Loss of genetic variation and increased population differentiation in geographically peripheral populations of Japanese char Salvelinus leucomaenis

In recent years, populations of the Japanese char, Salvelinus leucomaenis have decreased in central Honshu in Japan due to environmental changes and fishing pressure. Therefore, it is desirable to effectively increase the char resources. In order to formulate appropriate strategies for the development of sustainable fisheries in central Honshu, we compared the genetic variability and genetic differentiation between the char populations of central Honshu and those of northern Japan using five microsatellites and the mitochondrial control region. The number of alleles per locus, allelic richness, and expected heterozygosity were 1.4–2.4, 1.4–2.4, and 0.156–0.289, respectively, for the central Honshu populations and 6.8–10.6, 5.6–8.9, and 0.452–0.731, respectively, for the northern Japan populations. The genetic variability of the central Honshu populations was significantly lower than that of the northern Japan populations. The same tendency was observed for the nucleotide diversity of the mitochondrial control region. On the other hand, the FST estimates were significantly higher for the central Honshu populations than for the northern Japan populations. In this study, we did not observe linkage disequilibrium and deviation from the Hardy–Weinberg equilibrium. Thus, we think that the central Honshu populations have low genetic variability and high genetic differentiation due to restricted gene flow and small population size because these populations are landlocked and are located near the southern tip. In the northern Japan populations, the genetic variability of the mitochondrial control region was relatively low as compared to that of the microsatellite markers. We surmised that Salvelinus leucomaenis may have been subjected to a founder effect in the late Pleistocene period as has been reported in the Arctic char Salvelinus alpines.