Model-based multilocus, genomic, and phenotypic integration reveals species assignment inconsistencies and sampling...

Widespread amphibians often show inconsistent species assignments in public databases, complicating accurate range-wide biodiversity mapping and obscuring gaps in taxonomic resolution. We assessed three widespread cryptic Asian Dicroglossid genera (Fejervarya, Hoplobatrachus, Quasipaa) across Indomalayan and Palearctic ecozones, where diffuse boundaries, taxonomic uncertainty, and exotic introduction impact biodiversity patterns. Using a hierarchical, scenario-based species delimitation framework based on publicly available molecular datasets and targeted new data, we evaluated 18 species-delimitation scenarios across 14 nominal taxa, with GenBank-based assignment as a control model. All scenarios were based on shared multilocus Dicroglossidae datasets (up to 517 sequence entries), integrating GenBank data with targeted sampling across two ecozones. The best-supported scenario was further refined using genome-derived SNPs from heterogeneous data sources (GBS, RNA-seq, and WGS/WCS), together with a binary morphological trait. Across analyses, the best-supported Model A1 showed a lower MLE than GenBank-based assignments, indicating non-random taxonomic mismatches between updated local classifications and public database entries. The model delineated 17 dicroglossid clades, including a single Hoplobatrachus lineage in East Asia. Diverging over 19 Mya, Fejervarya showed pronounced cryptic structure, with two deeply divergent clades recovered within the F. limnocharis, F. kawamurai, and F. multistriata species complexes, while Quasipaa displayed deep divergences. Integration of ecological niche modelling and bioacoustic analyses for a selected sympatric pair at the ecozone boundary further showed differences in predicted habitat associations and selected acoustic traits between F. kawamurai [Clade II] and F. multistriata [Clade I], despite substantial range overlap. Fejervarya multistriata was associated with coastal lowlands, whereas F. kawamurai was more widely distributed inland. Our integrative framework highlights regions with high mismatch under dense sampling (e.g., the Yangtze-Huai transition and East Asian mainland), and regions with mismatch under limited sampling, particularly insular systems (e.g., Taiwan and Hainan), defining priorities for future genomic surveys.