Masafumi Matsui's research while affiliated with Kyoto University and other places

Publications (278)

Article
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Background Hynobius hirosei is a lotic-breeding salamander endemic to Shikoku Island in western Japan. Significant allozymic and morphological differences have been found among the populations of this species; however, the degree and pattern of intraspecific variation have not been surveyed using a sufficient number of samples. Methods For the tax...
Article
Glandirana rugosa is known to include several geographic groups differing in sex chromosomes, and has been proven to be paraphyletic in mitochondrial phylogeny with respect to G. susurra. By analyzing genetic and morphological variation in a large number of individuals of Glandirana, we studied their taxonomic relationships. A mitochondrial DNA phy...
Article
Previous phylogenetic studies based on mitochondrial DNA data have consistently suggested that Hynobius tokyoensis consists of two major clades, clade A (northern clade) and clade B (southern clade). In this study, we newly estimated their population genetic structure and phylogenetic relationships by nuclear SNPs, and the results suggested heteros...
Preprint
In order to interpret the degree of postmating isolation and the evolutionary relationships among Fejervarya species from Indonesia (Lesser Sunda), Bangladesh, China, and Japan, crossing experiments and molecular phylogenetic analyses were carried out using frogs of Fejervarya species from these countries. The crossing experiments revealed that the...
Article
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The Quaternary climate affected the present species richness and geographic distribution patterns of amphibians by limiting their activities during the glacial period. The present study examined the phylogenetic relationships of Japanese toads ( Bufo japonicus and B. torrenticola ) and the demography of each lineage from the past to the present bas...
Article
We developed eight novel microsatellite markers for the salamander Hynobius tsuensis, which is endemic to Tsushima Island, Japan. In H. tsuensis, the number of alleles, observed heterozygosity, and expected heterozygosity in each locus ranged from 1 to 10, 0.00 to 0.76, and 0.00 to 0.76, respectively. In cross-species amplification, five and four o...
Article
The genus Kalophrynus is represented by tiny to medium terrestrial or subfossorial frogs and is widely distributed in Southeast Asia. The diversity centre of this genus is Borneo, where almost half of all nominal species are distributed and all of these are endemic to this and the peripheral islands. Kalophrynus nubicola is the smallest species wit...
Article
The maintenance mechanisms of hybrid zones between two lineages/species and their gene flow dynamics are major topics for speciation studies. Elucidating these dynamics can help us to understand the process of speciation. The newt Cynops pyrrhogaster is distributed on the main islands of Japan and comprises five mitochondrial DNA (mtDNA) lineages....
Article
We found a uniquely colored dicroglossid frog of the genus Occidozyga from western Sarawak, East Malaysia. It is divergent from other congeners in morphology and mtDNA sequences. In a molecular phylogeny, this species is the sister lineage to the continental species O. lima and O. martensii with weak support. The species is small with SVL 16-18 mm...
Article
Fauna of the Central Ryukyus includes a high percentage of endemic species, and Hallowell's tree frog Hyla hallowellii Thompson, 1912 is one of such elements, occurring in a total of eight islands in the Amami and Okinawa Island groups. Using samples representing all of these eight island populations, we studied variations in morphology, karyotype,...
Article
The red-bellied form of Calliophis intestinalis (Laurenti, 1768) sensu lato was originally reported from Pahang, west Malaysia. To determine the taxonomic status of this form, we examined the type specimens of Elaps sumatranus Lidth De Jeude, 1890, Calliophis intestinalis everetti (Boulenger, 1896), and Callophis furcatus var. nigrotaeniatus Peters...
Article
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A Japanese microhylid, Microhyla okinavensis, originally described from Okinawajima Island, middle Ryukyus, was long synonymized with M. ornata from India. However, molecular phylogenetic studies revealed its distinct species status from M. ornata, and more recent phylogenetic study revealed the population from the Yaeyama Group of the southern Ryu...
Article
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Buergeria japonica, long thought to be a single species widely occurring on the Ryukyu Archipelago and Taiwan, proved to include three genetically differentiated clades, (1) the Northern and Central Ryukyu, (2) the Southern Ryukyu and Northern Taiwan, and (3) the Southern Taiwan clades. The Southern Taiwan clade has already been split from the othe...
Article
Micryletta inornata is a complex species that is widely distributed from Sumatra to mainland Asia, including the Thai-Malay Peninsula and Indochina. Recently, this species was confirmed to be endemic to regions near the type locality in Sumatra, and the populations from other regions were suggested to be different species. We examined phenotypic an...
