Molecular phylogenetic analysis of Violaceae (Malpighiales) based on plastid and nuclear DNA sequences

A phylogenetic analysis of Violaceae is presented using sequences from rbcL, atpB, matK and 18S rDNA from 39 species and 19 genera. The combined analysis of four molecular markers resulted in only one most parsimonious tree, and 33 of all 38 nodes within Violaceae are supported by a bootstrap proportion of more than 50%. Fusispermum is in a basal-most position and Rinorea, Decorsella, Rinoreocarpus and the other Violaceae are successively diverged. The monogeneric subfamily Fusispermoideae is supported, and it shares a number of plesiomorphies with Passifloraceae (a convolute petal aestivation, actinomorphic flowers and connate filaments). The other monogeneric subfamily Leonioideae is sunken within the subfamily Violoideae and is sister to Gloeospermum, sharing some seed morphological characteristics. The present molecular phylogenetic analysis suggests that the convolute, apotact and quincuncial petal aestivation is successively derived within the family. The evolutionary trends of the other morphological characteristics, such as a filament connation, the number of carpels and floral symmetry, are discussed. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Molecular phylogenetic analysis of Euphorbiaceae sensu stricto based on plastid and nuclear DNA sequences and ovule and seed character evolution

A phylogenetic analysis of Euphorbiaceae sensu stricto is presented using sequences from rbcL, atpB, matK and 18S rDNA from 85 species and 83 genera. The combined analysis of four molecular markers resulted in only one most parsimonious tree and also generated new supported clades, which include Euphorbioideae + Acalyphoideae s.s., subclades A2 + A3, subclades A5 + A6 and a clade uniting subclades A2–A8 within Acalyphoideae s.s. A palisadal exotegmen is a possible synapomorphy for all the Euphorbiaceae, except for the subfamily Peroideae. The presence of vascular bundles in the inner integument and a thick inner integument were shown to be synapomorphies for the clade of inaperturate and articulated crotonoids and for the large clade of Euphorbioideae, Acalyphoideae s.s., inaperturate and articulated crotonoids, respectively. Characters of the aril and vascular bundles in the outer integument are discussed. The selected embryological characters were seen to be highly correlated with the molecular phylogeny. When the results of molecular phylogenetic analysis of a previous study and this study were adjusted along with the selected embryological characters, all clades within Euphorbiaceae were supported except for a clade comprising Euphorbioideae + Acalyphoideae s.s. + inaperturate crotonoids + articulated crotonoids + Adenoclineae s.l. and a clade uniting subclades A4–A8 within Acalyphoideae s.s. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Systematic position of Asteropyrum (Ranunculaceae) inferred from chloroplast and nuclear sequences

Sequences of chloroplast gene rbcL and partial nuclear 26S rDNA were used to evaluate phylogenetic relationships of Asteropyrum. Four primary clades were recognized in Ranunculaceae, corresponding to subfamilies Hydrastidoideae, Coptidoideae, Thalictroideae, and Ranunculoideae. Our results place Asteropyrum in Ranunculoideae, sister to the tribe Actaeeae, which includes Beesia, Cimicifuga, and Eranthis. This is supported by chromosome characters, including chromosome size and basic number, and the stainability of prophase chromosomes and interphase nuclei. Our results do not support previous placements of Asteropyrum in either Coptidoideae or Thalictroideae. Considering its uniqueness in a few characters (e.g. simple peltate leaves, accumulating benzylisoquinoline alkaloids, vessel elements with only typical scalariform perforation plates), we recognize Asteropyrum as a monotypic tribe of Ranunculoideae, Asteropyreae W. T. Wang et C. Y. Chang.     

Molecular phylogenetic study of the basidiomycetous anamorphic yeast genusTrichosporon and related taxa based on small subunit ribosomal DNA sequences

Small subunit ribosomal DNA sequences of all species of the basidiomycetous anamorphic yeast genusTrichosporon were determined, and phylogenetic trees were constructed by the neighbor-joining and maximum likelihood methods. The sequence data showed that, with the exception ofT. pullulans, the genus is monophyletic, although its members have two different major ubiquinones, Q9 and Q10. The genus can be divided phylogenetically into three major clusters. Species with Q10 as the major ubiquinone constitute a single cluster, while those with Q9 form two clusters.Trichosporon pullulans was phylogenetically distinct from other taxa of the genus. It is located in a cluster containingCystofilobasidium capitatum, Mrakía frigida, Xanthophyllomyces dendrorhous and three species ofUdeniomyces. This result sugests thatT. pullulans does not belong to the genusTrichosporon.     

