Geographic allozyme variation in the Japanese clouded salamander, Hynobius nebulosus (Amphibia: Urodela)

Out of the ancient lake: Multiple riverine colonizations and diversification of the freshwater snails in the genus Semisulcospira around Lake Biwa

Ancient lakes are a hotspot of biodiversity. Freshwater species often experience spectacular species radiation after colonizing lakes from riverine habitats. Therefore, the relationship between the fauna of the ancient lakes and the surrounding riverine system has a special significance in understanding their origin and evolutionary history. The study of ancient lake species often focused on the lake colonization of riverine species. In contrast, far less attention has been placed on the reverse direction: the riverine colonization of the lake species, despite its importance in disentangling their complex evolutionary history. The freshwater snails in the genus Semisulcospira involve endemic groups that radiated in the ancient Lake Biwa. Using genetics and fossil records, we inferred that the ancestors of these lake-endemic Semisulcospira snails historically colonized the riverine habitats at least three times during the Middle Pleistocene. Each colonization resulted in the formation of a new lineage that was genetically and morphologically distinct from other lineages. Further, one of these colonizations was followed by hybridization with a cosmopolitan riverine species, which potentially facilitated the population persistence of the colonizers in the new environment. Despite their complex histories, all these colonizers were currently grouped within a single species, Semisulcospira kurodai, suggesting cryptic diversity in this species. This study highlights the significance of the riverine colonizations of the lake species to fully understand the diversification history of freshwater fauna in and around the ancient lakes.

Two single-point mutations in Ankyrin Repeat one drastically change the threshold temperature of TRPV1

TRPV1 plays an important role in the thermosensory system; however, the mechanism controlling its heat activation property is not well understood. Here, we determine the heat activation properties of TRPV1 cloned from tailed amphibians, which prefer cooler environments, finding the threshold temperatures were approximately 10 °C lower compared with rat TRPV1 (rTRPV1). We find that two amino acid residues (Gln, Leu/Val) in the Ankyrin Repeat 1 (ANK1) region of the N-terminal domain are conserved among tailed amphibians and different from those (Arg, Lys) in rTRPV1. We observe the activation by heat in all urodelan TRPV1s is markedly elevated by substitution of these two amino acids. Conversely, reciprocal substitutions of rTRPV1 apparently lowers the high threshold temperature. Our studies demonstrate that tailed amphibians express TRPV1 with a reduced heat-activation threshold by substitution of two amino acid residues in the ANK1 region that likely contribute to cool-habitat selection.

Taxonomic Reassessment of the Izumo Lineage of Hynobius utsunomiyaorum: Description of a New Species from Chugoku, Japan

Simple Summary

In the study, we investigated the true taxonomic composition of Hynobius utsunomiyaorum from Chugoku District, Japan. Our detailed morphological and molecular comparisons showed that H. utsunomiyaorum is clearly divided into two species: the true H. utsunomiyaorum and the Izumo Lineage of H. utsunomiyaorum, i.e., Hynobius kunibiki sp. nov. This new species does not satisfy the diagnosis of H. utsunomiyaorum, while these two species do not form a monophyletic group based on molecular data. Hynobius setoi is morphologically more similar to the new species than is H. utsunomiyaorum. Previous studies have suggested that H. setoi is distributed across the San’in region, i.e., the northern part of Chugoku District, Japan. However, our research revealed that H. setoi is not distributed in the northern part of Shimane Prefecture, located in the western part of the San’in region in Chugoku District. Rather than H. setoi, we found that the new species was distributed in the northern part of Shimane Prefecture. Additionally, results of phylogenetic analyses using all valid Japanese Hynobius species are provided in our study. Based on these results, we show that Japanese Hynobius species included in the subgenus Hynobius may be divided into four genetic clades. The information in our study will be vital for developing conservation management strategies and policies for these species.