Article
Females of some Asian salamanders of the genus Hynobius deposit in streams their eggs embedded in a translucent envelope called an ‘egg sac’. The edges of the envelope exhibit a spectacular blue-to-yellow iridescent glow, which instantaneously disappears when the sac is removed from water. First, our scanning electron microscopy analyses reveal tha...
Article
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The endangered crocodile newt, Echinotriton andersoni, is a relatively large species of the family Salamandridae and is distributed on six islands in the central part of the Ryukyu Archipelago, Japan. Because of an originally small distribution range and recent habitat loss, this species has been steadily declining in number. To elucidate fine-scal...
Article
Two lineages of stream toads in the genus Ansonia from Malaysian Borneo have long been suspected to be specifically distinct on the basis of molecular data. We assessed the taxonomic status of these lineages using morphological and additional genetic data. In mtDNA phylogeny, each lineage-one from Bario, Kelabit Highlands of Sarawak, the other from...
Article
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Kurixalus absconditus sp. nov., a new species of tree frog of the genus Kurixalus, described from West Kalimantan on the basis of molecular phylogenetic and morphological evidence. The new species can be distinguished from its congeners by a combination of following morphological characters: having smaller body size, more prominent of mandibular sy...
Article
Within Sundaland, the species diversity of the genus Megophrys is richest in Borneo, with some species restricted to the northern highlands of the island. On the basis of molecular, morphological and acoustic evidence, we describe a new species of large-sized Megophrys, once confused with M. nasuta. The new species Megophrys kalimantanensis sp. nov...
Article
A lotic-breeding salamander Hynobius stejnegeri, formerly called H. yatsui, from western Japan is revised based on genetic and morphological evidence, and three species are described: H. guttatus sp. nov. from Chubu-Kinki districts of Honshu Island, H. tsurugiensis sp. nov. from east highland of Shikoku Island, and H. kuishiensis sp. nov. from othe...
Article
We sequenced mitochondrial cytochrome b gene of 14 samples of Siberian salamander, Salamandrella keyserlingii, from a population newly found in Kamishihoro-cho, eastern Hokkaido, Japan, and conducted phylogenetic analysis to reveal genetic identity of the population. The Kamishihoro population was most closely related to the geographically adjacent...
Article
The Ryukyu Archipelago, located at the southwestern part of Japan, is known as a group of continental islands and harbours many endemic taxa, supposedly reflecting its fairly long isolation from the Eurasian continent, Taiwan and the Japanese main islands. Microhyla okinavensis has been known as an endemic member of the terrestrial fauna of this ar...
Article
The abundant clouded salamander from western Japan, Hynobius nebulosus, has long been considered a single widespread species, although some authors have suggested the inclusion of several cryptic species. This led to a molecular and morphological analysis of populations from all parts of the known range. Phylogenetic relationships were inferred fro...
Article
Larval morphology offers some of the more important characters for the taxonomy of Meristogenys, and larval information of almost all species has been reported for this genus. However, some larval assignments in previous studies were not based on reliable methods and should be reexamined using modern techniques. In this study, we used molecular met...
Article
Two new species of lotic-breeding salamanders, Hynobius sematonotos and H. oyamai, are described from Chugoku district and northeastern Kyushu district, respectively, western Japan. They are members of the so-called H. naevius group and are phylogenetically close to H. naevius, H. katoi, and H. hirosei but divergent from them with large genetic dis...
Article
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A new species of frog in the genus Microhyla is described from Sumatra, Indonesia based on molecular and morphological characters. This new species was previously confused with M. achatina, a Javan endemic. This new species is diagnosable from its congeners by possessing a medium size (SVL in adult males 18.20–21.32 mm, in adult females 20.37–25.51...
Article
Two new species of the dwarf litter frog genus Leptobrachella are described from North and Central Kalimantan, Indonesian part of the Borneo Island. Leptobrachella fusca n. sp. from Bulungan Regency, differs from all congeneric species in the following combination of characters: body small (SVL: 16.3 mm in a male); dorsum uniformly dark brown; side...
Article
Hybridizations on a secondary contact zone between 2 diverged lineages can have various evolutionary consequences, including the genetic replacement of one lineage by another. We detected such a case between 2 lineages (the Central and Western lineages) of the Japanese fire-bellied newt, Cynops pyrrhogaster in the Chugoku district of western Japan....
Data
Sampling numbers, vouchers, localities and GenBank Accession numbers of sequences used in this study “*” sequences were downloaded from GenBank. “#” sequences were retrieved form Zhao et al. (2012). CIB, Chengdu Institute of Biology, Chinese Academy Science; HNNU, Henan Normal University; IEBR, Institute of Ecology and Biological Resources; VNUH, V...
