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.     

A phylogeny inferred from large ribosomal subunit (26S) rDNA sequences suggests that Cuscuta is a derived member of Convolvulaceae

Cuscuta is a parasitic angiosperm that has been considered alternatively either as a genus within Convolvulaceae or as a monogeneric family in its own right. Although typically placed in the Solanales,Cuscuta has also been positioned within the Polemoniales. Extreme reduction of morphological and anatomical characters, as well as chloroplast genome reductions and rearrangements, has made the phylogenetic placement ofCuscuta uncertain. Analysis of 26S rDNA sequences suggests thatCuscuta is a derived member of Convolvulaceae. Molecular results are discussed in relation to the morphological and anatomical characters of autotrophic members of Convolvulaceae.     

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.     

Phylogeny and biosystematics ofPseudomonotes (Dipterocarpaceae) based on molecular and morphological data

The placement of a recently discovered South American monotypic genus,Pseudomonotes tropenbosii, in subfam.Monotoideae (Dipterocarpaceae) extends the geographical range of the subfamily from Africa to the Neotropics. Although morphological and anatomical evidence suggest similarities betweenPseudomonotes andMonotes, the close alliance of these two genera was questionable due to their disjunct distribution and a lack of phylogenetic analysis. In the present study, we reconstructed the phylogeny ofPseudomonotes and other putatively related taxa usingrbcL sequence data. The analysis ofrbcL sequences of 20 taxa belonging to 15 genera and eight families recovered a single most parsimonious tree. The genusSarcolaena (Sarcolaenaceae) formed a clade sister to the monophyleticDipterocarpaceae clade.Monotes andPseudomonotes formed a strongly supported group, sister to the monophyletic clade withPakaraimaea and the remaining Asiatic dipterocarp species studied. The study strongly supports the placement ofPseudomonotes within subfam.Monotoideae of theDipterocarpaceae.     

Molecular phylogeny of Pottiaceae (Musci) based on chloroplast rps4 sequence data

Comparative sequencing of the chloroplast rps4 gene was used to reconstruct the phylogenetic relationships within the family Pottiaceae (Musci). The results confirm that Ephemerum spinulosum, Splachnobryum obtusum, Goniomitrium acuminatum and Cinclidotus fontinaloides are clearly positioned within the Pottiaceae and that Hypodontium dregei is not a member. At subfamily level, the data support the subfamily Pottioideae as being a monophyletic clade. The Trichostomoideae are probably paraphyletic. Neither the subfamily Chionolomideae, represented in this study by Pseudosymblepharis schimperiana, nor the subfamily Erythrophyllopsoideae, represented by both known species, Erythrophyllastrum andinum and Erythrophyllopsis fuscula, are supported by the sequence data. The Timmielloideae should be excluded from the Pottiaceae. The Merceyoideae, represented in this study by Scopelophila cataractae, might form a sister clade to all other Pottiaceae, but their position is not fully resolved. At the genus level, Barbula is clearly polyphyletic since Barbula bolleana and Barbula indica appear in a clade clearly separated from Barbula unguiculata. Pottiopsis caespitosa and Leptobarbula berica are placed within the Trichostomoideae. Likewise, the genera Gymnostomum and Anoectangium are excluded from the Pottioideae and placed within the Trichostomoideae. Leptophascum leptophyllum is closely related with Syntrichia; Aloina is not closely related to Tortula or Crossidium. Evidence of a clade within the Pottioideae, formed of Leptodontium and Triquetrella, is provided.     

Incongruence among mitochondrial,chloroplast and nuclear gene trees in <Emphasis Type="Italic">Pinus</Emphasis> subgenus <Emphasis Type="Italic">Strobus</Emphasis> (Pinaceae)

Introgression has been considered to be one of main factors leading to phylogenetic incongruence among different datasets at lower taxonomic levels. In the plants of Pinaceae, the mtDNA, cpDNA, and nuclear DNA (nrDNA) may have different evolutionary histories through introgression because they are inherited maternally, paternally and biparentally, respectively. We compared mtDNA, cpDNA, and two low-copy nrDNA phylogenetic trees in the genus Pinus subgenus Strobus, in order to detect unknown past introgression events in this group. nrDNA trees were mostly congruent with the cpDNA tree, and supported the recent sectional and subsectional classification system. In contrast, mtDNA trees split the members of sect. Quinquefoliae into two groups that were not observed in the other gene trees. The factors constituting incongruence may be divided into the following two categories: the different splits within subsect. Strobus, and the non-monophyly of subsect. Gerardianae. The former was hypothesized to have been caused by the past introgression of cpDNA, mtDNA or both between Eurasian and North American species through Beringia. The latter was likely caused by the chimeric structure of the mtDNA sequence of P. bungeana, which might have originated through past hybridization, or through a horizontal transfer event and subsequent recombination. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Isolation and characterization of arsenite-oxidizing bacteria from arsenic-contaminated soils in Thailand

