Morphological discrimination of two genetic groups of a Japanese salamander, Hynobius naevius (Amphibia, Caudata)

Hynobius naevius, distributed on western Honshu, Shikoku, and Kyushu Islands of Japan, includes two genetically distinct groups (Groups A and B) that have never been delimited morphologically. Using specimens from the entire species range, we investigated the possibility of distinguishing these groups morphologically. Multivariate analyses of morphometric characters resulted in recognition of two groups that corresponded well to the two genetic groups. One (Group A) was characterized by larger body, compressed tail, shallower vomerine tooth series, bluish- or reddish-purple ground color, and pale-white lateral markings. In contrast, another (Group B) was characterized by smaller body, cylindrical tail, longer vomerine tooth series, reddish-brown ground color, and white lateral markings. Group A was composed of populations from the Chugoku District of Honshu and northern Kyushu, and could not be divided into subgroups, while Group B encompassed populations from the Chubu and Kinki Districts of Honshu, Shikoku and Kyushu, and was subdivided into three local subgroups that are geographically separated by marine straits. Morphometric differentiation in Group A is presumed to have been less affected by genetic factors than by other factors, such as ecological relationships with other, coexisting species. Differentiation in Group B is assumed to have been enhanced not only by genetic but also by climatological factors.     

Spatial framework of nine distinct local populations of the Japanese dormouse Glirulus japonicus based on matrilineal cytochrome b and patrilineal SRY gene sequences

We previously revealed the presence of six genetically distinct matrilineal populations of the Japanese dormouse Glirulus japonicus in the distribution range of Honshu, Shikoku, and Kyushu islands. In this study, we extended this analysis using mitochondrial cytochrome b gene sequences (n = 96) and Y-chromosome-specific SRY gene sequences (n = 22) from individuals collected from Honshu, Shikoku, Kyushu, and Oki Dogo I. The cytochrome b sequence data allowed us to define precise geographic ranges of the six previously known and three newly found distinct matrilineal lineages: northeastern Honshu (I), east-central Honshu (II), west-central Honshu and the Kii Peninsula (III), the western part of Honshu (IV), Shikoku (V), westernmost Honshu and Kyushu (VI), the northern part of central Honshu (VII), the southern part of central Honshu (VIII), and Oki Dogo I. (IX). Our inference of geographic borders suggests that regions of lower and higher altitudes in the mountain systems played important roles in driving the hosting and separation of lineages, respectively. Six matrilineal lineages (I, II, V, VI, VIII, and XI) were shown to possess their own SRY haplotypes, while lineages III and IV shared one haplotype. These data together with our previous observation of nuclear ribosomal RNA gene variation indicate advanced populational subdivision in this species. It is thus evident that each of the populations, including those living at high latitudes and in limited geographic spaces, have survived for several million years. A specific ability to tolerate cold may have permitted G. japonicus to preserve anciently diverged lineages in each locality.     

Onset of cryptic vicariance in the Japanese dormouse Glirulus japonicus (Mammalia, Rodentia) in the Late Tertiary, inferred from mitochondrial and nuclear DNA analysis

The sequences of the mitochondrial cytochrome b gene and restriction site variation in the spacer region of the nuclear ribosomal RNA gene [rDNA-restriction fragment length polymorphism (RFLP)] were analysed to determine the phylogeographic structure of the Japanese dormouse ( Glirulus japonicus ), which is threatened by deforestation and has been designated an endangered species in Japan. The phylogenetic tree of cytochrome b grouped G. japonicus into six geographical populations: north-eastern Honshu (I), central Honshu (II), west-central Honshu/Kii Peninsula (III), western Honshu (IV), Shikoku (V), and westernmost Honshu/Kyushu (VI); the genetic distances among these groups suggest divergence in the Late Tertiary. The lineage of group VI was located at the basal position in the phylogenetic tree, followed by the radiation of the other lineages. An rDNA-RFLP analysis of 15 restriction sites roughly supported such genetic isolation; groups I, II, III, IV, V and VI have five, two, one, one, one and four unique restriction sites, respectively, revealing four geographic groups as cryptic species: I, II, III + IV + V and VI. Our results reveal the ancient divergences of the local population, which has a complicated evolutionary history, and should be useful in developing a framework for the conservation of this species.     