Data
Ultrametric tree for the mitochondrial genes of Tylototriton s.l. resulted from GMYC analysis. Red shading branches indicate GMYC clusters. “*” individuals were used in *BEAST analyses Red shading branches indicate GMYC clusters. “*” individuals were used in *BEAST analyses.
Data
Primers for PCR and sequencing in this study
Data
Lineage through time plots for different lineage delimitating strategies based on 10,000 simulated trees under different sampling fractions Different lineage delimitating strategies: GMYC, 39 statistically inferred coalescent lineages using the Generalized Mixed Yule Coalescent method; NS, 23 currently nominal species; and NSP, 23 NS plus four inde...
Data
Testing diversification models in the genus Tylototriton s.l. using birth–death likelihood Different lineage delimitating strategies: GMYC, 39 statistically inferred coalescent lineages using the Generalized Mixed Yule Coalescent method; NS, 23 currently nominal species; NSP, 23 NS plus four independent lineages representing putative cryptic specie...
Article
Full-text available
Global climatic transitions and Tibetan Plateau uplifts are hypothesized to have profoundly impacted biodiversity in southeastern Asia. To further test the hypotheses related to the impacts of these incidents, we investigated the diversification patterns of the newt genus Tylototriton sensu lato , distributed across the mountain ranges of southeast...
Data
Divergence times within Salamandridae and fossil calibrations (C1–C4) for dating analyses The tree was resulted from the topology-constrained Beast analysis. Fossil calibrations C1–C4 were given in materials for details. Grey bars at nodes show 95% highest posterior density intervals of divergence times.
Article
Southeast Asia and southern China (SEA-SC) harbor a highly diverse and endemic flora and fauna that is under increasing threat. An understanding of the biogeographical history and drivers of this diversity is lacking, especially in some of the most diverse and threatened groups. The Asian leaf-litter frog genus Leptolalax Dubois 1980 is a forest-de...
Article
The taxonomic status of two populations of stream toads of the genus Ansonia from Thailand, previously suspected to be specifically distinct on the basis of molecular data, are assessed using morphological and additional genetic data. In mtDNA phylogeny, each of the two Thai lineages, one from Pilok Subdistrict, Kanchanaburi, and another from Phuke...
Article
The Japanese giant salamander, Andrias japonicus, is known to exhibit very low genetic diversity, but the number of individuals surveyed in a population is limited by now. We investigated partial sequences (673 bp) of mitochondrial cytochrome b gene in 180 specimens of a population from the Inuyama Head Works on the Kiso River, Central Japan, over...
Article
By examining mitochondrial DNA phylogeny using 2424bp of sequence data 12S rRNA, tRNAval, and 16S rRNA genes, we evaluated the taxonomic relationships among Javan litter frogs Leptobrachium hasseltii from southern Sumatra, Java, and Bali. Leptobrachium hasseltii formed a well-supported monophyletic group, which comprised two major clades. One major...
Article
Examination of the holotype of Hynobius stejnegeri Dunn, 1923 revealed that the species is identical with H. yatsui Oyama, 1947, recently resurrected from H. naevius (Temminck and Schlegel, 1838). The name H. yatsui is therefore relegated to a subjective junior synonym of H. stejnegeri. The latter name, however, has been widely applied to an amber-...
Article
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Few empirical studies have compared coalescent-based methods to distance-based methods for delimitation of less divergent species. In this study, we used two coalescent-based (BFD and BPP) and two distance-based barcoding (ABGD and jMOTU) methods to delimit closely related species in the Kurixalus odontotarsus species group. Phylogenetic analyses r...
Article
We report on biological notes of an enigmatic asterophryine Gastrophrynoides borneensis based on a male collected from western Sarawak. The male is immaculate brown in dorsal colour, without small white spots contrasting to previous descriptions. Whether this indicates intraspecific variation or specific differentiation requires further study. Mito...
Article
A new species of salamander, Hynobius mikawaensis, is described from the eastern part of Aichi Prefecture, central Japan. It is a lentic breeder of the so-called H. lichenatus species group, and is phylogenetically closest to H. nigrescens and H. takedai. Morphologically, it differs greatly from H. nigrescens, but is very similar to H. takedai, fro...
Article
We studied specimens of the genus Leptobrachella Smith, 1925 collected from West Kalimantan, Indonesian part of the island of Borneo, and housed in the Bogor Museum as L. mjobergi Smith, 1925. Our morphological examination proved that the specimens should be identified as L. juliandringi Eto, Matsui et Nishikawa 2015. This is the first record of L....
