Taxonomic reassessment of salamanders (genus Hynobius) from Tsushima Islands, Japan, with a resurrection of Hynobius tagoi Dunn, 1923 (Amphibia: Caudata).

To clarify the taxonomic status of salamanders from Tsushima Islands, Japan, we examined two species of salamanders, Hynobius tsuensis and Hynobius sp. from Tsushima Islands, and compared them with H. nebulosus from Kyushu. We found that the three taxa differ from each other in nuclear DNA, adult morphology, and egg-sac shape, and consider them to be independent species. Based on the investigation of type specimens of the synonyms, we identified Hynobius sp. as H. tagoi Dunn, 1923 and redescribe it herein. Also, we designate a neotype for H. tsuensis and redescribe H. tsuensis. The distribution areas of the two species partly overlap but they were distinguishable by their body colorations: H. tsuensis has uniformly blackish tail sides and a distinct yellow stripe on the upper tail edge; whereas H. tagoi has brown tail sides with numerous dark stippling and without a distinct yellow stripe on the upper tail edge.

Discovery of Two Lineages of Hynobius tsuensis (Amphibia, Caudata) Endemic to Tsushima Island, Japan.

The Tsushima salamander, Hynobius tsuensis, is a lotic-breeding species endemic to Tsushima Island, Japan. We investigated genetic variation in this species using samples covering all known localities on the island. Phylogenetic analyses based on mitochondrial cytochrome b gene sequences divided H. tsuensis populations into two genetic groups: true H. tsuensis and an unknown species (Hynobius sp.) showing a closer relationship to Hynobius nebulosus than to H. tsuensis. The genetic distance between the two groups was greater than the genetic distances between different species of Hynobius. Both groups were found to breed in mountain streams, sometimes in the same streams syntopically. Population structure analysis based on several nuclear microsatellite loci strongly indicated reproductive isolation between the two groups in the syntopic localities. This is the first report confirming the syntopic occurrence of two lotic salamanders of Hynobius on a small island. We propose that the lotic breeding habits of the two salamanders were independently acquired.

Complex Historical Biogeography of the Eastern Japanese Skink, Plestiodon finitimus (Scincidae, Squamata), Revealed by Geographic Variation in Molecular and Morphological Characters.

We investigated the geographic diversification of Plestiodon finitimus, which occurs in the central to northern parts of the Japanese Islands, based on a time-calibrated mitochondrial DNA (mtDNA) phylogeny and external morphological characters. The mtDNA phylogeny suggests that P. finitimus diverged from its sister species Plestiodon japonicus in western Japan 2.82-4.63 million years ago (MYA), which can be explained by geographic isolation due to the spread of sedimentary basins in the Pliocene. The primary intraspecific divergence was that between P. finitimus lineages in central and northeastern Japan 1.58-2.76 MYA, which could have been caused by the upliftings of major mountain ranges. In the northeastern lineage, mtDNA and morphological characters suggest a geographic differentiation between sub-lineages of the northwestern Tohoku District (α) and other areas (ß). Although the sub-lineage ß occurs in a disjunct geographic range, consisting of Hokkaido and the central to south of Tohoku, these areas are bridged by populations with intermediate characteristics along the Pacific side of northern Tohoku. Overall, the geographic variation in P. finitimus in northern Japan can be explained by an initial allopatric divergence of the sub-lineages α and ß at 0.71-1.39 MYA, a recent northward expansion of the sub-lineage ß, and subsequent secondary introgressive hybridization between the sub-lineages.

A reinvestigation of phylogeny and divergence times of Hynobiidae (Amphibia, Caudata) based on 29 nuclear genes.

Although several recent studies have investigated the major phylogenetic relationships within Hynobiidae, their evolutionary history remains partially resolved and the phylogenetic positions of some genera, particularly Pachyhynobius and Salamandrella are still disputed. Notably, previous studies relied primarily on mitochondrial DNA data and concatenated analyses; thus, a new investigation based on multiple nuclear genes and species-tree inference is needed. Here, we provide an in-depth phylogenetic analysis, based on 29 nuclear genes comprising 29,232bp of data from a comprehensive taxonomic sampling (24 hynobiids and 7 outgroups), using both concatenated and species-tree methods. Our results robustly resolved most genus-level relationships within Hynobiidae, including the placement of Salamandrella as the sister group to a clade containing Batrachuperus, Liua and Pseudohynobius, and the placement of Pachyhynobius as the sister group to a clade containing all hynobiids excluding Onychodactylus, Paradactylodon and Ranodon. Time estimates based on our data suggest that the major group of living hynobiids (excluding Onychodactylus) originated approximately 40Ma, ∼50% younger than estimates from mtDNA data (62.5Ma) but 10% older than estimates from three nuclear genes (36Ma). Our results highlight the benefits of using a large number of nuclear loci to infer both phylogeny and time for relatively old lineages.

