Resolving species-level diversity of Beringiana and Sinanodonta mussels (Bivalvia: Unionidae) in the Japanese archipelago using genome-wide data

•There are inconsistencies in phylogenies based on nuclear and mitochondrial DNA.•Two well-supported genome DNA-based clades show the presence of cryptic species.•Molecular clock shows Beringiana and Sinanodonta diverged >35 million years ago.•Ball-like shell morphology repeatedly appeared in the two genera in Lake Biwa.•The mtDNA-based classification of unionid mussels requires careful consideration.