Article
A new small, semi-Arboreal toad of the genus Pelophryne is described from western Sarawak, Malaysian Borneo, on the basis of molecular and morphological evidence. Of the two morphotypes recognized in the genus, the new species belongs to the one in which the tips of the fingers are expanded into truncate discs. Among the species in the morphotype,...
Article
We report a new microhylid frog of the genus Kalophrynus from Peninsular Malaysia and describe it as a new species Kalophrynus kiewi based on results of molecular and morphological analyses. The new species is a large-sized Kalophrynus (snout-vent length 34-47 mm) and is morphologically very similar to K. pleurostigma, in which it has long been unr...
Article
A new species of Asian rock gecko, genus Cnemaspis, is described from Padawan, western Sarawak, Malaysian Borneo. The new species forms a clade with C. paripari and C. nigridia of the C. nigridia group in a mitochondrial DNA phylogeny and is similar to them morphologically in some characters such as caudal scalation. It differs from the other Asian...
Article
Using preserved specimens, we studied the basic life history of the topotypic population of the unique Asian plethodontid salamander, Karsenia koreana. Of 51 individuals examined, 11 males and 13 females were judged as mature from the development of gonads. The ovarian eggs were large (diameter 3.7-4.8 mm) and yellow to orange in color, and the clu...
Article
Phylogenetic relationships within the genus Leptolalax have been insuiciently resolved, while the relationships of a related genus Leptobrachella with other genera are totally unknown. In order to improve these situations, we assessed the phylogenetic relationships among 19 species of Leptolalax and four species of Leptobrachella based on 2067-2527...
Article
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Chinese populations of the endangered Siberian salamander Ranodon sibiricus are reported to have diverged only about 120 years ago, and to have the lowest genetic diversity of any amphibian. However, these conclusions require verification, as the main range of the species is in Kazakhstan. Moreover, the generation time used for estimating divergenc...
Article
Full-text available
Using preserved specimens, we studied the basic life history of the topotypic population of the unique Asian plethodontid salamander, Karsenia koreana. Of 51 individuals examined, 11 males and 13 females were judged as mature from the development of gonads. The ovarian eggs were large (diameter 3.7-4.8 mm) and yellow to orange in color, and the clu...
Article
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The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009;...
Data
This plot is not part of the published stance but derives from it. The plot shows the number of authors by geographic region (courtesy of Dr. Diego Astua).
Article
A new highland species of the dwarf litter frog, Leptobrachella itiokai, is described from Gunung Mulu National Park, northern Sarawak, East Malaysia. It occurs syntopically with another highland species, L. brevicrus, but differs from it by a unique call that may be described as a chirp, with dominant frequency of ca. 10 kHz. The new species is mo...
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An unusual triploid individual (3N=42) was found in a population of Rana neba in nature. The individual had triplets of 14 chromosomes, which are apparently identical to those of diploid R. neba. This strongly suggests that this individual is autotriploid, although the mechanism of its emergence remains an open question.
Article
A fanged frog Limnonectes kuhlii was once thought to be wide-ranging in Southeast Asia, but is now confined to its type locality Java through recent phylogenetic studies, which clarified heterospecific status of non-Javanese populations, and monophyly of Bornean populations. However, large genetic differences among Bornean populations suggest occur...
Article
Full-text available
Using mitochondrial DNA sequences, we surveyed genetic features of 12 individuals of Cynops pyrrhogaster introduced into Hachijojima Island, in order to estimate their possible origin in the main islands of Japan. The phylogenetic analysis revealed that the 12 examined newts of the introduced population display no genetic diversity and share charac...
Article
Three species/subspecies of toads (Bufo japonicus japonicus, B. j. formosus, and B.Torrenticola) show parapatric/sympatric patterns of distribution in Japan, and usually they are morphologically indistinguishable at early developmental stages. For quick and easy genetic identification of these three toads, we validated LAMP assay. We designed taxon...
Article
We describe two well-preserved and articulated fossil anurans excavated from the Lower Cretaceous Sasayama Group in Hyogo Prefecture, Western Honshu, Japan, as new taxa on the basis of unique combinations of character states. We performed a phylogenetic analysis that included these new taxa, as well as Mesozoic and archaic anurans. This analysis st...
Article
Full-text available
A cryptic Bornean torrent frog of the genus Meristogenys, which is divergent genetically and morphologically from all known congeners, is described from mountain streams of western Sarawak, East Malaysia (Borneo). The species occurs sympatrically with the type species of the genus, M. jerboa, but apparently differs from it in adult coloration and l...