Geography-linked phylogeny of theDamaster ground beetles inferred from mitochondrial ND5 gene sequences

We have constructed phylogenetic trees based on sequence comparisons of mitochondrial NADH dehydrogenase subunit 5 gene for 11Damaster blaptoides specimens from various localities of Japan. The specimens consist of eight subspecies.Coptolabrus fruhstorferi, Acoptolabrus gehinii, andProcrustes kolbei, which are taxonomically related toDamaster, have also been analyzed for comparison.Damaster is more related toAcoptolabrus than toCoptolabrus in the ND5 trees, in contrast to the generally accepted view thatDamaster is derived fromCoptolabrus, whereasAcoptolabrus is the sister group ofDamaster/Coptolabrus. The emergence ofProcrustes is much earlier than the rest of the genera. TheDamaster subspecies are monophyletic. Four major lineages are recognized, which are geography linked within the Japanese archipelago. The origin and diversification process have been discussed based on these findings.The nucleotide sequence data reported in this paper will appear in the GSDB, DDBJ, EMBL, and NCBI nucleotide sequence databases with the accession numbers D50422-D50429     

Pattern of morphological diversification in the Leptocarabus ground beetles (Coleoptera: Carabidae) as deduced from mitochondrial ND5 gene and nuclear 28S rDNA sequences

Most of the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene and a part of nuclear 28S ribosomal RNA gene were sequenced for 14 species of ground beetles belonging to the genus Leptocarabus. In both the ND5 and the 28S rDNA phylogenetic trees of Leptocarabus, three major lineages were recognized: (1) L. marcilhaci/L. yokoael/Leptocarabus sp. from China, (2) L. koreanus/L. truncaticollis/L. seishinensis/L. semiopacus/L. canaliculatus/L. kurilensis from the northern Eurasian continent including Korea and Hokkaido, Japan, and (3) all of the Japanese species except L. kurilensis. Clustering of the species in the trees is largely linked to their geographic distribution and does not correlate with morphological characters. The species belonging to different species groups are clustered in the same lineages, and those in the same species group are scattered among the different lineages. One of the possible interpretations of the present results would be that morphological transformations independently took place in the different lineages, sometimes with accompanying parallel morphological evolution, resulting in the occurrence of the morphological species belonging to the same species group (= type) in the different lineages.     

A salmon id phylogeny inferred from mitochondrial cytochrome b gene sequences

Partial mitochondrial cytochrome b gene sequences of eight salmonid species were used in a PAUP analysis to generate a phylogeny of the group. The four genera represented are Salmo, Salvelinus, Oncorhynchus and Thymallus . The inferred phylogenetic tree coincides well with the classically derived one for these genera. The recent reclassification of the rainbow trout as a member of the genus Oncorhynchus is supported. The assignment of grayling as the outgroup is vindicated. The utility of gene sequence data to infer the phylogenetic relationships of the Salmonidae is discussed.     

Resolving phylogeny at the family level by mitochondrial cytochrome oxidase sequences: phylogeny of carrion beetles (Coleoptera, Silphidae)

We investigated the phylogenetic relationships of carrion beetles (Coleoptera, Silphidae) using 2094 bp of their mitochondrial cytochrome oxidase subunit I and II and tRNA leucine gene sequences. Shorter fragments of this gene region previously have been used to establish generic relationships in insects. In this study, they provided more than sufficient resolution, although the third positions of the protein-coding sequences reached saturation for the deeper divergences. This first published phylogeny for the Silphidae comprises 23 species from 13 genera sampled across the geographic range of the family. In addition, we included species from three related families as outgroups. One of these families, the Agyrtidae, was, until recently, included in the Silphidae, but its resolution here justifies its current position as a separate family. The silphid subfamilies Nicrophorinae and Silphinae are monophyletic in all analyses. All genera for which several species were sampled are supported as monophyletic groups, with the exception of the genus Silpha. European and North American representatives of two Nicrophorus species described from both continents are supported as each others' closest relatives. The lineage that colonized Gondwanaland and that most likely originated in the Palearctic is the most basal within the Silphinae.     