Towards the phylogeny of the Curculionoidea (Coleoptera): Reconstructions from mitochondrial and nuclear ribosomal DNA sequences

With about 60,000 described species, Curculionoidea represent the most species-rich superfamily in the animal kingdom. The immense diversity apparently creates difficulties in the reconstruction of the phylogenetic relationships. Independent morphological studies have led to very different classifications. This study is based on molecular data from two independent molecular sources, the 16S and 18S rDNA. Sensitivity analyses were conducted for the sequence alignment (gap costs were varied) as well as the phylogenetic reconstruction algorithms and some of their parameters. The higher-level relationships reconstructed within Curculionoidea are sensitive to alignment and reconstruction method. Nemonychidae or Oxycorynidae+Belidae were found to be sister to all remaining Curculionoidea in many analyses. The 16S rDNA sequence data (obtained from 157 species) corroborate many tribes and genera as monophyletic. It is observed that the phylogenetic reconstruction of genera with specific genetic features such as polyploidy and parthenogenetic reproduction is difficult in weevils. The curculionid subfamily Lixinae appears monophyletic. A new monophylum consisting of Entiminae, Hyperinae, Cyclominae, Myllorhinus plus possibly the Cossoninae is distinguished and we call it Entiminae s.l. For most other subfamilies and families homoplasy concealed the phylogenetic signal (due to saturation of the 16S sequences), or the species sampling was insufficient, although our sampling scheme was rather broad. We observed that although data from one source can easily be misleading (16S) or hardly informative (18S), the combination of the two independent data sets can result in useful information for such a speciose group of organisms. Our study represents the most thorough analysis of molecular sequence data of the Curculionoidea to date and although the phylogenetic results appear less stable than expected, they reflect the information content of these sequence data realistically and thus contribute to the total knowledge about the phylogeny of the Curculionoidea.     

Comparative phylogenetic analyses of Halomonas variabilis and related organisms based on 16S rRNA, gyrB and ectBC gene sequences

Halomonas variabilis and phylogenetically related organisms were isolated from various habitats such as Antarctic terrain and saline ponds, deep-sea sediment, deep-sea waters affected by hydrothermal plumes, and hydrothermal vent fluids. Ten strains were selected for physiological and phylogenetic characterization in detail. All of those strains were found to be piezotolerant and psychrotolerant, as well as euryhaline halophilic or halotolerant. Their stress tolerance may facilitate their wide occurrence, even in so-called extreme environments. The 16S rDNA-based phylogenetic relationship was complemented by analyses of the DNA gyrase subunit B gene (gyrB) and genes involved in the synthesis of the major compatible solute, ectoine: diaminobutyric acid aminotransferase gene (ectB) and ectoine synthase gene (ectC). The phylogenetic relationships of H. variabilis and related organisms were very similar in terms of 16S rDNA, gyrB, and ectB. The ectC-based tree was inconsistent with the other phylogenetic trees. For that reason, ectC was inferred to derive from horizontal transfer.     

Systematics and morphological evolution within the moss family Bryaceae: a comparison between parsimony and Bayesian methods for reconstruction of ancestral character states

The Bryaceae are a large cosmopolitan moss family including genera of significant morphological and taxonomic complexity. Phylogenetic relationships within the Bryaceae were reconstructed based on DNA sequence data from all three genomic compartments. In addition, maximum parsimony and Bayesian inference were employed to reconstruct ancestral character states of 38 morphological plus four habitat characters and eight insertion/deletion events. The recovered phylogenetic patterns are generally in accord with previous phylogenies based on chloroplast DNA sequence data and three major clades are identified. The first clade comprises Bryum bornholmense, B. rubens, B. caespiticium, and Plagiobryum. This corroborates the hypothesis suggested by previous studies that several Bryum species are more closely related to Plagiobryum than to the core Bryum species. The second clade includes Acidodontium, Anomobryum, and Haplodontium, while the third clade contains the core Bryum species plus Imbribryum. Within the latter clade, B. subapiculatum and B. tenuisetum form the sister clade to Imbribryum. Reconstructions of ancestral character states under maximum parsimony and Bayesian inference suggest fourteen morphological synapomorphies for the ingroup and synapomorphies are detected for most clades within the ingroup. Maximum parsimony and Bayesian reconstructions of ancestral character states are mostly congruent although Bayesian inference shows that the posterior probability of ancestral character states may decrease dramatically when node support is taken into account. Bayesian inference also indicates that reconstructions may be ambiguous at internal nodes for highly polymorphic characters.     

