Mitochondrial–nuclear discordance in the amago salmon, Oncorhynchus masou ishikawae, in the River Miya, Japan

Abstract

The amago salmon, Oncorhynchus masou ishikawae, is an endemic subspecies of O. masou in Japan. Populations in the River Miya, located at the entry of Ise Bay, central Japan, represent indigenous wild populations. They have been isolated in small tributaries as a result of environmental degradation in recent decades, with some populations also partially affected by stocking of hatchery fish of River Miya origin. We examined the genetic structure of these populations, using mitochondrial (mtDNA) and microsatellite DNA markers, in order to devise strategies for their long-term management and conservation. For mtDNA, sympatry of two genetically distinct clades was observed in some River Miya populations, together with populations from other rivers flowing into Ise Bay drainage. Taking into consideration paleogeographical information, it is conceivable that large-scale genetic admixture of the two clades in O. m. ishikawae occurred in Ise Bay in the past. For microsatellites, inter-population genetic divergence was small and genetic bottlenecks were detected in small-sized populations, with many microsatellite loci monomorphic. Although a Bayesian-based assignment test suggested two clusters in River Miya populations, they are likely to have been caused by anthropogenic effects in recent years since these clusters reflect population bottlenecks, not mtDNA clades. In conclusion, indigenous wild populations of O. m. ishikawae in the River Miya should be treated as a single conservation unit and the exchange of individuals between tributaries is needed to prevent the progress of genetic bottlenecks.