Repeated adaptation of the freshwater goby Rhinogobius kurodai from lotic to lentic environments in the Kanto Plain, Japan: morphological, behavioural and genetic approaches

Habitat generalists, which occupy a variety of environments, provide valuable systems for investigating how microgeographic adaptation drives population differentiation and range expansion, ultimately promoting speciation. This study focused on Rhinogobius kurodai, a freshwater goby widely distributed across the diverse aquatic landscapes of the Kanto Plain, the largest plain in Japan, which includes both lotic and lentic environments. We investigated whether adaptation to lentic environments from lotic ancestors has repeatedly occurred at a microgeographic scale. Seventeen local populations (nine lotic and eight lentic) from seven river systems were sampled to analyse their morphological traits, behavioural characteristics, and genetic population structure. The analyses revealed that the lentic populations, compared to the lotic populations, had more elongated pelvic fins and more frequently utilized the upper and middle water layers of the tank, accompanied by reduced sticking behaviour. In addition, lentic group exhibited greater variation in body shape. Nuclear single nucleotide polymorphism data obtained using the multiplexed ISSR genotyping by sequencing (MIG-seq) indicated that population structure largely reflected geographic patterns, with some gene flow detected between lotic and lentic populations within each region. However, morphological similarity in pelvic fins was better explained by habitat type (lotic or lentic) than by either geographic proximity or genetic similarity. These results suggest that R. kurodai has repeatedly adapted to lentic environments at a microgeographic scale through both convergent and divergent adaptations in functional traits. This study presents a clear case of how fine-scale adaptation enables organisms to colonize diverse environments.