Phylogenetic analyses of Malpighiales using plastid and nuclear DNA sequences, with particular reference to the embryology of Euphorbiaceae sens. str.

We present phylogenetic analyses of Malpighiales, which are poorly understood with respect to relationships within the order, using sequences from rbcL, atpB, matK and 18SrDNA from 103 genera in 23 families. From several independent and variously combined analyses, a four-gene analysis using all sequence data provided the best resolution, resulting in the single most parsimonious tree. In the Malpighiales [bootstrap support (BS) 100%], more than eight major clades comprising a family or group of families successively diverged, but no clade containing more than six families received over 50% BS. Instead, ten terminal clades that supported close relationships between and among families (>50% BS) were obtained, between, for example, Balanopaceae and Chrysobalanaceae; Lacistemataceae and Salicaceae; and Phyllanthaceae and Picrodendraceae. The monophyly of Euphorbiaceae sens. str. were strongly supported (BS 100%), but its sister group was unclear. Euphorbiaceae sens. str. comprised two basally diverging clades (BS 100%): one leading to the Clutia group (Chaetocarpus, Clutia, Pera and Trigonopleura), and the other leading to the rest of the family. The latter shared a palisadal, instead of a tracheoidal exotegmen as a morphological synapomorphy. While both Acalyphoideae (excluding Dicoelia and the Clutia group) and Euphorbioideae are monophyletic, Crotonoideae were paraphyletic, requiring more comprehensive analyses.     

The phylogenetic utility of chloroplast and nuclear DNA markers and the phylogeny of the Rubiaceae tribe Spermacoceae

The phylogenetic utility of chloroplast (atpB-rbcL, petD, rps16, trnL-F) and nuclear (ETS, ITS) DNA regions was investigated for the tribe Spermacoceae of the coffee family (Rubiaceae). ITS was, despite often raised cautions of its utility at higher taxonomic levels, shown to provide the highest number of parsimony informative characters, in partitioned Bayesian analyses it yielded the fewest trees in the 95% credible set, it resolved the highest proportion of well resolved clades, and was the most accurate region as measured by the partition metric and the proportion of correctly resolved clades (well supported clades retrieved from a combined analysis regarded as “true”). For Hedyotis, the nuclear 5S-NTS was shown to be potentially as useful as ITS, despite its shorter sequence length. The chloroplast region being the most phylogenetically informative was the petD group II intron.We also present a phylogeny of Spermacoceae based on a Bayesian analysis of the four chloroplast regions, ITS, and ETS combined. Spermacoceae are shown to be monophyletic. Clades supported by high posterior probabilities are discussed, especially in respect to the current generic classification. Notably, Oldenlandia is polyphyletic, the two subgenera of Kohautia are not sister taxa, and Hedyotis should be treated in a narrow sense to include only Asian species.     

基于核基因和线粒体基因序列的中国Singhardina亚属系统发育（半翅目：叶蝉科：小叶蝉亚科：小叶蝉族）

测定了中国Singhardina亚属15个代表种的核糖体28S基因D2区和线粒体16S基因、COI基因部分序列,分别采用最大简约法、最大似然法和贝叶斯法构建分子系统树。系统发育树显示了相似的拓扑结构,明晰了各分支间的关系。首次探讨了中国Singhardina亚属4个种团间的系统发育关系。结果显示,Singhardina亚属构成了1个独立支系,代表1个单系群。本研究首次提出种团Eurhadina(Singhardina)rubra,并推测该种团可能是Singhardina亚属中最原始的种团。种团Eurhadina(Singhardina)robusta和E.(Singhardina)mamata为姐妹群。种团E.(Singhardina)vittata不能从种团E.(Singhardina)punjabensis中分出得到了分子数据的支持。     

Relationship among coelacanths,lungfishes, and tetrapods: A phylogenetic analysis based on mitochondrial cytochrome oxidase I gene sequences

To clarify the relationship among coelacanths, lungfishes, and tetrapods, the amino acid sequences deduced from the nucleotide sequences of mitochondrial cytochrome oxidase subunit I (COI) genes were compared. The phylogenetic tree of these animals, including the coelacanth Latimeria chalumnae and the lungfish Lepidosiren paradoxa, was inferred by several methods. These analyses consistently indicate a coelacanth/lungfish clade, to which little attention has been paid by previous authors with the exception of some morphologists. Overall evidence of other mitochondrial genes reported previously and the results of this study equally support the coelacanth/lungfish and lungfish/tetrapod clades, ruling out the coelacanth/tetrapod clade.Correspondence to: K. Watanabe 0592     

