Population genetic structure of an androdioecious freshwater clam (<i>Corbicula fluminea</i>) and its clonal reproduction analysed through GRAS-Di sequencing technology

Abstract The freshwater clam Corbicula fluminea is a simultaneous hermaphrodite that reproduces through androgenesis. However, we found the coexistence of males and hermaphrodites (androdioecy) of C. fluminea in the Yasu River in Shiga Prefecture and in the Shirakawa River in Kyoto, Japan. In this study, we investigated the genetic structure of the androdioecious populations and the genetic relationship between brooding clams and brooded juveniles in their egg pouches, using genotyping by random amplicon sequencing–direct (GRAS-Di) to detect single nucleotide polymorphisms in gill tissue samples. Principal component analysis and assignment tests showed that males collected from the Yasu River were genetically distinct from males collected from the Shirakawa River and from hermaphrodites collected from both rivers. The results reveal maintenance of a male lineage in the Yasu River from 2009 to 2018, whereas in the Shirakawa River males were not distinct from hermaphrodites. In the study locations, this species exhibited two shell colour phenotypes (‘yellow’ and ‘green’), but correspondence between shell colour and genotype was not detected. A perfect match of all 6968 single nucleotide polymorphisms was found between the brooding clams and brooded juveniles, which confirmed the clonal reproduction with androgenesis reported previously from cytological observations.