Two hundred and eighty-eight arsenic-resistant bacteria were isolated by an enrichment culture method from a total of 69 arsenic-contaminated soil-samples collected from Dantchaeng district in Suphanburi province (47 samples), and from Ron Phiboon district in Nakhon Sri Thammarat province (22 samples), in Central and Southern Thailand, respectively. Twenty-four of the 288 isolated arsenic-resistant bacteria were found to be arsenite-oxidizing bacteria. On the basis of their morphological, cultural, physiological, biochemical and chemotaxonomic characteristics, and supported by phylogenetic analysis based upon their 16S rRNA gene sequences, they were divided into five groups, within the genera Acinetobacter, Flavobacterium, Pseudomonas, Sinorhizobium and Sphingomonas, respectively. Within genera, phylogenetic analysis using the 16S rRNA gene sequences suggested that they were comprised of at least ten species, five isolates being closely related to known bacteria (Acinetobacter calcoaceticus NCCB 22016^T, Pseudomonas plecoglossicida FPC951^T, Ps. knackmussii B13^T, Sinorhizobium morelense Lc04^T, and Sphingomonas subterranea IFO16086^T). The other five proposed species are likely to be new species closely related to Flavobacterium johnsoniae, Sinorhizobium morelense, Acinetobacter calcoaceticus and Pseudomonas plecoglossicida, but this awaits further characterization for confirmation of the taxonomic status. No overlap in isolated species or strains was observed between the two sites. The strain distribution and characterization are described.     

Is the evolutionary history of the O-type P element in the saltans and willistoni groups of Drosophila similar to that of the canonical P element?

We studied the occurrence of O-type P elements in at least one species of each subgroup of the saltans group, in order to better understand the phylogenetic relationships among the elements within the saltans group and with those of species belonging to the willistoni group. We found that the O-type subfamily has a patchy distribution within the saltans group (it does not occur in D. neocordata and D. emarginata), low sequence divergence among species of the saltans group as well as in relation to species of the willistoni group, a lower rate of synonymous substitution for coding sequences compared to Adh, and phylogenetic incongruities. These findings suggest that the evolutionary history of the O-type subfamily within the saltans and willistoni groups follows the same model proposed for the canonical subfamily of P elements, i.e., events of horizontal transfer between species of the saltans and willistoni groups.     

哀牢山兜兰,中国兰科一新天然杂种

报道了中国云南省兰科（Orchidaceae）兜兰属（Paphiopedilum）一新天然杂交种：哀牢山兜兰（Paphiopedilum×ailaoshanense B. Liu & S. P. Chen）。哀牢山兜兰与白旗兜兰（P. spicerianum）和沧源兜兰（P. gratrixianum var. cangyuanense）近缘,与前者的区别在于哀牢山兜兰花梗和子房有毛,中萼片带紫色晕以及紫色斑点,花瓣上侧暗绿色带紫色晕,下侧黄绿色;与后者的区别在于中萼片具1条宽阔的紫褐色中带,退化雌蕊紫色。哀牢山兜兰与天然杂种泸水兜兰（Paphiopedilum×lushuiense）相似,而哀牢山兜兰的中萼片下部边缘不后卷,近基部具紫红色晕,合萼片具2条明显紫色粗脉,花瓣匙形,上边缘波状,长6.0~6.2 cm,唇瓣长5.0~5.5 cm。为厘清哀牢山兜兰,沧源兜兰及白旗兜兰之间的关系,基于3个叶绿体基因片段（matK、rbcL、trnL）,构建了兜兰属部分植物系统发育树。鉴于形态和分子数据,认为哀牢山兜兰是天然杂交种。凭证标本存放于福建农林大学标本馆。     

Molecular Systematics of the Subfamily Caprinae (Artiodactyla, Bovidae) as Determined from Cytochrome b Sequences

We have sequenced the complete mitochondrial DNA cytochrome b gene from 18 species of the subfamily Caprinae and two outgroup taxa. Additional sequences retrieved from the literature were used to constitute a data set of 32 cytochrome b sequences comprising all genera usually included within the Caprinae. Phylogenetic relationships were assessed by PAUP using three new weighting schemes based on homoplasy analyses. Each type of substitution considered at each of the three codon positions was weighted according to its homoplasy level, as measured by the consistency index (CI), the slope of saturation (S), or their product (CIS). These differentially weighted parsimony analyses indicate that (1) the subfamily Caprinae is monophyletic, but only with the exclusion of Saiga from the group; (2) there is no support for monophyly of the four tribes currently recognized (Caprini, Rupicaprini, Ovibovini, and Saigini), suggesting relationships different from those traditionally accepted; (3) the caprine group consists of three major clades corresponding to (a) Budorcas and Ovis, (b) Capricornis, Ovibos, and Naemorhedus, and (c) Capra, Hemitragus, and Pseudois; and (4) the basal branching pattern is very weakly supported by bootstrap or branch support values except for the sister-group relationship of Pantholops with all other caprines, and the phylogenetic positions of Ammotragus, Oreamnos, and Rupicapra remain unclear.     

