Atsushi Kurabayashi

Nagahama Institute of Bio-Science and Technology · Department of Bioscience

The rice frog (Fejervarya kawamurai) is found in western Japan, and the western area of Lake Biwa used to be its eastern distribution limit. However, since around 2010, the habitat range of F. kawamurai has expanded to the eastern area of Lake Biwa. The formation of this new population cannot be explained only by a simple distribution expansion fro...

Blindsnakes of infraoder Scolecophidia (order Squamata) are the most basal group of extant snakes, comprising of more than 450 species with ecological and morphological features highly specialized to underground living. The Brahminy blindsnake, Indotyphlops braminus , is the only known obligate parthenogenetic species of snakes. Although the origin...

The islands of the river Padma of Rajshahi district, Bangladesh is rich in various plants, wild animals and adorned with natural beauty. Here, wildlife is facing severe threat due to constant river erosion, flood and human-environment conflict. Poor communication system and lack of stable land, the Padma islands have been considered one of the safe...

Horizontal transfer (HT) of genes between multicellular animals, once thought to be extremely rare, is being more commonly detected, but its global geographic trend and transfer mechanism have not been investigated. We discovered a unique HT pattern of Bovine-B (BovB) LINE retrotransposons in vertebrates, with a bizarre transfer direction from pred...

The complete sequence of the mitochondrial genome (mitogenome) of Tachysurus nudiceps (family Bagridae; order Siluriformes) was determined using next-generation sequencing. The composition of its mitogenome is the same as that observed in most other vertebrates and consists of 37 genes, an L-strand replication origin and a control region. As in pre...

Biodiversity monitoring is important for the conservation of natural ecosystems in general, but particularly for amphibians, whose populations are pronouncedly declining. However, amphibians' ecological traits (e.g. nocturnal or aquatic) often prevent their precise monitoring. Environmental DNA (eDNA) metabarcoding-analysis of extra-organismal DNA...

The Itasenpara bitterling, Acheilognathus longipinnis Regan, 1905, in the family Cyprinidae, is an endangered freshwater fish endemic to Japan. Designated a Japanese natural monument, research on A. longipinnis specimens is strictly restricted by law. In this study, we supplement existing genetic information and provide a resource for future studie...

Biodiversity monitoring is important for the conservation of natural ecosystems in general, but particularly for amphibians, whose populations are pronouncedly declining. However, amphibians ecological traits (e.g., nocturnal or aquatic) often prevent their precise monitoring. Environmental DNA (eDNA) metabarcoding-analysis of extra-organismal DNA...

A Correction to this paper has been published: https://doi.org/10.1007/s00248-021-01693-z

There are two distinct lungless groups in caudate amphibians (salamanders and newts) (the family Plethodontidae and the genus Onychodactylus, from the family Hynobiidae). Lunglessness is considered to have evolved in response to environmental and/or ecological adaptation with respect to oxygen requirements. We performed selection analyses on lungle...

A poorly-known proboscidate leech species, Torix tukubana (Oka, 1935), in which the mid-body somites are biannulate dorsally and triannulate ventrally, is redescribed based on new specimens collected from its type locality, Mt. Tsukubasan in Honshu, Japan. The redescription provides the internal digestive and genital organs of T. tukubana for the f...

Logging and human-induced conversion of natural forests into agricultural areas are major drivers of biodiversity loss in the tropics. Anuran larvae can be highly diverse, can reach high biomass and can play important roles in tropical streams; yet, compared to the adult frog communities, relatively little is known about how larval communities resp...

The mitochondrial (mt) genome of the bushveld rain frog (Breviceps adspersus, Brevicipitidae, Afrobatrachia) is the largest (28.8 kbp) among the vertebrates investigated to date. The major cause of genome size enlargement in this species is the duplication of multiple genomic regions. To investigate the evolutionary lineage, timing, and process of...

For more than a century, Hylarana tytleri (Theobald, 1868) has been confused with two congeneric species, H. taipehensis and H. erythraea, in Bangladesh and neighboring countries, due to phenetic similarities as well as a lack of sufficient molecular and morphometric data. To resolve these problems, we conducted molecular and morphological surveys...