Abstract

Here, we describe a new species of the genus Hynobius from Chugoku, Japan. In populations from central to eastern Shimane Prefecture, the Izumo Lineage of Hynobius utsunomiyaorum was clearly distinguished from the true Hynobius utsunomiyaorum based on morphological and molecular evidence. Thus, we describe the former lineage as a new species, Hynobius kunibiki sp. nov. Morphological comparisons revealed that H. utsunomiyaorum lacks a distinct yellow line on the ventral side of its tail, whereas the new species possesses this yellow line; most H. utsunomiyaorum individuals have distinct white spots on the lateral sides of their body and lack a fifth toe, whereas the new species largely lacks these spots, and all examined individuals had a fifth toe. The two species also differed significantly by several other morphological characteristics. The lentic species Hynobius setoi is morphologically similar to H. kunibiki sp. nov., but they differ significantly by various morphological characteristics. Despite their partial morphological similarity, these two species differed substantially in terms of their genetics. Finally, we show, in a phylogenetic tree including all Japanese Hynobius species, that the subgenus Hynobius can be divided into four genetic clades. Overall, this information will help develop conservation management strategies and policies for these species.

Influence of Quaternary environmental changes on mole populations inferred from mitochondrial sequences and evolutionary rate estimation

Quaternary environmental changes fundamentally influenced the genetic diversity of temperate-zone terrestrial animals, including those in the Japanese Archipelago. The genetic diversity of present-day populations is taxon- and region-specific, but its determinants are poorly understood. Here, we analyzed cytochrome b gene (Cytb) sequences (1140 bp) of mitochondrial DNA (mtDNA) to elucidate the factors determining the genetic variation in three species of large moles: Mogera imaizumii and Mogera wogura, which occur in central and southern mainland Japan (Honshu, Shikoku, and Kyushu), and Mogera robusta, which occurs on the nearby Asian continent. Network construction with the Cytb sequences revealed 10 star-shaped clusters with apparent geographic affinity. Mismatch distribution analysis showed that modes of pairwise nucleotide differences (τ values) were grouped into five classes in terms of the level, implying the occurrence of five stages for rapid expansion. It is conceivable that severe cold periods and subsequent warm periods during the late Quaternary were responsible for the population expansion events. The first and third oldest events included island-derived haplotypes, indicative of the involvement of land bridge formation between remote islands, hence suggesting an association of the ends of the penultimate (PGM, ca. 130,000 years ago) and last (LGM, ca. 15,000 years ago) glacial maxima, respectively. Since the third event was followed by the fourth, it is plausible that the termination of the Younger Dryas and subsequent abrupt warming ca. 11,500 years ago facilitated the fourth expansion event. The second event most likely corresponded to early marine isotope stage (MIS) 3 (ca. 53,000 years ago) when the glaciation and subsequent warming period were predicted to have influenced biodiversity. Utilization of the critical times of 130,000, 53,000, 15,000, and 11,500 years ago as calibration points yielded evolutionary rates of 0.03, 0.045, 0.10 and 0.10 substitutions/site/million years, respectively, showing a time-dependent manner whose pattern was similar to that seen in small rodents reported in our previous studies. The age of the fifth expansion event was calculated to be 5800 years ago with a rate of 0.10 substitutions/site/million years ago during the mid-Holocene, suggestive of the influence of humans or other unspecified reasons, such as the Jomon marine transgression.

Historical museum collections clarify the evolutionary history of cryptic species radiation in the world's largest amphibians

Inaccurate taxonomic assessment of threatened populations can hinder conservation prioritization and management, with human-mediated population movements obscuring biogeographic patterns and confounding reconstructions of evolutionary history. Giant salamanders were formerly distributed widely across China, and are interpreted as a single species, Andrias davidianus. Previous phylogenetic studies have identified distinct Chinese giant salamander lineages but were unable to associate these consistently with different landscapes, probably because population structure has been modified by human-mediated translocations for recent commercial farming. We investigated the evolutionary history and relationships of allopatric Chinese giant salamander populations with Next-Generation Sequencing methods, using historical museum specimens and late 20th-century samples, and retrieved partial or near-complete mitogenomes for 17 individuals. Samples from populations unlikely to have been affected by translocations form three clades from separate regions of China, spatially congruent with isolation by either major river drainages or mountain ranges. Pliocene-Pleistocene divergences for these clades are consistent with topographic modification of southern China associated with uplift of the Qinghai-Tibet Plateau. General Mixed Yule Coalescent model analysis indicates that these clades represent separate species: Andrias davidianus (Blanchard, 1871) (northern Yangtze/Sichuan), Andrias sligoi (Boulenger, 1924) (Pearl/Nanling), and an undescribed species (Huangshan). Andrias sligoi is possibly the world's largest amphibian. Inclusion of additional reportedly wild samples from areas of known giant salamander exploitation and movement leads to increasing loss of biogeographic signal. Wild Chinese giant salamander populations are now critically depleted or extirpated, and conservation actions should be updated to recognize the existence of multiple species.

