Population genetic structure and demographic history of Rhodeus atremius suigensis , an endangered bitterling in Japan

Demographic events can shape genetic diversity through genetic drift, often leaving a persistent signal in the genetic characteristics of species. Rhodeus atremius suigensis is an endangered bitterling fish endemic to the Okayama Plain, Japan. In this study, we inferred its demographic history and genetic structure using a comprehensive analysis of the mtDNA ND1 gene, microsatellite markers (MS) and MHC class IIB gene. Based on mtDNA, R. a. suigensis included two sublineages; A and B. While the former was widely distributed, the latter was restricted to eastern populations that were monomorphic in MHC. Phylogenetic analysis revealed that R. a. suigensis , together with R. a. atremius , experienced a substantial bottleneck in the middle Pleistocene. In MS and MHC, genetic diversity was low in all populations; ranked as the lowest among bitterling species. Bayesian clustering suggested that two clusters of MS had been widely introgressed in the centre of its distribution. These clusters seem to have been formed by the disruption of the distribution in the last Pleistocene, and later admixed by a large-scale reclamation in the Okayama Plain since the sixteenth century, which triggered a decline in effective population size ( N e ) in many populations. Based on coalescence analysis, all populations reached their lowest N e around the middle of the twentieth century. Accordingly, R. a . suigensis seems to have experienced two large bottlenecks in the past. While the first bottleneck was probably due to climatic changes in the middle Pleistocene, the second is due to anthropogenic degradation and fragmentation of habitats in recent years.