Speeding up taxonomy in the digital age: A deep learning approach for identifying cryptic freshwater snails

Cryptic species complexes pose fundamental challenges to biologists, as species exhibit minimal morphological differences that require integrating morphology, genetics, and biogeography for identification. Here, we present a deep learning approach to support species identification in the freshwater snail genus Radomaniola (Hydrobiidae), a morphologically cryptic group from the Balkans. Our approach mirrors the integrative workflow of expert taxonomists by combining shell images, morphometric measurements, and collection‑site metadata, with optional phylogenetic information. Despite being trained on fewer than 700 specimens across 20 visually similar species with strongly imbalanced class sizes, the system achieved high identification performance. Careful control of spurious correlations, such as those arising from site‑specific imaging conditions or overly precise geographic metadata, was essential to ensure that the network learned biologically meaningful features. Across all experiments, integrating multiple data types and jointly optimizing meaningful embeddings and classification consistently improved performance over image‑only and classification‑only baselines. On specimens from collection sites seen during training we achieved a macro-averaged F1 score of 0.93. Even though this dropped as low as 0.14 when evaluating on specimens from previously unsampled localities, it could be rapidly recovered by retraining with 2-3 newly labeled specimens. Additionally, model top-3 accuracy stayed consistently above 80% in all settings. These results show that relatively lightweight deep learning models can provide practical decision support in real taxonomic workflows.