Animal-associated microbiomes are integral to host health, yet key biotic and abiotic factors that shape host-associated microbial communities at the global scale remain poorly understood. We investigated global patterns in amphibian skin bacterial communities, incorporating samples from 2,349 individuals representing 205 amphibian species across a...

Two species of the clawed frog family, Xenopus laevis and X. tropicalis, are widely used as tools to investigate both normal and disease-state biochemistry, genetics, cell biology, and developmental biology. To support both frog specialist and non-specialist scientists needing access to these models for their research, a number of centralized resou...

Torix is a leech genus containing freshwater proboscidate species, and several members of this taxon are ectoparasites specific to amphibians. Torix tukubana inhabits mountain streams in Japan, and only two frog species are known to be hosts. We collected this leech from two other amphibians, Onychodactylus japonicus (Japanese clawed salamander) an...

The rich biodiversity of frogs and toads in Bangladesh is unexpectedconsidering the rather simple topographic features of the country. Indeed, anew species, Microhyla nilphamariensis, has recently been described fromNilphamari District (northern region), Bangladesh. However, additionalgenetic, acoustic, and morphometric data are necessary to precis...

Systematics and classification of Asian frogs of the genus Fejervarya and related genera (family Dicroglossidae; hereafter referred to as fejervaryan frogs) have been the subject of intensive debates in the past few years. We complement previous phylogenetic studies with analyses of concatenated sequences from 14 nuclear loci and mitochondrial gene...

Andrias japonicus, the Japanese giant salamander, is the second largest amphibian species in the world. The biology of this long-lived, fully aquatic salamander is still incompletely known, and studying the threats it experiences is important for conservation management. We used 16S amplicon sequencing to provide the first data on the composition a...

To elucidate reproductive isolating mechanisms in the Bangladesh coastal bullfrog Hoplobatrachus litoralis and its congeneric species, we performed crossing experiments using three species: H. litoralis, H. tigerinus and H. rugulosus. In addition, we conducted histological observations on spermatogenesis of the hybrids. The reciprocal hybrids betwe...

The cutaneous microbiota plays a significant role in the biology of their vertebrate hosts, and its composition is known to be influenced both by host and environment, with captive conditions often altering alpha diversity. Here, we compare the cutaneous bacterial communities of 61 amphibians (both wild and captive) from Hiroshima, Japan, using hig...

We have succeeded in creating see-through frogs from natural color mutants of the Japanese brown frog Rana japonica, which usually possesses an ochre or brown back; this coloration enables the organs, blood vessels, and eggs to be observed through the skin without performing dissection. We crossed two kinds of recessive color mutant (black-eyed and...

Transcription activator-like effector nucleases (TALENs) have previously been used for targeted genome editing in various organisms including Xenopus laevis. However, because of genomic polyploidization, X. laevis usually possess homeologous genes (homeologs) with quite similar sequences that make the analysis of gene function difficult. In the pre...

Abstract The diploid Xenopus tropicalis, with its small nuclear genomic size and short generation time compared to the traditional experimental amphibian X. laevis, is considered a next-generation model animal. Several experimental X. tropicalis lines have been used in research studies. Previous studies showed that the mtDNA sequence of the Asashim...

Abstract Sichuan torrent frog, Amolops mantzorum (family Ranidae, suborder Neobatrachia), possesses heteromorphic sex chromosomes unusual characteristics among amphibians. We determined the complete nucleotide sequence of the A. mantzorum mitogenome. This genome is 17,744 bp in length and contains 37 genes, 1 control region, and 1 light strand repl...

To elucidate the genetic divergences of several Asian frog taxa, the mitochondrial 16S rRNA gene (16S) sequences of 81 populations across 6 Asian countries were analyzed. In total, 109 haplotypes were found, and the concept of a 3% difference in 16S sequence corresponding to species threshold was applied to define candidate amphibian species, for w...

