Genetic structure and demographic connectivity of marbled flounder (Pseudopleuronectes yokohamae) populations of Tokyo Bay

Abstract Marine populations are generally well connected through larval exchange, and juvenile and adult migration. Genetic differentiation and/or local adaptation among populations are sometimes observed at small spatial scales. The marbled flounder ( Pseudopleuronectes yokohamae ) is a commercially important coastal species in Tokyo Bay, Central Japan, exhibiting different spawning phenology at a small scale. Using 30 highly polymorphic microsatellite loci, including the 16 new microsatellite loci developed in the present study, we estimated the genetic structure and demographic connectivity of specimens collected along Tokyo Bay in 2012–2013 and 2015–2016. F -statistics indicated a genetic differentiation between adult populations collected within and outside Tokyo Bay during both collection periods, but almost no difference was detected between the populations from the inner and outer parts of Tokyo Bay. Assignment tests directly estimated demographic connectivity between the inner and outer bays via larval dispersal and juvenile and adult migration. The average movement distance of marbled flounder was 13.1–29.6 km, with a maximum distance of 42.8–54.0 km. This movement distance contributed to the strong demographic connectivity between the inner and outer bays. Meanwhile, an indirect method using the isolation by distance (IBD) theory underestimated the average movement distance (5.0–7.8 km) because the isolated setting of Tokyo Bay resulted in a higher IBD slope. Based on the results of F -statistics and assignment tests, we suggest that a multilayered management by local and regional organizations may benefit the fishery in Tokyo Bay.