Dataset: Resolving species assignment in public data refines biodiversity mapping of widespread amphibians in Asian ecozones

Amphibians with wide distributions are often subject to misidentification and inconsistent taxonomic labeling in open-access databases and published studies, leading to confusion over species boundaries. This dataset supports a multifaceted species delimitation framework applied to three dicroglossid frog genera: Fejervarya, Hoplobatrachus, and Quasipaa, distributed across the Indomalayan and Palearctic ecozones. The datasets includes (a) multilocus (4,044 bp), (b) concatenated supermatrix of genome-wide SNP data (~700,000 sites), and (c) 147 genome-wide loci from open-source GBS, RNA-seq, and WGS/WCS datasets, yielding 155 loci with 20 variants per split locus from 517 taxon entries and representing 14 recognised species across the two ecozones.

These data were used to evaluate 18 competing topological hypotheses using Bayesian species delimitation, model selection, and iterative genomic refinement. Complementary data layers include ecological niche models (ENMs) and advertisement call recordings from key populations in East Asia. The dataset enables the identification of cryptic clades and provides ecological and acoustic evidence supporting taxonomic divergence within the Fejervarya kawamurai, F. multistriata, and F. limnocharis species complexes.

Environmental variables such as precipitation of the driest month, elevation, and diurnal temperature range were identified as key predictors shaping distribution patterns. Additionally, call analysis validated the distinctiveness of sympatric clades within the Eastern Yangtze River Basin. The genomic and ecological datasets provided here support the correction of mislabeled GenBank records and offer a reusable framework for future taxonomic revision, comparative phylogeography, and amphibian biodiversity research.