Parallel evolution in radiation ofOhomopterus ground beetles inferred from mitochondrial ND5 gene sequences

Molecular phylogenetic analyses using mitochondrial NADH dehydrogenase subunit 5 (ND5) gene sequences representing all 15 species and the majority of subspecies or races of theOhomopterus ground beetles from all over the Japanese archipelago have uncovered a remarkable evolutionary history. Clustering of the species in the molecular phylogenetic tree is linked to their geographic distribution and does not correlate with morphological characters. Taxonomically the same species or the members belonging to the same species-group fall out in more than two different places on the ND5 tree. Evidence has been presented against a possible participation of ancestral polymorphism and random lineage sorting or of hybrid individuals for the observed distribution of mitochondrial DNA haplotypes. The most plausible explanation of our results is that parallel evolution took place in different lineages. Most notably,O. dehaanii, O. yaconinus, andO. japonicus in a lineage reveal almost identical morphology with those of the same species (or subspecies) but belonging to the phylogenetically remote lineages.The nucleotide sequence data reported in this paper will appear in the DDBJ, EMBL, and GenBank nucleotide sequence databases with accession numbers D50711-DD-50733 and D87131-D87186.     

五种啮齿类动物mtDNA蛋白编码基因序列变化的比较

目的利用本实验室测定的中国地鼠、金黄地鼠和GenBank中田鼠、小鼠、大鼠的线粒体全基因组序列,比较分析五种啮齿类动物的mtDNA蛋白编码基因序列的变异,探讨其分子进化关系。方法将五种动物各自的13个蛋白编码基因分别连接成一个序列,用DNAstar-EditSeq分析软件计算每个序列的碱基长度和组成,计算蛋白编码基因的碱基和氨基酸的差异。以人为外群,基于连接在一起的13个蛋白编码基因的氨基酸序列,用MEGA4.0软件通过最大简约性法(MP)和非加权成对平均数法(UPGMA)构建进化树。结果在五种啮齿动物的13个蛋白基因序列中,A、T、C、G碱基的平均含量为32.4%、29.6%、26.2%和11.9%,中国地鼠mtDNA各蛋白编码序列以及其编码的氨基酸序列与其他物种相比,与金黄地鼠的相应序列差异最小,与大鼠mtDNA各蛋白编码序列以及其编码的氨基酸序列差异较大。分子进化树也显示中国地鼠和金黄地鼠的亲缘关系最近,与小鼠、大鼠存在的差异相对大。结论五种动物的碱基组成的百分比中显示G的相对缺乏,相互之间的进化关系与传统的分类地位基本吻合。     

Molecular and morphological congruence in hominoid trans-species polymorphisms

Molecular and morphological data increasingly have confirmed thatHomo sapiens is more closely related to the African apes than to the Asian orangutan. At the same time, this evolutionary relationship has been questioned persistently from the standpoint of cladistic analyses of morphological characteristics, such as the incisive foramen; some proponents of cladistic approaches to phylogeny propose instead thatHomo sapiens is closer to the orangutan. This contrast can be resolved, and various kinds of evidence brought into consistency, by (1) demonstrating that particular morphological traits, including the incisive foramen, are variable across taxa, not taxon-specific; and (2) utilizing the principle of polyclinal variation to describe the preservation of widespread, shared genetic diversity among mammalian populations, particularly those of hominoid primates.     

Molecular phylogeny of cockroaches (Blattaria) based on mitochondrial COII gene sequences

Phylogenetic relationships among five cockroach families (Cryptocercidae, Polyphagidae, Blattidae, Blattellidae and Blaberidae) using seventeen species, were estimated based on the DNA sequences of the mitochondrial cytochrome oxidase subunit II (COII) gene. A cladogram inferred using the neighbour‐joining method indicated that Polyphagidae and Cryptocercidae are closely related to each other, and that these two groups are a sister group to the remaining cockroach families. The monophyly of this clade, however, was not strongly supported in terms of bootstrap percentages. Blaberidae and Blattellidae were shown to be sister groups as previously proposed, with Blattidae as a sister group to that clade. Non‐weighted and weighted parsimony analyses were also performed following analyses of nucleotide substitution patterns that indicated saturation of the COII gene among these taxa had occurred. These parsimonious cladograms suggested that Polyphagidae was the basal family, and Polyphaginae, including Cryptocercus as proposed by Grandcolas 1994a ), was not monophyletic. The inferred relationships among cockroach families (Polyphagidae, Cryptocercidae + (Blattidae + (Blattellidae + Blaberidae))) is partly in agreement with some previously published analyses. Additionally, based on molecular data, Asian and American Cryptocercus are suggested to have diverged from one another before the Oligocene (～20 mya).     

