenic activity and glacial-interglacial cycles have played key roles in the speciation and diversification of Apodemus in China. These results highlight the challenges of species delimitation in taxonomically complex groups and demonstrate that relying solely on molecular methods is insufficient. We advocate an integrative taxonomic framework that combines molecular, morphological, and ecological data to address these taxonomic puzzles.