Genetic Diversity among Clouded Salamanders (Hynobius nebulosus) in Shiga Prefecture

The Japanese clouded salamander (Hynobius nebulosus) is a lentic-breeding species distributed throughout western Japan. Threats, such as habitat loss, have led to it being categorized as a vulnerable species. To explore the phylogeographic features and population differentiation among clouded salamanders in Shiga prefecture, we analyzed sequences of the mitochondrial cytochrome b gene. DNA samples were collected from 29 distinct breeding sites, and 53 cytochrome b haplotypes were identified. On the basis of comparison of the composition and frequency of haplotypes in each breeding site, salamanders in each habitat appeared to have distinct characteristics. Significant genetic differentiation was observed in 93.3% of possible pairs of habitats in Shiga prefecture, and 67.7% of habitat pairs within the same locality were found to be significantly different. These results suggest that the salamanders' poor locomotion combined with topographic effects may have contributed to the diversity of locally distributed salamanders in Shiga. Phylogenetic analysis showed that haplotypes of H. nebulosus in Shiga can be divided into five groups (the Nagahama-Maibara group, Otsu group, Konan group 1, Konan group 2, and Takashima group), each with a distinct geographical distribution. Haplotypes of the Otsu group, however, were exceptionally widely distributed. The results of the present study will contribute to the future of H. nebulosus conservation management in Shiga.

Hynobiidae origin in middle Cretaceous corroborated by the new mitochondrial genome of Hynobius chinensis

Hynobius chinensis was first described by Günther in the nineteenth century. At present, the origins of the extinct Hynobius chinensis on the Zhoushan Island (Hynobius chinensis-ZI) remain a mystery. It is the only species of family Hynobiidae on the Zhoushan Island. However, there is very little empirical evidence regarding Hynobius chinensis-ZI phylogenetic relationship, and when or how did its ancestors colonized the island. Here, we used mitochondrial genome data to recover the phylogeny of family Hynobiidae. Results suggested that the origin of Hynobiidae was most likely in Middle Cretaceous (~112.9 Mya), and some Hynobius species of Taiwan and Japan diverged earlier than that of the mainland of China. Hynobius chinensis-ZI diverged from its closest living relative (Hynobius yiwuensis) around 6.5 Mya, and Hynobius chinensis-ZI was isolated on Zhoushan Island since the postglacial transgression in Holocene period.

Fin whale MDH-1 and MPI allozyme variation is not reflected in the corresponding DNA sequences

The appeal of genetic inference methods to assess population genetic structure and guide management efforts is grounded in the correlation between the genetic similarity and gene flow among populations. Effects of such gene flow are typically genomewide; however, some loci may appear as outliers, displaying above or below average genetic divergence relative to the genomewide level. Above average population, genetic divergence may be due to divergent selection as a result of local adaptation. Consequently, substantial efforts have been directed toward such outlying loci in order to identify traits subject to local adaptation. Here, we report the results of an investigation into the molecular basis of the substantial degree of genetic divergence previously reported at allozyme loci among North Atlantic fin whale (Balaenoptera physalus) populations. We sequenced the exons encoding for the two most divergent allozyme loci (MDH-1 and MPI) and failed to detect any nonsynonymous substitutions. Following extensive error checking and analysis of additional bioinformatic and morphological data, we hypothesize that the observed allozyme polymorphisms may reflect phenotypic plasticity at the cellular level, perhaps as a response to nutritional stress. While such plasticity is intriguing in itself, and of fundamental evolutionary interest, our key finding is that the observed allozyme variation does not appear to be a result of genetic drift, migration, or selection on the MDH-1 and MPI exons themselves, stressing the importance of interpreting allozyme data with caution. As for North Atlantic fin whale population structure, our findings support the low levels of differentiation found in previous analyses of DNA nucleotide loci.