Xenopus tropicalis has many advantages as a next-generation model animal for biological research. However, the temperature tolerance range of this frog is narrow, making transportation of live specimens difficult under extreme air temperatures in the summer and winter. This seasonal constraint diminishes the usefulness of X. tropicalis as an experi...

Two new frog species belonging to genus Microhyla from the southeast, central and northeast regions of Bangladesh are described. Based on a molecular phylogeny derived from mitochondrial DNA sequences, one of the new species forms a clade with M. fissipes, while the second new species is sister to this clade. The DNA sequences of the mitochondrial...

Two new frog species belonging to genus Microhyla from the southeast, central and northeast regions of Bangladesh are described. Based on a molecular phylogeny derived from mitochondrial DNA sequences, one of the new species forms a clade with M. fissipes, while the second new species is sister to this clade. The DNA sequences of the mitochondrial...

Mitochondrial genomic (mitogenomic) reorganizations are rarely found in closely-related animals, yet drastic reorganizations have been found in the Ranoides frogs. The phylogenetic relationships of the three major ranoid taxa (Natatanura, Microhylidae, and Afrobatrachia) have been problematic, and mitogenomic information for afrobatrachians has not...

Anderson's crocodile newt (Echinotriton andersoni) is distributed in the Central Ryukyu Islands of southern Japan, but environmental degradation and illegal collection over the last several decades have devastated the local populations. It has therefore been listed as a class B1 endangered species in the IUCN Red List, indicating that it is at high...

Genus Babina is a member of Ranidae, a large family of frogs, currently comprising 10 species. Three of them are listed as endangered species. To identify mitochondrial (mt) genes suitable for future population genetic analyses for endangered species, we determined the complete nucleotide sequences of the mt genomes of 3 endangered Japanese Babina...

Pelophylax nigromaculatus, P. porosus porosus, and P. p. brevipoda are three pond frog species distributed in Japan. Their distributions overlap at two basins in central Japan (P. nigromaculatus and P. p. porosus in the Matsumoto basin, and P. nigromaculatus and P. p. brevipoda in the Ina basin), and hybrid descendants have been found in these area...

To survey the diversity of anuran species in Bangladesh, we compared mitochondrial 16S rRNA gene sequences (approximately 1.4 kbp) from 107 Bangladesh frog specimens. The results of genetic divergence and phylogenetic analyses incorporating data from related species revealed the occurrence of at least eight cryptic species. Hoplobatrachus tigerinus...

Crocodile newts, which constitute the genera Echinotriton and Tylototriton, are known as living fossils, and these genera comprise many endangered species. To identify mitochondrial (mt) genes suitable for future population genetic analyses for endangered taxa, we determined the complete nucleotide sequences of the mt genomes of the Japanese crocod...

Odorrana ishikawae is listed as a class IB endangered species in the IUCN Red List and is protected by law in both Okinawa and Kagoshima Prefectures, Japan. Here, in an effort to help effectively preserve the genetic diversity of this endangered species in the laboratory, we tested a farming technique involving the artificial breeding of frogs, and...

Due to an originally small distribution range and over-exploitation of primary forest, Ishikawa’s frog (Odorrana ishikawae) has been steadily declining in number. For effective conservation of this species, a greater amount of genetic information of this species is needed. Here, we isolated and characterized 12 microsatellite loci of O. ishikawae u...

Microhylidae is a geographically widespread family of anurans. Although several extensive molecular analyses have attempted to elucidate their subfamilial relationships, and correlate these with Mesozoic and Cenozoic continental drifts, consensus has not been reached. Further, generic level relationships have not been well investigated in some micr...

The endangered frog, Odorrana ishikawae (Anura, Ranidae), is a species endemic to the mami and Okinawa Islands ofthe Ryukyu Archipelago, Japan. Segmentation of these islands has een considered to occur middle or upper Pleistocene. Our morphometric analyses revealed bvious differences between the Amami and Okinawa populations. Two distinct morphotyp...

In this study we sought to clarify the evolutionary relationships and biogeographic history of the bell-ring frog, Buergeria buergeri (family Rhacophoridae), and two congeneric species Buergeria japonica and Buergeria robusta, by analyzing three mitochondrial (mt) genes: 12S rRNA, Cytb, and ND5. Phylogenetic analyses based on gene data showed the m...