Phylogenetic differentiation between Atlantic <Emphasis Type="Italic">Scomber colias</Emphasis> and Pacific <Emphasis Type="Italic">Scomber japonicus</Emphasis> based on nuclear DNA sequences

In the classical taxonomy, three Scomber species are distinguished: S. scombrus, S. australasicus, and S. japonicus. Yet, some fish taxonomists have recently recognized Scomber colias, inhabiting the Atlantic Ocean, as a separate species from S. japonicus, distributed in the Pacific Ocean. Such proposal was based on significant mitochondrial DNA divergence as well as great phenotypic variation among individuals from these two ocean basins. However, in the absence of nuclear DNA data this issue remains still controversial. In this study, a phylogenetic analysis of nuclear 5S rDNA sequences was performed. A total of 30 individuals of S. colias collected in the Atlantic and 34 specimens of S. japonicus from the Pacific were characterized. Moreover, nine individuals of Pacific S. australasicus and eight of Atlantic S. scombrus were included. Maximum likelihood, maximum parsimony, and neighbor-joining analyses revealed the presence of two well-supported distinct clades corresponding to S. colias and S. japonicus, respectively. Altogether, morphologic and genetic data are in agreement with the recognition of two different species, S. colias in the Atlantic, and S. japonicus in the Pacific.     

Monophyly and phylogenetic relationships of the catfish genus Glyptothorax (Teleostei: Sisoridae) inferred from nuclear and mitochondrial gene sequences

GlyptothoraxBlyth (1860) is the most species-diverse and widely-distributed genus in the Sisoridae, but few studies have examined monophyly of the genus and phylogenetic relations within it. We used the nuclear RAG2 gene and mitochondrial COI and Cyt b genes from 50 of the approximately 70 species to examine monophyly of Glyptothorax and phylogenetic relationships within the genus. Molecular phylogenetic trees were constructed using maximum parsimony, maximum likelihood and Bayesian inference methods. All methods strongly supported monophyly of Glyptothorax, with Bagarius as its sister group. Both analyses of two- and three-gene datasets recovered nine major subclades of Glyptothorax, but some internal nodes remained poorly resolved. The phylogenetic relationships within the genus and existing taxonomic problems are discussed.     

Orientobilharzia turkestanicum is a member of Schistosoma genus based on phylogenetic analysis using ribosomal DNA sequences

In the present study, samples representing Orientobilharzia turkestanicum from cattle, sheep, cashmere goat and goat in Heilongjiang Province, China, were characterized and grouped genetically by sequences of internal transcribed spacer (ITS, including ITS-1 and ITS2) and 28S ribosomal DNA (28S rDNA). The ITS and 28S rDNA were amplified by polymerase chain reaction (PCR) and then sequenced and compared with that of other members of the Schistosomatidae available in GenBank™, and phylogenetic relationships between them were re-constructed using the neighbor-joining and maximum parsimony methods. The lengths of ITS-1, ITS-2 and 28S rDNA sequences for all O. turkestanicum samples from different hosts were 384 bp, 331 bp and 1304 bp, respectively. While the ITS-1 sequences of O. turkestanicum from each of the four different hosts, and ITS-2 of O. turkestanicum from cattle, sheep and cashmere goat were identical, respectively, the ITS-2 of O. turkestanicum from goat differed from that of O. turkestanicum from cattle, sheep and cashmere goat by one nucleotide. The 28S rDNA sequences of O. turkestanicum from sheep and cashmere goat were identical, but differed from that of O. turkestanicum from cattle and goat by two nucleotides, with the latter two also having identical 28S rDNA sequence. Phylogenetic analyses based on the combined sequences of the ITS-1 and ITS-2, or the 28S rDNA sequences placed O. turkestanicum within the genus Schistosoma, and it was phylogenetically closer to the African schistosome group than to the Asian schistosome group. These results should have implications for studying the origin and evolution of O. turkestanicum and other members of the Schistosomatidae.     