Phylogenetic Relationships Among Mycoplasmas Based on the Whole Genomic Information

With the rapid increase in available bacterial whole-genome information, comparison of bacteria at the whole-genome level has proven to be highly useful in microbial phylogenetic research. Here we constructed a phylogenetic tree based on 15 whole genomes of Mycoplasma and the related bacteria. First, 143 orthologous gene families that are shared by all of the 15 bacteria were selected and 143 multiple alignments were generated. Next, a concatenated multiple alignment inferred from the 143 multiple alignments was generated. A total of 43,370 amino acid sites were considered in the neighbor-joining analysis. The phylogenetic tree based on the whole-genomic information indicated that the 15 bacteria were divided into four major groups with 100% bootstrap support, i.e., the M. hyopneumoniae (Mhy) group, the M. mycoides (Mmy) group, the M. pneumoniae (Mpn) group, and the Bacillus-Phytoplasma (BP) group. In the phylogenetic tree, the Mhy group was more closely related to the Mpn group than the Mmy group. The relationships among the Mhy, Mmy, Mpn, and BP groups were supported with 100% in bootstrap analysis. The phylogenetic tree based on the whole-genome comparison is different from the 16S rRNA tree. Thirty-nine of the 143 phylogenetic trees had the same type of the topology based on the whole-genome comparison. However, we could not identify a gene family contributing or solely belonging to the topology of the 39 proteins. In this study, we showed that some proteins, such as RpoA, RpoB, RpoC, and RpoD, are not suitable for evolutionary studies on relationships among major groups of mycoplasmas. We also showed that glycolysis-related genes of Ureaplasma have a higher substitution rate than the other bacteria. The phylogenetic approaches at the whole-genome level are very important and will be essential for microbial evolutionary studies. Electronic supplementary material The online version of this article (doi: ) contains supplementary material, which is available to authorized users. Reviewing Editor: Dr. John Oakeshott     

Reconciling classical and molecular phylogenies in the stichotrichines (Ciliophora, Spirotrichea), including new sequences from some rare species

We performed a comparative morphological and molecular study on oxytrichid and urostylid stichotrichs (=part of the former hypotrichs). Included are new small subunit (18S) ribosomal RNA (rRNA) gene sequences from five rare oxytrichids (Gonostomum namibiense, Cyrtohymena citrina, Hemiurosoma terricola, Onychodromopsis flexilis, Orthoamphisiella breviseries) and published sequences, based on cultures provided by the senior author, of two key stichotrichid genera, viz., Gastrostyla and Engelmanniella. These and other sequences, altogether 27 species representing 23 genera, were used to analyze how 18S rRNA-based phylogenetic trees can be reconciled with the morphological and ontogenetical data. In 18S rRNA trees, the oligotrichine family Halteriidae invariably clusters within the oxytrichid clade, usually near Oxytricha granulifera, type species of the genus. This position is hardly supported by morphological and ecological evidence and, especially, it contradicts the current ontogenetic findings; possibly, it is an artifact caused by taxa undersampling and/or special molecular evolutionary events. In contrast, most morphological and DNA sequence data of the stichotrichs can be harmonized with the CEUU (Convergent Evolution of Urostylids and Uroleptids) hypothesis which suggests that the urostylid midventral pattern evolved from an oxytrichine ancestor, developing a second time within the Oxytrichidae. The systematic position of one of the two key genera could be clarified with the 18S rRNA sequences: Gastrostyla is a stylonychine oxytrichid. Based on the molecular data and a reassessment of ontogenesis, a new genus, Styxophrya nov. gen., is established for Onychodromus quadricornutus Foissner, Schlegel & Prescott, 1987.     