Comments on cephalometrical configurations of the Japanese

Cephalometrical configurations of Japanese people were investigated on two hundred and sixteen groups living on the four main islands of Japan: Hokkaido, Honshu, Shikoku, and Kyushu. The Japanese in Honshu were divided geographically into a narrow-featured eastern major group and a broad-featured western major group. A physical characteristic of Japanese living in the western mid-Honshu was the lengthened feature of their cephalic measurement, an influence of a long-headed group of Korean people; Japanese residents in eastern mid-Honshu, however, showed the result of mixing with a short-headed group of Korean people. Japanese people living in Hokkaido, the northernmost island, and in the Ryukyu Islands in the South of Japan, presented no important finding which suggests their influence on the physical characteristics of the Japanese. Ongoing studies indicating physical relationships between Kyushu or Shikoku residents and Honshu residents, are as yet insufficient.     

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

Using starch gel electrophoresis, geographical enzyme variation was surveyed in 46 populations of the Japanese salamander Hynobius nebulosus , which occurs widely in western Japan. This species exhibits substantial local genetic differentiation and is more diverse in inland regions than on small islands. In several different analyses, two groups of populations, one from Kyushu Island to the westernmost part of Chugoku district, Honshu (western group), and another from Shikoku through Kinki to Chubu district, Honshu (eastern group), were consistently recognized. Most of the remaining populations were placed in two less clearly-defined groups: the montane group from the Chugoku Mountains and the Chugoku group from the coastal regions of Chugoku district. The divergence patterns of H. nebulosus are thought to be related to the geological history of its range. The populations near the boundary of the western group were found to share several alleles that were predominant on both sides of the boundary, indicating past secondary contact. Differentiation in the montane group did not follow the isolation by distance model, probably because several populations included were genetically mixed with lowland populations of the Chugoku group.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 311–330.     

Color polymorphism and historical biogeography in the Japanese patellogastropod limpet Cellana nigrolineata (Reeve) (Patellogastropoda: Nacellidae)

Cellana nigrolineata is amongst the most common and largest patellogastropod limpets in Japan, and has two color morphs. Analyses of anatomical and morphological characters, shell structure, and mitochondrial COI data (658bp) of these color morphs suggested that they represent intraspecific genetic variation. Molecular analysis demonstrated that the species can be subdivided into three genetically distinct groups: (Clade 1) Honshu, Shikoku to Eastern Kyushu, (Clade 2) Western Kyushu and (Clade 3) Southern Kyushu. Clade 1 and Clade 2 + 3 are distributed on the coastlines adjacent to two warm-water currents, the Kuroshio and Tsushima Currents, respectively. The southern population (Clade 3) is currently isolated by inhospitable sandy shores. The subdivision of these groups likely dates from the glacial period of Plio-Pleistocene time.     

Phylogenetic relationships and biogeography of the Japanese clawed salamander, Onychodactylus japonicus (Amphibia: Caudata: Hynobiidae), and its congener inferred from the mitochondrial cytochrome b gene

Using the mitochondrial cytochrome b gene, we investigated phylogenetic relationships between and within the Japanese clawed salamander, Onychodactylus japonicus, and its close continental relative O. fischeri. Monophyly of O. japonicus was well supported, and O. japonicus was clearly distinguished from O. fischeri. However, O. fischeri comprises genetically distinct populations from Russia, NE China, and Korea that do not form a monophyletic group. Within O. japonicus, four major clades were clearly recognized: Clade I from northern Tohoku district, Clade II from southern Tohoku district and the Tsukuba Mountains, Clade III from southwestern Honshu, and Clade IV from Kinki and Chugoku districts in Honshu and from Shikoku. Although genetic distances among these clades were large (5.5-9.6%), relationships among the clades were unresolved. All clades except Clade I contained two or three distinct subclades. In several localities in Kinki and Chugoku, Clades III and IV were sympatric. The estimated divergence times and available geohistorical data suggest that O. japonicus began to differentiate in the Upper Late Miocene and that the pattern of genetic differentiation of this species has been affected strongly by climate changes and geohistorical events such as volcanic activity and mountain formation. Our results suggest that both O. fischeri and O. japonicus comprise multiple cryptic species.     