We determined the complete nucleotide sequences of mitochondrial (mt) genomes from two dicroglossid frogs, Hoplobatrachus tigerinus (Indian Bullfrog) and Euphlyctis hexadactylus (Indian Green frog). The genome sizes are 20462 bp in H. tigerinus and 20280 bp in E. hexadactylus. Although both genomes encode the typical 37 mt genes, the following uniq...

We determined the complete nucleotide sequence of the mitochondrial (mt) genome of an endangered Japanese frog, Odorrana ishikawae (family Ranidae). We also sequenced partial mt genomes of three other Odorrana and six ranid species to survey the diversity of genomic organizations and elucidate the phylogenetic problems remaining in this frog family...

Studies using amphibians have contributed to the progress of life science including developmental biology and cell biology for more than one hundred years. Since the 1950s Xenopus laevis in particular has been used by scientists in many fields for experiments, resulting in the development of various techniques such as microsurgery on early embryos,...

Consensus on the taxonomic system and phylogenetic relationships for the anuran genus Fejervarya has yet to be established. Morphological characters in this genus are generally unsuitable for species identification. To carry out molecular species identification and solve phylogenetic problems, we collected 67 Fejervarya specimens from 12 Asian coun...

Neobatrachia is a phylogenetically-nested anuran group and contains approximately 85% of amphibian species. It is difficult to analyze the neobatra-chian mitochondrial (mt) genome due to accelerated nucleotide substitution rates and occasional gene rearrangements. To overcome these problems, we designed 15 PCR primers. These primers, together with...

Two new frog species of the genus Euphtyctls, which were shown to be two distinct taxa by mitochondrial DNA analyses, are described from Karnataka State, southwestern India. On the molecular phylogenetic tree, the first new species appears as a sister group with respect to E hexadactylus. The second new species forms a group with E cyanophlyctis. T...

In Malagasy frogs of the family Mantellidae, the genus Mantella is known to possess highly reorganized mitochondrial (mt) genomes with the following characteristics: 1) some rearranged gene positions, 2) 2 distinct genes and a pseudogene corresponding to the transfer RNA gene for methionine (trnM), and 3) 2 control regions (CRs) with almost identic...

To elucidate the species composition, genetic divergence, evolutionary relationships, and divergence time of Hoplobatrachus and Euphlyctis frogs (subfamily Dicroglossinae, family Ranidae) in Bangladesh and other Asian countries, we analyzed the mitochondrial Cyt b, 12S, and 16S rRNA genes of 252 specimens. Our phylogenetic analyses showed 13 major...

To clarify the genetic divergence in the F. limnocharis complex from Thailand and neighboring countries and to elucidate the phylogenetic problems of this taxon, we analyzed partial sequences of the mitochondrial 12S and 16S rRNA genes and the nuclear CXCR4, NCX1, RAG-1, and tyrosinase genes. The F. limnocharis complex from Thailand had three disti...

We sequenced the whole mitochondrial (mt) genomes of three neobatrachian species: Japanese tree frog Hyla japonica, Japanese common toad Bufo japonicus, and narrow-mouthed toad Microhyla okinavensis. The gene arrangements of these genomes diverged from that of basal anurans (suborder Archaeobatrachia), but are the same as that of the members of der...

We compared six taxa of the genus Fejervarya from central Western Ghats, southwestern India, including F. rufescens, F. sahyadris, and four taxa that possess distinct mtDNA haplotypes as demonstrated by our previous studies. Morphological comparisons with F. brevipalmata, F. keralensis, F. nilagirica, and F. syhadrensis on the basis of literature d...

In the tropics, certain didemnid ascidians harbor the prokaryotic photosymbiont Prochloron. To date, this photosymbiosis has been found in four didemnid genera that include non-symbiotic species. Here, we report the molecular phylogeny of symbiotic and non-symbiotic didemnids based on their 18S rDNA sequences. The data cover all four genera contain...