Ribosomal RNA gene sequences and hominoid phylogeny

Sequences totaling 3,500 bases from the 28S rRNA gene and from one of the ribosomal internal transcribed spacers (ITS1) have been determined for human, chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), and orangutan (Pongo pygmaeus). Analyses of the rRNA alignments show (1) a clustering of substitutions in the variable regions of the 28S gene, (2) a 1.5-3-fold increase in divergence in the transcribed spacer over that in the exon, and (3) that human and chimpanzee are the most closely related pair, in agreement with the results of Miyamoto et al., Sibley and Ahlquist, and Caccone and Powell.     

Molecular phylogeny of the Drosophila auraria species complex and allied species of Japan based on nuclear and mitochondrial DNA sequences

We studied the phylogenetic relationships among the six species of the Drosophila auraria species complex and three species of the montium species subgroup endemic to Japan. To do this, we examined the DNA sequences of the nuclear ITS1 and the mitochondrial COII of these species. Intraspecific variation in ITS1 was observed for most of the species studied. However, interspecific variation was small and of the same magnitude as intraspecific variation among D. auraria, D. triauraria, and D. quadraria. In addition, the amount of intraspecific variation between COII sequences from D. auraria and D. triauraria was almost the same as that of the interspecific variation between these species. Phylogenetic trees based on ITS1 or COII data reveal that, with the exception of D. pectinifera, these species can be separated into two taxonomic groups. D. rufa formed a taxonomic lineage with two Japanese endemic species, D. asahinai and D. lacteicornis. Physiological and behavioral differences between D. auraria and D. triauraria have been reported, but our results differed from those previously reported. Such differences may be better explained by hybridization between D. auraria and D. triauraria than by similarity due to recent common ancestry. Both the ITS1- and COII-based phylogenetic trees placed D. pectinifera outside the auraria complex. However, D. pectinifera sequences were more similar to those of the auraria complex than those of D. punjabiensis, another species thought to be closely related to members of the auraria complex.     

五种色蟌Cyt b基因序列及其系统发育关系

以昆虫mtDNA的Cytb基因作为分子遗传标记,用其特异性引物进行PCR扩增及DNA测序,共获得蜻蜓目束翅亚目色蟌科4属5种及1外群的Cytb基因部分序列(576bp),该片段中碱基T,C,A,G的平均含量分别为31.6,21.6,31.4和15.4%,A+T平均含量为63%,明显高于G+C含量(37%)。密码子第3位点的A+T平均含量较高,为66.4%。碱基替换多发生在密码子的第3位点。以巨齿尾溪蟌Bayadera melanopteryx作为外群构建系统发育树,结果显示,绿色蟌属Mnais和单脉色蟌属Matrona是单系群,绿色蟌属是单脉色属、细色蟌属Vestalis及艳色蟌属Neurobasis的姐妹群,是较早分化出来的一个类群。     

A phylogeny of Chinese species in the genus Phrynocephalus (Agamidae) inferred from mitochondrial DNA sequences

We investigated the phylogenetic relationships among most Chinese species of lizards in the genus Phrynocephalus (118 individuals collected from 56 populations of 14 well-defined species and several unidentified specimens) using four mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b, and ND4-tRNA(LEU)). The partition-homogeneity tests indicated that the combined dataset was homogeneous, and maximum-parsimony (MP), neighbor-joining (NJ), maximum-likelihood (ML) and Bayesian (BI) analyses were performed on this combined dataset (49 haplotypes including outgroups for 2058bp in total). The maximum-parsimony analysis resulted in 24 equally parsimonious trees, and their strict consensus tree shows that there are two major clades representing the Chinese Phrynocephalus species: the viviparous group (Clade A) and the oviparous group (Clade B). The trees derived from Bayesian, ML, and NJ analyses were topologically identical to the MP analysis except for the position of P. mystaceus. All analyses left the nodes for the oviparous group, the most basal clade within the oviparous group, and P. mystaceus unresolved. The phylogenies further suggest that the monophyly of the viviparous species may have resulted from vicariance, while recent dispersal may have been important in generating the pattern of variation among the oviparous species.     

DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers

DNA barcoding has been successfully implemented in the identification of previously described species, and in the process has revealed several cryptic species. It has been noted that such methods could also greatly assist in the discovery and delineation of undescribed species in poorly studied groups, although to date the feasibility of such an approach has not been examined explicitly. Here, we investigate the possibility of using short mitochondrial and nuclear DNA sequences to delimit putative species in groups lacking an existing taxonomic framework. We focussed on poorly known tropical water beetles (Coleoptera: Dytiscidae, Hydrophilidae) from Madagascar and dung beetles (Scarabaeidae) in the genus Canthon from the Neotropics. Mitochondrial DNA sequence variation proved to be highly structured, with >95% of the observed variation existing between discrete sets of very closely related genotypes. Sequence variation in nuclear 28S rRNA among the same individuals was lower by at least an order of magnitude, but 16 different genotypes were found in water beetles and 12 genotypes in Canthon, differing from each other by a minimum of two base pairs. The distribution of these 28S rRNA genotypes in individuals exactly matched the distribution of mtDNA clusters, suggesting that mtDNA patterns were not misleading because of introgression. Moreover, in a few cases where sequence information was available in GenBank for morphologically defined species of Canthon, these matched some of the DNA-based clusters. These findings demonstrate that clusters of close relatives can be identified readily in the sequence variation obtained in field collected samples, and that these clusters are likely to correspond to either previously described or unknown species. The results suggest that DNA-assisted taxonomy will not require more than a short fragment of mtDNA to provide a largely accurate picture of species boundaries in these groups. Applied on a large scale, this DNA-based approach could greatly improve the rate of species discovery in the large assemblages of insects that remain undescribed.     

Phylogenetic relationships and evolution of the Japanese Carabinae ground beetles based on mitochondrial ND5 gene sequences

The phylogenetic relationships of the Japanese Carabinae ground beetles were analyzed by comparing 1,069 nucleotide sequences in the mitochondrial gene encoding NADH dehydrogenase subunit 5 (ND5). The ND5 phylogenetic tree revealed that the hind-wingless Carabina and the hind-wingedCalosoma/Campalita (Calosomina) diverged from the common ancestor, andCychrus (Cychrini) is the outgroup of them. Five distinct clusters (groups) can be recognized in the Carabina, i.e.,CARABUS, HEMICARABUS, LEPTOCARABUS, APOTOMOPTERUS, andPROCRUSTES/DAMASTER. The ancestors of these lineages diverged almost at the same time more than 10 Myr ago. TheCarabus cluster includes two subclusters,Carabus andOhomopterus. Two species ofCarabus examined are phylogenetically rather remote, while five species amongOhomopterus are closely related to each other. The results suggest that diversification ofCarabus started much earlier than that ofOhomopterus, presumably in the Eurasian continent, and that ofOhomopterus in the Japanese archipelago. The branching order in theLEPTOCARABUS lineage was established,Authenocarabus/Pentacarabus being their outgroup. In theDAMASTER/PROCRUSTES lineage,Procrustes is placed as the outgroup ofDamaster, with the branching order ofCoptolabrus andAcoptolabrus/Damaster. The diversification of theDamaster subspecies appeared to have occurred in the Japanese archipelago earlier thanOhomopterus, and its phylogeny reflects their geographic distribution in the archipelago rather than the morphological characters.The nucleotide sequence data reported in this paper will appear in the GSDB, DDBJ, EMBL, and NCBI nucleotide sequence databases with the accession numbers D50339-D50365     

Molecular phylogeny of Japanese Catocala moths based on nucleotide sequences of the mitochondrial ND5 gene

Phylogenetic relationships of 31 Japanese Catocala species were analyzed based on the partial nucleotide sequences of the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene (762 bp). When several non-Catocala Noctuidae moths were designated as the outgroup, these Catocala species formed a monophyletic group. However, divergences between these Catocala species were very deep, and no close phylogenetic relationships were recognized among them except for that between the two recently separated species, C. xarippe and C. fulminea. The remote relationships implied for several pairs of species suggest that the color of the hindwings is a changeable characteristic, and does not reflect phylogenetic lineage. Continental specimens were analyzed in 20 of 31 Catocala species, and all of them showed a close relationship with their Japanese counterpart. However, the closeness of the nucleotide sequences between the Japanese and continental individuals of the same species varied from species to species, indicating that isolation between the Japanese and continental populations of these species occurred at many different times. The two analyzed species endemic to North America showed a close relationship with their morphologically inferred Japanese counterparts, indicating that the geographic separation and following speciation between these Eurasian and American species occurred much more recently compared with the speciation events among the Catocala species now found in Japan.     