Phylogeny of Caragana (Fabaceae) based on DNA sequence data from rbcL, trnS–trnG, and ITS

Phylogenetic relationships of 48 species of Caragana (Fabaceae: tribe Hedysareae) and one representative each of Astragalus, Calophaca, Halimodendron, and Hedysarum are estimated from DNA sequences of the rbcL gene, trnS–trnG intron and spacer, and ITS region. At least one representative of all five sections and 12 series within Caragana are included. Analyses yielded strongly supported clades corresponding to sections Caragana, Bracteolatae, and Frutescentes. The species of section Jubatae are distributed among three strongly supported clades, i.e., one with the species of section Bracteolatae, another with two species of section Spinosae, and a third as sister to section Frutescentes. All but the last of these six clades are corroborated by at least one unambiguously traced morphological character. The placement of the other four species of section Spinosae are not well supported and lack unambiguous morphological synapomorphies, and the samples of Calophaca and Halimodendron nest within Caragana with weak support.     

Phylogenetic relationships in Magnoliaceae subfam. Magnolioideae: a morphological cladistic analysis

Relationships within Magnolioideae have been the subject of persistent debate; the main point at issue mostly being the disposition of tribes, genera and sections. A morphological cladistic analysis of the subfamily using Liriodendron as the out-group showed that Magnolioideae consisted of a large basal polytomy, but with five resolved and variously supported clades. Manglietia constituted a clade with sect. Rytidospermum of Magnolia subg. Magnolia. Kmeria and Woonyoungia formed a pair. Pachylarnax, Parakmeria and Manglietiastrum were grouped together, and sect. Splendentes and Dugandiodendron also formed a pair. The largest and best supported clade consisted of Magnolia subg. Magnolia sects. Oyama and Maingola, Magnolia subg. Yulania, Michelia, Aromadendron, Alcimandra, Elmerrillia, Paramichelia and Tsoongiodendron, with sect. Oyama of Magnolia subg. Magnolia is sister to the remainder. Although Magnolia sect. Maingola, Aromadendron, Alcimandra and Elmerrillia constituted a poorly resolved subclade, Aromadendron formed a monophyletic clade with Alcimandra. Within the Michelia/Magnolia subgen. Yulania subclade, Paramichelia was sister to Tsoongiodendron. These results are supported by similar placement of taxa within various molecular analyses of the family, but the low level of resolution indicates that more morphological data are needed to improve phylogenetic signal. Our results support the molecular analyses in suggesting that Magnolia is best considered to be a large and diverse genus, but that the relationships between the taxa within it require more detailed clarification, with more extensive sampling and a combined molecular and morphological approach being needed.     

Phylogeny of the East Asian botiine loaches (Cypriniformes,Botiidae) inferred from mitochondrial cytochrome <Emphasis Type="Italic">b</Emphasis> gene sequences

The Botiinae have traditionally represented a subfamily of the Cobitidae. At present, the classification and phylogenetic relationships of the Botiinae are controversial. To address systematic and phylogenetic questions concerning this group, we sequenced the complete cytochrome b gene from 34 samples, of which 24 represented 13 species of the East Asian botiine fishes, while the other 10 were non-botiine loach species. For the 1140 bp sequences determined, 494 sites were variable ones, of which 424 were parsimony informative. With Myxocyprinus asiaticus as an outgroup, molecular phylogenetic trees were constructed using the neighbor-joining, maximum parsimony, maximum likelihood and Bayesian methods. All molecular phylogenetic trees revealed that botiine fishes form a monophyletic group and are distantly related to other loaches, suggesting that the Botiinae should be placed in their own family. Within the Botiinae, there are three genera; Botia, Parabotia, andLeptobotia, each genus forming a monophyletic group, with the genus Botia as the most ancestral split. Our molecular results are in agreement with morphological analyses of botiines, suggesting that Botia is the ancestral genus, while Leptobotia and Parabotia were resolved as more derived sister groups.     

Phylogenetic utility and comparative morphology of the composite scale brushes in male phycitine moths (Lepidoptera, Pyralidae)

Male pyralid moths in the subfamily of Phycitinae are known to possess composite scale brush structures associated with the 8th abdominal sternite, but the histology and the structural morphology of these organs have not been adequately explored. As such, the phylogenetic utility of these structures is unknown. We examine the pre-genitalic abdominal histology of male Dioryctria reniculelloides (Pyralidae: Phycitinae) associated with the composite scale brushes, as well as structural morphology within the genus Dioryctria and two closely related genera. The composite scale brushes are composed of fused scales. The musculature associated with the base of sternum 8 shows considerable modification compared to previously described Lepidoptera. Complex glandular tissue was also found associated with the scale brush structures, suggesting secretory function. Phylogenetic utility of ultrastructure and gross morphology was examined for major Dioryctria species groups. Many characters were homoplasious, but several supported the monophyly of the genus, as well as some internal relationships. In conclusion, the combination of ultrastructural, gross morphological and histological characters can be a rich source of information for elucidating a range of evolutionary relationships within the subfamily.