Exploring patterns and extent of bias in estimating divergence time from mitochondrial DNA sequence data in a particular lineage: a case study of salamanders (order Caudata).

In the practice of molecular dating, substitution saturation will bias the results if not properly modeled. Date estimates based on commonly used mitochondrial DNA sequences likely suffer from this problem because of their high substitution rate. Nevertheless, the patterns and extent of such expected bias remain unknown for many major evolutionary lineages, which often differ in ages, available calibrations, and substitution rates of their mitochondrial genome. In this case study of salamanders, we used estimates based on multiple nuclear exons to assess the effects of saturation on dating divergences using mitochondrial genome sequences on a timescale of ~200-300 My. The results indicated that, due to saturation for older divergences and in the absence of younger effective calibration points, dates derived from the mitochondrial data were considerably overestimated and systematically biased toward the calibration point for the ingroup root. The overestimate might be as great as 3-10 times (about 20 My) older than actual divergence dates for recent splitting events and 40 My older for events that are more ancient. For deep divergences, dates estimated were strongly compressed together. Furthermore, excluding the third codon positions of protein-coding genes or only using the RNA genes or second codon positions did not considerably improve the performance. In the order Caudata, slowly evolving markers such as nuclear exons are preferred for dating a phylogeny covering a relatively wide time span. Dates estimated from these markers can be used as secondary calibrations for dating recent events based on rapidly evolving markers for which mitochondrial DNA sequences are attractive candidates due to their short coalescent time. In other groups, similar evaluation should be performed to facilitate the choice of markers for molecular dating and making inferences from the results.

Mosaic gene conversion after a tandem duplication of mtDNA sequence in Diomedeidae (albatrosses).

Although the tandem duplication of mitochondrial (mt) sequences, especially those of the control region (CR), has been detected in metazoan species, few studies have focused on the features of the duplicated sequence itself, such as the gene conversion rate, distribution patterns of the variation, and relative rates of evolution between the copies. To investigate the features of duplicated mt sequences, we partially sequenced the mt genome of 16 Phoebastria albatrosses belonging to three species (P. albatrus, P. nigripes, and P. immutabilis). More than 2,300 base pairs of tandemly-duplicated sequence were shared by all three species. The observed gene arrangement was shared in the three Phoebastria albatrosses and suggests that the duplication event occurred in the common ancestor of the three species. Most of the copies in each individual were identical or nearly identical, and were maintained through frequent gene conversions. By contrast, portions of CR domains I and III had different phylogenetic signals, suggesting that gene conversion had not occurred in those sections after the speciation of the three species. Several lines of data, including the heterogeneity of the rate of molecular evolution, nucleotide differences, and putative secondary structures, suggests that the two sequences in CR domain I are maintained through selection; however, additional studies into the mechanisms of gene conversion and mtDNA synthesis are required to confirm this hypothesis.

The role of nick formation in delayed quinacrine mustard fluorescence in the C-heterochromatin of Apodemus argenteus.

Chromosomes stained with fluorochromes, including quinacrine mustard (QM), emit the brightest fluorescence immediately after exposure to excitation light, and the fluorescence gradually fades with an increase in exposure time. However, in the QM-stained chromosomes of the small Japanese field mouse Apodemus argenteus, most C-heterochromatic regions emit weak fluorescence immediately after exposure to blue light, and they become brightly fluorescent by prolonged exposure (delayed QM fluorescence). We proposed recently that the delayed QM fluorescence is somehow related to nicks produced in C-heterochromatic DNA by blue light irradiation. To test this possibility, we examined the chromosomal distribution of nicks by in-situ nick translation and changes, if any, in the QM fluorescence pattern after methylene blue (MB) -mediated photooxidation, which is considered to induce nicks in chromosomal DNA. It was found that C-heterochromatic regions fluoresced brightly without any delay after exposure to blue light, and that nicks increased considerably in the same regions after the MB-mediated photooxidation. It seems, therefore, that photooxidation and strand breaks in DNA (including nicks) are responsible for the induction of delayed QM fluorescence. Trypsin digestion, on the other hand, abolished delayed QM fluorescence. Thus, not only DNA but also chromosomal protein(s) are involved in the unusual sequence of QM fluorescence patterns in A. argenteus.

