Recent reduction of genetic diversity in markless form of the red-spotted masu salmon Oncorhynchus masou ishikawae in the Ono River, Kyushu, Japan

Markless form of masu Oncorhynchus masou masou and red-spotted masu salmon O. masou ishikawae (iwame) is distributed in a few rivers within Japan. Iwame is thought to be an intraspecific color variation that has evolved independently in each river. We investigated the genetic variation of iwame and red-spotted masu salmon (amago) in the Kohbaru River system using 21 microsatellite loci in 299 individuals collected in 2005 and 2013–2014. Overall, the genetic diversity within iwame was almost lost as of 2013 (allelic richness: 1.0–1.1, H E : 0.01–0.02), and all microsatellite loci were fixed, except for two loci. In comparisons between temporal samples (i.e., 2005 vs. 2013), a remarkable reduction of genetic diversity was observed within the iwame collected in the middle reach. In contrast, amago did not show a reduction of genetic diversity, although the levels of genetic diversity were very low (allelic richness: 1.4–2.7, H E : 0.14–0.40). The effective number of breeders using linkage disequilibrium (LD) method and the effective population size using temporal method were very small (LD Method: <45; temporal method: <17). Significant genetic differentiation was found among most iwame and amago samples despite their geographic proximity. This genetic differentiation is probably due to the recent genetic drift caused by the isolation and reduction of the population size. We suggest that continuous genetic monitoring focused on further loss of genetic diversity and genetic introgression of non-native amago should be prioritized to make management plans for long-term persistence of iwame and amago in this river.