The phylogenetic positions of the conifer genera Amentotaxus,Phyllocladus, and Nageia inferred from 18s rRNA sequences

To determine the evolutionary positions of the conifer genera Amentotaxus, Phyllocladus, and Nageia, we obtained 18S rRNA sequences from 11 new taxa representing the major living orders and families of gymnosperms. With the published Chlamydomonas as an outgroup, phylogenetic analyses of our new data and available sequences indicate that (1) the Gnetales form a monophyletic group, which is an outgroup to the conifers, (2) the conifers are monophyletic, (3) Taxaceae, Cephalotaxaceae, Cupressaceae, and Taxodiaceae form a monophyletic group, (4) Amentotaxus is closer to Torreya than to Cephalotaxus, suggesting that Amentotaxus is better to be classified as a member of Taxaceae, (5) Phyllocladus, Dacrycarpus, Podocarpus, and Nageia form a monophyletic group, and (6) Pinaceae is an outgroup to the other families of conifers. Our finding that Phyllocladus is a sister group of the Podocarpaceae disagrees with the suggestion that the phylloclade of the genus is an ancient structure and that the genus is a terminal taxon within the Podocarpaceae. The genus Nageia is more closely related to Podocarpus than to Dacrycarpus and was derived from within the Podocarpaceae. In conclusion, our data indicate that in conifers, the uniovulate cone occurred independently in Taxacaeae and Cephalotaxaceae, and in Podocarpaceae after the three families separated from Pinaceae, and support the hypothesis that the uniovulate cone is derived from reduction of a multiovulate cone.Correspondence to: S.-M. Chaw     

Attributes and congruence of three molecular data sets: inferring phylogenies among Septoria-related species from woody perennial plants

To improve our understanding of phylogenetic relationships within the anamorphic genus Septoria, three molecular data sets representing 2,417 bp of nuclear and mitochondrial genes were evaluated. Separate gene analyses and combined analyses were performed using first, the maximum parsimony criterion and second, a Bayesian framework. The homogeneity of data partitions was evaluated via a combination of homogeneity partition tests and tree topology incongruence tests before conducting combined analyses. A last incongruence re-evaluation using partitioned Bremer support was performed on the combined tree, which corroborated the previous estimates. After each separate data set attributes were examined, simple explanations were advocated as the causes of the significant incongruences detected. The analysis of multiple gene partitions showed unprecedented phylogenetic resolution within the genus Septoria that supported the results from previously published single gene phylogenies. Specifically, we have delimited distinct but closely related species representing monophyletic groups that frequently correlated with their respective host families. Conversely, the occurrence of well-supported groups including closely related but distinct molecular taxa sampled on unrelated host-plants allowed us to reject, in these particular cases, the co-evolutionary concept expected between a parasite and its host and to discuss alternative evolutionary models recently proposed for these pathogens.     

Putative basidiomycete teleomorphs and phylogenetic placement of the coelomycete genera: Chaetospermum, Giulia and Mycotribulus based on nu-rDNA sequences

Few basidiomycetes are known to have a coelomycete anamorph. The partial SSU and LSU of nu-rDNA of three coelomycete genera (Chaetospermum, Giulia, Mycotribulus) were sequenced to determine their phylogenetic relationship. M. mirabilis was well placed in the Physalacriaceae, Agaricales, whereas G. tenuis clusters with the Corticiaceae, Corticiales. C. camelliae and C. artocarpi form a close relationship with the Sebacinaceae, Sebacinales. Although morphologically these coelomycetes are pycnidial and with appendaged conidia, they show no consistency in their phylogenetic relationship, belonging to disparate major taxonomic groups with putative teleomorphs in the Agaricales, Corticiales and Sebacinales. Further molecular studies of coelomycetes may be rewarding to evaluate their phylogenetic affinities.     

Relationships of Afroablepharus Greer, 1974 skinks from the Gulf of Guinea islands based on mitochondrial and nuclear DNA: patterns of colonization and comments on taxonomy

Partial sequences of three mitochondrial DNA genes, 12S rDNA, 16S rDNA and cytochrome b, and one nuclear gene, c-mos, were used to assess the phylogenetic relationships of species belonging to the genus Afroablepharus from the volcanic islands of the Gulf of Guinea (West Africa) and neighboring continental Africa. Additionally, partial sequences of cytochrome b were used to compare levels of sequence divergence within populations. The three forms from S?o Tomé, Príncipe and Annobon (one per island) are genetically distinct, with high levels of divergence, supporting the recognition of a distinct species in each island. Populations within each island contain very low levels of genetic diversity. These three forms form a monophyletic group suggesting a single initial colonization followed by radiation to the other islands, possibly from S?o Tomé to Príncipe and Annobon. This is contrary to what was found in other reptiles from these islands such as Mabuya (sensu lato) and Hemidactylus, which colonized the islands multiple times. Assuming a molecular clock for cytochrome b of about 2% divergence per million years (usually applied to Sauria), the lineage on Annobon island exceeds the age of the island, thus casting further doubt on this widely used divergence estimate. Partial sequences of c-mos showed no variation within islands. Five to seven sites were variable among islands, which is a high value further supporting the treatment of each island form as a distinct species.