Nuclear DNA restriction site polymorphisms and the phylogeny and population structure of an intertidal snail species complex (Littorina)

Primers for amplification of four novel, unlinked nuclear DNA loci, the first reported for the rough periwinkles of the genus Littorina, are described. Patterns of restriction site polymorphism for these loci are detailed within the rough periwinkles. RFLPs are not found to be diagnostic for any of the currently accepted species within this group, nor for any of the contentious subspecies, or forms, whose taxonomic status is uncertain. However, there are important differences in allele frequencies between these taxa and certain of these mirror differences detected in a previous study of the mitochondrial DNA. These allele frequency data are used to construct a phylogeny in which groupings of the three recognised species are obvious when either Nei's genetic distances or Reynold's distances are clustered. Contentious forms (L. neglecta, L. saxatilis 'b' and L. tenebrosa) do not cluster as distinct taxa, although populations of L. neglecta have important allele frequency differences from L. saxatilis. These four loci have confirmed the consensus view of Littorina phylogeny and provided important information on population structure-however four loci is insufficient for reaching definitive conclusions. Since analysis of nuclear DNA polymorphisms such as these is invaluable for analysis of phylogeny, population structure and phylogeography, identification of additional loci is considered imperative.     

基于线粒体基因cyt b的鹟亚科部分鸟类系统发育

采用分子系统学方法对鹟亚科(Muscicapinae)6属31种鸟类的cytb基因序列992bp进行系统发生分析。以荒漠伯劳(Lanius isabellinus)和发冠卷尾(Dicrurus hottentottus)为外群,采用贝叶斯法(Bayesian,BI)、最大似然法(Maximum-likelihood,ML)和最大简约法(Maximumparsimony,MP)分别构建鹟亚科的系统发育树。结果支持:寿带属(Terpsiphone)、扇尾鹟属(Rhipidura)与方尾鹟属(Culicicapa)可从鹟亚科中移出,其中寿带属归入王鹟科(Monarchidae),扇尾鹟属与方尾属归入扇尾鹟科(Rhipiduridae);鹟属(Muscicapa)、仙鹟属(Niltava)为单系发生,并聚为姐妹群,亲缘关系较近;姬鹟属(Ficedula)并非单系发生,白眉姬鹟(Ficedulazanthopygia)在3种系统发生树中的位置差别较大,研究结果未能确定其分类地位;铜蓝(Muscicapa thalassina)与白腹蓝(Cyanoptila cyanomelana)亲缘关系较近,前者应从属中移出,后者应从姬属移出,共同归入仙属或列为仙属的姐妹属。上述结论解决了亚科部分有争议属、种间的进化关系,为亚科分类系统提供了DNA水平证据。     

Intraspecific phylogeny of the New Zealand short-tailed bat Mystacina tuberculata inferred from multiple mitochondrial gene sequences

An intraspecific phylogeny was established for the New Zealand short-tailed bat Mystacina tuberculata using a 2,878-bp sequence alignment from multiple mitochondrial genes (control region, ND2, 12S ribosomal RNA [rRNA], 16S rRNA, and tRNA). The inferred phylogeny comprises six lineages, with estimated divergences extending back between 0.93 and 0.68 million years to the middle Pleistocene. The lineages do not correspond to the existing subspecific taxonomy. Although multiple lineages occur sympatrically in many populations, the lineages are geographically structured. This structure has persisted despite repeated cycles of range expansion and contraction in response to climatic oscillations and catastrophic volcanic eruptions. The distribution of lineages among populations in central North Island indicates that a hybrid zone was formed by simultaneous colonization from single-lineage source populations inhabiting remote forest refugia. The observed pattern is not typical of microbats, which because of their high mobility generally exhibit low levels of genetic differentiation and geographic structure over continental ranges. Although lineages of M. tuberculata occur sympatrically in many populations, genetic distances between them are sufficiently large to suggest that they may be considered evolutionary significant units or taxonomic subspecies.