Spatial and temporal aspects of occurrence of Mogera species in the Japanese islands inferred from mitochondrial and nuclear gene sequences

We assessed dispersal and vicariant events in four species of Japanese moles in the genera Mogera and Euroscaptor to better understand the factors shaping intra- and interspecific differentiation in Japanese moles. We used the combined viewpoints of molecular phylogeny and historical geology using nucleotide sequences of mitochondrial (cytochrome b; Cytb) and nuclear (A2ab, Bmp4, Tcf25, vWf) genes. The divergence times estimated from the molecular data were verified with available geological data on the chronology of fluctuations in sea level in the Korea Strait, assuming sequential migration and speciation events. This produced possible migration times of 5.6, 3.5, 2.4, and 1.3 million years ago for four species of Japanese moles, Euroscaptor mizura, Mogera tokudae, M. imaizumii, and M. wogura, respectively. For the western Japanese mole M. wogura, Cytb sequences revealed four major phylogroups with strong geographic affinities in southwestern Central Honshu (I), western Honshu/Shikoku (II), Kyushu/westernmost Honshu (III), and Korea/Russian Primorye (IV). The nuclear gene sequences supported the distinctiveness of phylogroups I and IV, indicating long, independent evolutionary histories. In contrast, phylogroups II and III were merged into a single geographic group based on the nuclear gene data. Intraspecific divergences in M. imaizumii and M. tokudae were rather apparent in Cytb but not in nuclear gene sequences. The results suggest that repeated dispersal events have occurred between the Asian continent and the Japanese Islands, and intensive vicariant events associated with abiotic and biotic factors have created higher levels of species and genetic diversities in moles occurring on the Japanese Islands.

A skeletochronological study of breeding females in a population of Japanese clouded salamanders (Hynobius nebulosus)

The age structure of breeding females of Hynobius nebulosus has not been studied sufficiently. We estimated the ages of 76 individuals from a population in Kyoto by using skeletochronology. The mean age and snout-vent length (SVL) of this population were 4.6 years and 55.7 mm, respectively. It was estimated that the youngest females breed two years post hatching at a mean SVL of 46.5 mm, but a larger number of individuals begins breeding at three years and a mean SVL of 52.2 mm. Because most males also start to breed at three years, there seems to be no gender difference in the timing of sexual maturation. The age of the oldest female was estimated to be 11.8 years. It is possible that the life history of H. nebulosus is characterized by early maturation and arrested growth, and short longevity.

Allozymic variation and phylogeography of two genetic types of Onychodactylus japonicus (Amphibia: Caudata: Hynobiidae) sympatric in the Kinki District, Japan

On the basis of allozyme and mtDNA sequence variation, we elucidated genetic relationships between two sympatric genetic types of Onychodactylus japonicus in Kinki and adjacent districts, and investigated their phylogeography. Allozymic analysis revealed the presence of two distinct genetic types (the SW-Honshu and Kinki groups) in this area, and their sympatric occurrence in three of 10 sampling sites. Fixed or nearly fixed allele differences in several loci strongly suggested reproductive isolation between the two types, although one hybrid specimen was found in a locality. Analyses of mtDNA using 194 specimens from 22 localities also demonstrated two genetic types. From phylogeographic and population genetic analyses, it was surmised that these two types diverged allopatrically, and secondarily contacted to become sympatric by the Pleistocene uplift of mountains. Our results indicate different specific status for these two types and separation of the Kinki group from O. japonicus, to which the SW-Honshu group belongs.

Morphological variation in a Japanese salamander, Hynobius kimurae (Amphibia, Caudata)

We studied variation in morphometric and meristic characters and color pattern in the salamander Hynobius kimurae, examining 282 males from 24 localities encompassing the whole distributional range of the species in Honshu, the mainland of Japan. Multivariate analyses of 24 morphometric characters resulted in the separation of two groups, (1) eastern populations from the Kanto District to Shizuoka Prefecture of the Chubu District, and (2) central-western populations from Aichi Prefecture of the Chubu District westwards. Similar groups were recognized in meristic characters and color pattern. These geographic patterns of morphological variation coincided with the pattern of genetic differentiation inferred from allozymes in this species, except for the position of one population from the intermediate region. Some of the morphometric and meristic characters significantly correlated with environmental parameters of sampling sites, and suggested effects of differential habitat conditions among populations on the geographic morphological variation in this species.