Intraspecific variation of cuticular hydrocarbon composition in Formica japonica Motschoulsky (Hymenoptera: Formicidae)

Cuticular hydrocarbons and morphological features were compared among 80 Formica japonica colonies collected in Japan. Although a few morphological differences were found in workers among the colonies, four different types of cuticular hydrocarbon composition were observed. This was supported by a principal component analysis. We further compared the cuticular hydrocarbons among a total of approximately 400 F. japonica colonies, and categorized the hydrocarbon components into four types based on the result of discriminant analyses for the first 80 colonies. Type 1 was observed in colonies mainly collected in southern Honshu, Shikoku, and Kyushu. Types 2, 3, and 4 were from colonies with primary collections in Southern Honshu, central and Pacific coast northern Honshu, and the Sea of Japan coasts of northern Honshu and Hokkaido, respectively. The occurrence of four distinct types of CHC composition suggests that the colonies that produce them are separate species.     

Phylogenetic relationships of Hynobius naevius (Amphibia: Caudata) as revealed by mitochondrial 12S and 16S rRNA genes

Using mitochondrial 12S and 16S rRNA sequences, we investigated phylogenetic relationships among populations of the endemic Japanese salamander Hynobius naevius. Monophyly of this species was recovered only in the maximum parsimony tree and was unresolved in maximum likelihood and Bayesian trees. Instead the following four haplotype clades consistently emerged clearly: Clade 1 from northwestern Kyushu, Clade 2 from Chugoku and northeastern Kyushu, Clade 3 from western Shikoku and Kyushu, and Clade 4 from Chubu-Kinki and central-eastern Shikoku. Of these, Clades 1 and 2, and Clades 3 and 4, respectively, correspond to Groups A and B previously recognized from the analyses of allozyme data in this species, but monophyly of these groups was not strongly supported. Unlike the previous results, the western and eastern samples from Shikoku did not form a clade, and were grouped with Kyushu-B in Clade 3 and Chubu-Kinki in Clade 4, respectively. The reason for this conflict between mtDNA and allozyme results is unknown, but might be related to retention of ancestral mtDNA polymorphism in Shikoku populations. Nearly simultaneous divergence of as many as four lineages in wide-ranging H. naevius is inferred for the late Miocene-Pliocene history of this taxon.     

Morphological relationships among populations in the Sorex caecutiens/shinto group (Eulipotyphla, Soricidae) in East Asia, with a description of a new subspecies from Cheju Island, Korea

We investigated the morphological relationships among eight populations of Sorex caecutiens/shinto group in East Asia using 11 cranial and dental characters and four external characters. Univariate and multivariate analyses of these characters failed to distinguish S. caecutiens and S. shinto. Morphological characters were, in fact, continuous between populations. Sorex shinto from Honshu was similar to S. caecutiens from the Korean peninsula and Primorye in skull dimensions and to S. caecutiens from Hokkaido-Sakhalin in external dimensions. Sorex caecutiens from Cheju Island is morphologically similar to S. shinto from Sado and Shikoku islands. These three insular populations were characterized by having large body sizes. Sorex caecutiens from Cheju was the largest of the S. caecutiens/shinto group in East Asia. This shrew from Cheju was classified definitively as S. caecutiens on DNA data, but has a unique morphology among S. caecutiens populations in East Asia. We therefore regard this Sorex shrew on Cheju Island as a new subspecies of S. caecutiens and designate it S. c. hallamontanus Abe and Oh.     

Taxonomic review of Agraphydrus from Japan (Coleoptera: Hydrophilidae: Acidocerinae)

The Japanese species of the genus Agraphydrus are revised. Five species are recognized, including Agraphydrus ogatai sp. nov. from Honshu, Shikoku and Kyushu. The new species can be distinguished by the coarse ground punctures on the pronotum and elytra, and by the shape of parameres. All species except A. luteilateralis are redescribed. All species are diagnosed, relevant morphological characters are illustrated, distributional records are summarized and an updated key is provided.     

Molecular phylogeny of the genus Apatrobus (Coleoptera: Carabidae: Patrobinae) in western Japan

We performed a molecular phylogenetic analysis of the ground beetles Apatrobus (Carabidae), endemic to Japan, using the mitochondrial cytochrome c oxidase subunit I (COI) and the nuclear 28S rRNA (28S) genes. We focused on the species divergence in Kyushu, Shikoku and western Honshu and used 15 of 19 species and three populations with undetermined species in the DNA analysis. The gene trees showed that, of the Apatrobus species studied, A. hayachinensis Nakane from northern Honshu was not included in the monophyletic group of the other Apatrobus species and likely to be of a different genus. Divergence time estimation suggested that Apatrobus species excluding A. hayachinensis diverged 5.2 million years ago and the subsequent divergence of species occurred during the Pliocene and Pleistocene. In each of the main islands, Kyushu, Shikoku and Honshu, two or more distinct lineages occurred and all species had restricted distribution areas, suggesting that ancient dispersal and vicariance among the three main islands resulted in the nested biogeographical pattern of species distribution.     

