Current Genetic Status of Nagaremon-charr, a Threatened Morphotype of Salvelinus leucomaenis in the Ane River, Lake Biwa System, Central Japan, With Comments on Its Conservation.

Stream-dwelling white-spotted charr, Salvelinus leucomaenis, populations tend to have unique color and spot patterns in different regions and may even display stream-specific patterns. An extreme edge of such diversity, found in individuals with atypical body color patterns (so-called nagaremon-type charr, a rare morphotype of Salvelinus leucomaenis [hereafter termed nagaremon-charr]), sympatrically occurring with normal-charr, has been reported from only six small isolated populations in Japan. Based on morphological and ecological perspectives, nagaremon-charr has been considered as an intraspecific color variant of white-spotted charr, although the genetic status of nagaremon-charr has not been determined. In this study, genetic diversity and population structure of the nagaremon-charr in a tributary of the Ane River (Lake Biwa system) were investigated through microsatellite and mtDNA analyses. Nagaremon-charr and sympatric normal-charr in the tributary shared the mtDNA haplotypes and were assigned to the same cluster in the STRUCTURE analysis and discriminant analysis of principal components (DAPC). These results suggested that nagaremon-charr in the Ane River is an intra-populational specific color variant of white-spotted charr. Above a waterfall, nagaremon-charr specimens exhibited extremely reduced genetic diversity, indicating that genetic drift may account for the fixation of the nagaremon-morphotype. Normal-charr below the waterfall clustered separately from hatchery-reared charr, indicative of native status of the former. Thus, both nagaremon-charr and normal-charr in the entire Ane River tributary should be conserved.

Mitochondrial DNA population structure of the white-spotted Charr (Salvelinus leucomaenis) in the Lake Biwa water system.

A phylogeographic analysis of mitochondrial DNA sequences was performed in order to elucidate the origin, dispersal process, and genetic structure of white-spotted charr in the Lake Biwa water system. Two haplotypes were most common in the Lake Biwa water system, and were also common in the adjacent inlet rivers of the Sea of Japan. These results suggest that in the glacial periods of the Pleistocene, white-spotted charr dispersed into the northern inlet rivers of Lake Biwa from adjacent inlet rivers of the Sea of Japan by watershed exchanges, colonizing the whole of the Lake Biwa water system. Mitochondrial DNA diversity contrasted sharply between the western and eastern parts of the system, suggesting that the populations in the western part might be more reduced than those in the eastern part in relation to the smaller habitat size. The high overall FST estimate (0.50), together with pairwise comparisons of FST, indicated significant genetic divergence between populations due to isolation and small population size. Hierarchical analysis (AMOVA) also showed that genetic variation was more pronounced among regions (28.39%) and among populations within regions (47.24%) than within populations (24.37%). This suggests that each population in and around the Lake Biwa water system should be treated as a significant unit for conservation and management.

Conformation and the sodium ion condensation on DNA and RNA structures in the presence of a neutral cosolute as a mimic of the intracellular media.

Water-soluble neutral cosolutes can be used to quantify biomolecular properties in the particular molecular environment occurring in a cell. We studied the conformation and the thermal stability of DNA and RNA structures in the presence of PEG [poly(ethylene glycol)] and smaller cosolutes of glycerol, ethylene glycol, 1,3-propanediol, 2-methoxyethanol, and 1,2-dimethoxyethane. Although the neutral cosolutes destabilized the oligonucleotide duplex and the hairpin structures, the left-handed Z-form duplex was more energetically favored in the cosolute-containing solutions. These observations were due to the contribution of water molecule on the nucleotide structure formations because the cosolutes act as an osmolyte to reduce the water activity of a solution. Moreover, the sodium ion condensation for the duplex and the hairpin formations was reduced in the presence of PEG, while that for the transition from the B-form to the Z-form was unaltered. The CD (circular dichroism) and EPR (electron paramagnetic resonance) spectra demonstrated that the cosolutes changed the helical conformation of the unstructured oligonucleotides, but not those of the ordered structures. The results of the favorable formation of the noncanonical nucleotide structures, and minimized conformational and thermal perturbations of the ordered nucleotide structures in the cosolute-containing solutions implicate the significance of the intracellular environment on DNA and RNA structures in a cell.

Molecular phylogenetic relationships of Eastern Asian Cyprinidae (pisces: cypriniformes) inferred from cytochrome b sequences.

Complete mitochondrial cytochrome b sequences of 54 species, including 18 newly sequenced, were analyzed to infer the phylogenetic relationships within the family Cyprinidae in East Asia. Phylogenetic trees were generated using various tree-building methods, including Neighbor-joining (NJ), Maximum Parsimony (MP) and Maximum Likelihood (ML) methods, with Myxocyprinus asiaticus (family Catostomidae) as the designated outgroup. The results from NJ and ML methods were mostly similar, supporting some existing subfamilies within Cyprinidae as monophyletic, such as Cultrinae, Xenocyprinae and Gobioninae (including Gobiobotinae). However, genera within the subfamily "Danioninae" did not form a monophyletic group. The subfamily Leuciscinae was divided into two unrelated groups: the "Leuciscinae" in East Asia forming as a monophyletic group together with Cultrinae and Xenocyprinae, while the Leucisciriae in Europe, Siberia, and North America as another monophyletic group. The monophyly of subfamily Cyprininae sensu Howes was supported by NJ and ML trees and is basal in the tree. The position of Acheilognathinae, a widely accepted monophyletic group represented by Rhodeus sericeus, was not resolved.