Reduced genetic variation in the Japanese giant salamander, Andrias japonicus (Amphibia: Caudata)

The phylogenetic relationships among 46 samples from 27 populations of the Japanese giant salamander, Andriasjaponicus and its congener, A. davidianus from China was investigated, using 3664 bp sequences of the mitochondrial genes NADH1, NADH3, cyt b and CR, partial NADH6 and intervening genes. In phylogenetic trees constructed by MP, ML, and Bayesian methods, the family Cryptobranchidae and the genus Andrias both form monophyletic groups. Japanese A. japonicus and Chinese A. davidianus are sister taxa and can be regarded as separate species despite a small degree of genetic differentiation. Andriasjaponicus is divided into central and western clades, but the phylogenetic relationships within the latter clade are unresolved. As previously reported from allozyme analyses, A. japonicus exhibits little genetic differentiation, in strong contrast to salamanders of the genus Hynobius with which their distributions overlap. This reduced genetic variability in A. japonicus is attributable to a unique mating system of polygyny, delayed sexual maturity, notable longevity, life in a stable aquatic environment, and gigantism, as well as bottleneck effects following habitat fragmentation and extinction of local populations during Quaternary glaciations. The species is thus susceptible to extinction by potential environmental fluctuations, and requires extensive conservation measures.

Genetic relationships among salamanders of the genus Hynobius (Amphibia, Caudata) from Korea and southwestern Japan

We performed allozyme analysis for three Korean (Hynobius leechii, H. quelpaertensis, and H. yangi) and three Japanese (H. nebulosus, H. tsuensis, and H. dunni) salamanders to clarify their interspecific relationships using H. naevius as an outgroup. The genetic distances (Nei's D) within ingroup species ranged from 0.11 to 0.78 with a mean of 0.33. In the NJ and CONTML trees, monophyly of the ingroup was not supported and Korean H. quelpaertensis and H. leechii diverged first from the remaining species, which together formed a weakly supported clade. Korean H. yangi, long identified as H. leechii, was closer to Japanese H. nebulosus (D=0.108) and H. tsuensis (D=0.138) than to Korean H. leechii (D=0.197) and H. quelpaertensis (D=0.305). Hynobius tsuensis and H. nebulosus were very close (D=0.108) despite their different breeding habits. A geohistorical hypothesis is proposed to explain the divergence of the six species.

Systematic Relationships of Hynobius okiensis among Japanese Salamanders (Amphibia: Caudata)

We conducted an electrophoretic survey to examine systematic relationships of a lotic-breeding salamander Hynobius okiensis endemic to Dogo Island of the Oki Islands, Japan, with several lentic and lotic-breeding Japanese species. Genetically H. okiensis with 2n=56 chromosomes was closer to the lentic-breeding H. nebulosus group (H. nebulosus and H. dunni) with the same chromosome number than to the lotic-breeding H. naevius group (H. naevius and H. kimurae) and H. boulengeri with 58 chromosomes. Chromosome number reduction from 58 to 56, possibly accompanied with a change in breeding environment from streams to still waters, is estimated to have first occurred in the nebulosus group of Hynobius. A reversal only in breeding habits then seems to have followed in steep, montane environments of the small island of Dogo, resulting in the speciation of H. okiensis.

Morphological and Allozymic Variation in Hynobius boulengeri and H. stejnegeri (Amphibia: Urodela: Hynobiidae)

We studied morphological and allozymic variation in populations of Japanese salamanders, Hynobius boulengeri and H. stejnegeri. Adult H. boulengeri showed sexual dimorphism, and juveniles differed greatly from adults in many morphological characters. From the results of multivariate analyses of morphological characters, the populations were divided into four groups: (I) H. boulengeri from Honshu, (II) H. boulengeri from Shikoku, (III) H. boulengeri from the Sobo-Katamuki Mountains of Kyushu and H. stejnegeri, and (IV) H. boulengeri from the Amakusa Islands and the Osumi Peninsula. Phenotypic relationships among the four groups were identical to relationships clarified by allozymic analyses, except for group IV, which was included in group III in the allozyme tree. Some morphometric characters were significantly correlated with environmental variables. We consider H. stejnegeri to be a valid species based on its unique color pattern, morphometric characters, and allelic composition, even though it was nested within group III of H. boulengeri by both morphological and allozymic analyses. We propose that group I from Honshu and group II from Shikoku should be treated as H. boulengeri sensu stricto and H. hirosei, respectively. Resolving the taxonomic status of the remaining populations of groups III and IV from Kyushu requires further study.