Occurrence of Cryptosporidium sp. in snakes in Japan.

The aim of this study was to determine the prevalence of Cryptosporidium in snakes in Japan. Fecal samples or intestinal contents of 469 snakes, consisting of five species, were analyzed and Cryptosporidium oocysts were detected only from the Japanese grass snake Rhabdophis tigrinus. The mean prevalence of Cryptosporidium sp. in Japanese grass snakes was approximately 26% in the region studied. Histopathological observations revealed that the organism caused proliferative enteritis in the small intestine. Sequence analysis of a fragment of the small subunit rRNA gene has shown that the partial sequence of Cryptosporidium sp. isolated from the snakes was identical to that of the Cryptosporidium snake genotype W11 from New Guinea viper boa.

The delayed quinacrine mustard fluorescence from the C-blocks of Apodemus argenteus is due to the introduction of nicks into the DNA.

"Delayed QM-fluorescence" refers to the unusual kinetics of fluorescence from most of the C-heterochromatic regions of the chromosomes of the small Japanese field mouse Apodemus argenteus. When stained with quinacrine mustard (QM-stained), these C-heterochromatic regions emit weak fluorescence immediately after exposure to blue light (BL); they emit bright fluorescence within a few minutes; and the intensity of the fluorescence gradually decreases after maximum fluorescence has been recorded. To elucidate the mechanism of this phenomenon, we used acridine orange staining (AO-staining) and a modified version of the in situ nick-translation method. Focusing on the large C-heterochromatic region (C-block) of the X chromosome, we noted that AO-stained C-blocks emitted greenish fluorescence, while QM-stained and BL-exposed (QM-BL-processed) C-blocks emitted reddish fluorescence upon AO-staining after removal of QM. These findings suggested that the C-block DNA of A. argenteus might undergo a structural change, such as strand breaks, during QM-BL processing. Application of the modified in situ nick-translation method revealed the generation of an appreciable number of nicks in the C-block DNA by QM-BL processing. No such nick formation was observed in the C-blocks of three other mammalian species: Apodemus peninsulae, Microtus montebelli, and Urotrichus talpoides. Our findings support the hypothesis that nick formation due to exposure to BL might play a primary role in inducing delayed QM-fluorescence in the C-blocks of A. argenteus. On the basis of the present and earlier findings, we propose a probable mechanism for delayed QM-fluorescence in A. argenteus chromosomes.

Cytogenetic studies of Hynobiidae (Urodela) XIX. Morphological variation of sex chromosomes pairing behavior of sex lampbrush chromosomes in Hynobius quelpaertensis (Mori) from Cheju Island, South Korea.

Using Giemsa staining, C-banding and Ag-NOR staining techniques, we analyzed chromosomes in adult male and female Hynobius quelpaertensis and in embryos of this species in egg sacs collected from eight localities of Cheju Island, South Korea. Chromosome pair 21 was consistently homomorphic in male specimens, while it was heteromorphic in female specimens, suggesting the occurrence of ZZ/ZW sex chromosome constitution in this species. The W chromosome, being much larger than the Z chromosome, was of three morphologically distinct types: WA, WB and WC. Lampbrush chromosomes examined in the oocytes of one female specimen having the WA chromosome showed that the short arm of the WA chromosome and the long arm of the Z chromosome paired closely and hence are genetically homologous. We also tried to analyze the structural relationship among the three types of W chromosomes based on their C-banding and Ag-NOR patterns.

Application of mFISH for the analysis of chemically-induced chromosomal aberrations: a model for the formation of triradial chromosomes.

Using a human lymphoblastoid cell line WTK-1, we applied multicolor fluorescence in situ hybridization (mFISH) technique to analyze mitomycin C (MMC)-induced chromatid exchanges, focusing especially on the triradial chromosomes. It was found that the triradial chromosomes were formed with a specific rearrangement, "recipient and donor" relationship. The exchange sites of the recipient chromosomes were on single chromatid breaks and distributed randomly throughout the interstitial, pericentromeric, and terminal regions. In counterpart, donor chromosomes exchanged on isochromatid breaks of their telomeric and/or subtelomeric regions with the single chromatid breaks of recipient chromosomes. More than 80% of the scored triradial chromosomes were formed with such rearrangements, and few acentric chromosome fragments derived from the donor chromosomes could be detected in the metaphases observed. We therefore suggest that biological mechanisms of breakages between the recipient and donor chromosomes are different: the former due to direct DNA-damage by MMC, but the latter due to indirect DNA-damage depending on telomeric specific structure/function.