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The bitterling Tanakia lanceolata is a primary freshwater fish with wide distribution range in Japan; therefore, analysis of this species will yield much information on the formation of Japanese freshwater fish fauna. However, populations of this species are threatened by several human activities. To reveal the genetic population structure of T. lanceolata and the process of its formation, as well as its genetic status, we conducted phylogenetic analyses and estimated divergence times based on partial sequences of the mitochondrial DNA cytochrome b gene, using specimens collected across the distribution range. The results of the analysis showed that Japanese T. lanceolata is monophyletic and consists of seven local population groups that diverged from the Late Pliocene to the Middle Pleistocene. The population structure in western Japan was similar to that of other freshwater fishes (e.g., separation by the Suzuka Mountains), although there were several differences in population boundaries and the presence/absence of a secondary contact zone. The Central Highlands in central Honshu are the primary, or at least the most effective, geological barrier responsible for population divergence in Japanese freshwater fish species. However, the small genetic differentiation of the T. lanceolata population between the western and eastern sides of the Central Highlands suggested recent dispersal and gene flow across the region after uplift of the highlands. The genetic population structure indicated extensive genetic disturbance in the Kanto Region. Our results provide information on the formation process of the Japanese freshwater fish fauna, which could aid conservation efforts toward T. lanceolata.

Two new species of pike gudgeon, Pseudogobio agathonectris from western Honshu, Japan, and P. polysticta from eastern Honshu, Japan, are described, and P. esocinus (Temminck and Schlegel 1846) is redescribed. The two new species were previously considered to be P. esocinus, which had been only a nominal species of the genus from Japan. The two species are distinguishable from P. esocinus by following a combination of characters: tip of pectoral spiny soft ray not reaching that of 6th soft fin ray, and tip of outer edge of pectoral fin strongly curved posteriorly; long barbel (15.3–36.9% of HL in P. agathonectris, 16.9–34.8% in P. polysticta, respectively), with the tip commonly extending beyond vertical through anterior edge of eye; 10–14 (modally 13) and 12–14 (13) pectoral soft fin rays; long mouth (33.2–45.3% of HL and 29.6–42.0%); short length between anus and anal fin origin (16.5–21.4% of SL and 15.9–22.4%), with 11–14 (12) and 11–16 (12) scales; and small body size (at most 150 mm SL). Pseudogobio agathonectris is distinguishable from P. polysticta by the canonical discriminant functions based on five meristic and 25 morphometric characters, and distinct dark blotches and obscure black spots on dorsal and lateral body (vs. obscure blotches and many distinct spots).

The Chinese false gudgeon, Abbottina rivularis, is a common cyprinid fish that is widely distributed throughout continental East Asia, but exhibits a restricted, discontinuous distribution in western Japan, including Honshu and Kyushu islands. In this study, analyses of mitochondrial (cytochrome b) and nuclear (glyt, myh6, and RAG1) genes were conducted to investigate patterns and magnitudes of intraspecific differentiation among A. rivularis populations in Japan and adjacent continental areas. Phylogenetic analysis of the mitochondrial gene sequences resolved four major lineages—the Japan lineage (JL), a northern continental lineage (NCL), and two southern continental lineages (SCL1 and SCL2)—with uncorrected pairwise sequence distances of 9.4–15.2% (estimated divergence times, 7.9–17.1 Myr). Two lineages (JL and SCL1) occurred in both the Honshu and Kyushu districts of Japan. Compared with populations in continental areas, most Japanese populations exhibited less genetic diversity. The JL was divided into two well-differentiated sub-lineages distributed on Honshu and Kyushu islands, respectively. Kyushu Island, as well as areas on Honshu where the species is known to have been introduced, also harbored the SCL1 lineage, which constituted most of the populations on Kyushu. The applied nuclear DNA data strongly suggest that hybridization between the Japan and continental lineages has occurred on Kyushu Island. The artificial introduction hypothesis, instead of a two-origin scenario, best explains the origin of the SCL1 in Japan.

To reveal the primary historical events that affected the geographic differentiation in freshwater organisms in the Japanese archipelago, we investigated the phylogeny and phylogeographic structure of the widely distributed freshwater fish Pseudogobio esocinus. We conducted comprehensive phylogeographic analyses based on partial sequences of the mitochondrial DNA cytochrome b (cyt b) gene in 1,212 P. esocinus specimens from 201 locations in 136 river systems along with sequence data from related species. We also examined the entire cyt b sequence and three nuclear gene sequences for a subset of individuals to estimate the phylogenetic relationships and divergence times. Historical processes shaping the present phylogeographic patterns were inferred by the Bayesian skyline plot, mismatch distribution and nested clade phylogeographic analyses. The mitochondrial and nuclear DNA phylogenies showed that the Japanese P. esocinus was not monophyletic and consisted of three largely differentiated groups. Divided by the Central Highlands, two groups were distributed in southwestern Japan, with a third group in northeastern Japan. The estimated divergence time indicated that the framework of the present ranges of the three groups was formed during or before the Early Pliocene. In southwestern Japan, the two groups often occurred sympatrically and included several regional subgroups bounded by major mountain systems uplifted in the early Pleistocene, while in the northeastern Japanese group, recent (since about 0.3 million years ago) range expansion from the northwestern area was inferred. The results suggest the importance of the uplifting of the Central Highlands and interconnection with the continental area in the distribution and divergence of P. esocinus, which may have also influenced regional heterogeneity in the Japanese freshwater fauna. The contrasting phylogeographic patterns between northeastern and southwestern Japan probably reflect their topographic and geohistorical differences, and imply differences in the formation process of freshwater fauna between the two regions.

The genetic population structure of the small cyprinid Hemigrammocypris rasborella, distributed widely in lowlands of western Japan, was examined using partial sequence data of mitochondrial DNA (mtDNA). Molecular phylogenetic analysis revealed that the populations of the western Kyushu region were markedly differentiated from all eastern populations, such that the groups would be comparable to different species; their divergence was inferred to have occurred in the Late Miocene–Pliocene. Also, a largely divergent mtDNA group (with divergence in the early Pleistocene) was found in the Sanyo and northeastern Shikoku regions, forming a secondary contact zone in the western Kinki with the eastern mtDNA group. To date, these aspects of the population structure of H. rasborella appear to be unique among lowland fishes in western Japan. Deeper understanding of the formation processes of freshwater faunas in western Japan will require further comparisons of the phylogeographic patterns and ecological traits of constituent species.

To elucidate the genetic population structure of Pseudogobio esocinus (Cyprinidae) in central Honshu, Japan, we performed phylogeographic analysis based on partial mitochondrial cytochrome b gene sequences. We found not only differentiation of mtDNA lineages between basins (uncorrected p ≈ 2%), presumably associated with uplifting of the Suzuka Mountains in the early Pleistocene, but also more diverged two mtDNA lineages within basins (p ≈ 8%). No evidence of mtDNA introgression from related sympatric species was found. The phylogeographic history of these two lineages should be elucidated by further analysis based on the specimens of P. esocinus from the entire distribution range.