Japanese Freshwater Fishes: Biogeography and Cryptic Diversity

Abstract

More than 300 species of freshwater fishes are present in Japan. Because their distribution is expected to reflect geological history consequent to their low dispersal ability, they are a suitable group for studying historical relationships between land and biota. The strictly freshwater fish fauna in the Japanese Archipelago is primarily separated into two groups: those in northeastern Hokkaido, and those in other southwestern areas. The latter is further divided into two endemic faunas in the eastern and western regions across the Fossa Magna area. Recent phylogenetic and phylogeographic studies, primarily using mitochondrial DNA markers, support the importance of the Fossa Magana area in isolating related forms or intraspecific populations since the Late Miocene–Pliocene. This isolation, however, is not a primary one in some species. In western Japan, which has a rich and endemic freshwater fish fauna, both similar and different phylogeographic patterns have been observed among species, which may reflect differences in distribution histories and ecological traits of species. Further analyses using nuclear DNA loci, or genomic data, are necessary to elucidate the true processes of distribution, demography, and adaptation. Currently, 181 species/subspecies that depend heavily on freshwater environments are recognized in the Japanese Archipelago, but at least 244 evolutionary units (i.e., deep lineages with a long, unique history) are included in its freshwater fish fauna. The introduction of nonindigenous species is the primary driver for the decrease in β-diversity among regions, but the effects of species transplanted from other regions within Japan (i.e., the mixture and loss of endemic evolutionary units) remain underevaluated. Evolutionarily distinct units of freshwater fishes are historical legacies and should be maximally protected and passed on to future generations.