Notes on two species of the subgenus Lyrothorax Chaudoir (Coleoptera: Carabidae; genus Pterostichus), Pterostichus amagisanus Tanaka and Ishida and Pterostichus fujitai Tanaka and Ishida

Two species of the subgenus Lyrothorax Chaudoir (Coleoptera: Carabidae; genus Pterostichus ), Pterostichus amagisanus Tanaka and Ishida and Pterostichus fujitai Tanaka and Ishida, were revised based on the male endophallus (inner sac everted from aedeagus). P. amagisanus was newly recorded based on a single male from Kyushu, southwest Japan, far from its known distribution (Honshu; the Fuji-Hakone-Izu volcano area), although additional materials are necessary to confirm this record. Despite a highly disjunct distribution, no conspicuous difference was recognized in either external or genital characters between the materials from Honshu and Kyushu. The nominal species P. fujitai was separated into two species, P. fujitai (Honshu) and Pterostichus eoyoritomus sp. nov. (Shikoku; type locality: Mount Jingayama); these two species have some significant differences in the endophallic structures. Character states in male genitalia suggest a sister relationship between P. eoyoritomus sp. nov. and Pterostichus yoritomus Bates.     

Morphometric and meristic characteristics of two groups ofLethenteron reissneri

Morphometric and meristic characteristics were compared between two genetically divergent groups ofLethenteron reissneri, collected from Hokkaido and Honshu islands, Japan. Whereas significant differences were found in some morphometric and meristic characters, the ranges overlapped somewhat in all of the characters examined between the two groups. Thus, it was difficult to distinguish exactly between the two groups using only the morphological characters. In sympatric populations of the two groups, no significant differences were found in almost all of the morphometric and meristic characters examined. The two groups ofL. reissneri, which are reproductively isolated from each other, should be regarded as sibling species. Assortative mating, based on morphological features, appears unlikely as the reproductive isolating mechanism between the two groups.     

Geographic variation in the greater Japanese shrew-mole,Urotrichus talpoides: Combining morphological and chromosomal patterns

Although much information on the species dynamics of small mammals may be gleaned from the integration of morphological and molecular data sets, the two are not routinely combined when species boundaries and definitions are investigated. The greater Japanese shrew-mole (Urotrichus talpoides) presents a rare example of intraspecific and geographical euchromatic chromosomal variation. In this study a combination of 2D landmark-based and outline-based geometric morphometric methods were used to provide the first quantitative examination of variation in skull morphology occurring between populations of U. talpoides. Geographic variation was found to be most conspicuous in ventral and dorsal cranial morphology, and less evident for outline-based analyses of the dentary, thereby indicating differing magnitudes of skeletal plasticity associated with geographic variation in each system. Both ventral and dorsal cranial morphology differed significantly between shrew-moles from western and eastern Honshu, in agreement with previously identified chromosomal variation boundaries. Inclusion of other island populations revealed shape differences between shrew-moles in Kyushu, Tsushima and North Honshu. These results lend general support for the unification of morphological and chromosomal data when assessing species boundaries.     

Distribution of the four flagellar (H) antigenic subserotypes of Bacillus thuringiensis H serotype 3 in Japan

A total of 302 strains of Bacillus thuringiensis flagellar (H) serotype 3, collected from sericultural environments and soils of the three main islands (Honshu, Shikoku and Kyushu) of Japan, were examined for their H antigenic subserotypes. Of these strains, 259 (85.8%) were identified as the H subserotype 3a : 3c (subsp. alesti ), 16 (5.3%) were referable to the subserotype 3a : 3b : 3c (subsp. kurstaki ), 26 (8.6%) belonged to the subserotype 3a : 3d : 3e (subsp. fukuokaensis ) and one strain (0.3%) was the subserotype 3a : 3d (subsp. sumiyoshiensis ). The subserotypes 3a : 3c and 3a : 3b : 3c were present in sericultural environments only; the former was distributed in Honshu and Shikoku Islands but not in Kyushu Island, and the latter was distributed in Honshu and Kyushu Islands but not in Shikoku Island. The subserotype 3a : 3d : 3e, mainly found in soils but occasionally in sericultural environments, was distributed in the three main islands. It also appeared that the subserotype 3a : 3d : 3e, a recently described subserotype, was distributed in Japan more widely than the globally disseminated subserotype 3a : 3b : 3c. The results clearly showed geographical and ecological differences in the distribution of subserotypes.     

Discrimination of two Japanese water pennies,Eubrianax granicollis Lewis and E. ramicornis Kiesenwetter (Coleoptera: Psephenidae), based on laboratory rearing and molecular taxonomy

Two psephenid beetles, Eubrianax granicollis Lewis and E. ramicornis Kiesenwetter, are common species on the main islands of Japan (i.e. Honshu, Shikoku and Kyushu), but diagnostic characters for larval identification are unknown. Two types of field‐collected Eubrianax larvae from Honshu and Kyushu were discriminated based on the distributions of granules on the dorsal surface. These larvae were assigned to E. granicollis and E. ramicornis by comparing them with larvae of the two species obtained via laboratory rearing. The two species were also identified unambiguously on the basis of their mitochondrial cytochrome oxidase subunit I (COI) gene sequences. Larval and pupal morphology are described based on laboratory‐reared specimens.     

Phylogeography of Japanese population of Phelotrupes auratus (Coleoptera, Geotrupidae) inferred from mitochondrial DNA sequences

A partial sequence of the mitochondrial cytochrome c oxidase subunit I (COI) gene (745 bp) was determined for 57 specimens of a geotrupid beetle (Phelotrupes auratus) from throughout the Japanese archipelago. Of the 57 beetles examined, 42 haplotypes were identified. Phylogenetic trees inferred using maximum parsimony, neighbor joining, and Bayesian inference methods were highly congruent. Reconstructed phylogenetic relationships indicated that P. auratus from the Japanese archipelago was separated into two distinct lineages: Group A, which consisted of 35 haplotypes from Honshu, Shikoku, and Hokkaido Islands, and Group B, which consisted of seven haplotypes from Kyushu and Yakushima Islands. In addition, two sublineages were also recognized within Group A: Subgroup A-1, which consisted of 11 haplotypes from eastern Honshu and Hokkaido, and Subgroup A-2, which consisted of 10 haplotypes from western Honshu and Shikoku. Average genetic distances within Group A were positively correlated to geographic distance between sampling localities. Phylogenetic relationships among haplotypes did not correspond to subspecies classification.     

Cytogeographical study of four aneuploids ofCarex oxyandra Kudo in Japan

Chromosome numbers were determined for 342 clones ofCarex oxyandra collected from 35 localities in Hokkaido, Honshu, Shikoku and Kyushu, Japan. Four intraspecific aneuploids, 2n=18, 20, 24 and 26, were found. In meiotic division, only bivalent chromosomes were observed in all clones at metaphases I and II, suggesting that the aneuploids are established gamodemes. In the mitotic metaphase chromosomes, trimodal variation in chromosome length was observed. The 2n=26 clones found on Mt. Hiko had two particularly small chromosomes. The cytodemes with higher number of chromosomes are distributed in more southern areas of Japan.Carex oxyandra, therefore, accompanied with chromosome fragmentations, might spread the geographical distribution to the southern parts. The morphological characters of leaves, spikes, scales, perigynia and nuts were similar among the four cytodemes, except for the small leaves on plants from Yaku Island.     

Chromosome polymorphism in the ant,Pheidole nodus

A survey of chromosome polymorphism was made in populations of Pheidole nodus (Hymenoptera, Formicidae). A total of 1,666 males were collected from 11 localities in Japn. Four polymorphic karyotypes were observed: (1) n = 17 with 4 metacentrics (abbreviated as 4M), (2) n = 18(3M), (3) n = 19(2M) and (4) n = 20(1M). These differences are due to the Robertsonian type rearrangement. The karyotype 18(3M) is found in all the populations examined, but the others are more or less localized in their distribution. The 17(4M) appears mainly in Shikoku and the northern Kyushu populations, 19(2M) along the Pacific coast of Honshu, Shikoku and Kyushu, and 20(1M) in the eastern part of Honshu and Shikoku. This distribution pattern indicates that 18(3M) is the oldest, 19(2M) and 20(1M) are derived from 18(3M) by centric fission, and 17(4M) by centric fusion. The most probable mechanism of karyotype evolution in this species is considered to be the centric fission.