Phylogenetic position of the genus Dobinea: Evidence from nucleotide sequences of the chloroplast gene rbcL and the nuclear ribosomal ITS region

Dobinea Buch.-Ham. ex D. Don, a genus with two species endemic to east Asia, has been placed in three different families, the Podoaceae, tribe Acerineae of the Sapindaceae, and tribe Dobineeae of the Anacardiaceae. In this paper, phylogenetic relationships of the genus were examined based on DNA sequences of the chloroplast rbcL gene and the ITS region of nuclear ribosomal DNA. Our data support the monophyly of Dobinea and its placement in the Anacardiaceae.     

Phylogenetic relationships of Cornaceae and close relatives inferred from matK and rbcL sequences

Phylogenetic relationships were inferred using nucleotide sequences of the chloroplast gene matK for members of Cornales, a well-supported monophyletic group comprising Cornaceae and close relatives. The shortest trees resulting from this analysis were highly concordant with those based on previous phylogenetic analysis of rbcL sequences. Analysis of a combined matK and rbcL sequence data set (a total of 2652 bp [base pairs]) provided greater resolution of relationships and higher internal support for clades compared to the individual data sets. Four major clades (most inclusive monophyletic groups) of Cornales are indicated by both sets of genes: (1) Cornus-Alangium, (2) nyssoids (Nyssa-Davidia-Camptotheca)- mastixioids (Mastixia, Diplopanax), (3) Curtisia, and (4) Hydrangeaceae-Loasaceae. The combined evidence indicates that clades 2 and 3 are sisters, with clade 4 sister to the remainder of Cornales. These relationships are also supported by other lines of evidence, including synapomorphies in fruit and pollen morphology and gynoecial vasculature. Comparisons of matK and rbcL sequences based on one of the most parsimonious rbcL-matK trees indicate that matK has a much higher A-T content (66.9% in matK vs. 55.8% in rbcL) and a lower transition:transversion ratio (1.23 in matK vs. 2.21 in rbcL). The total number of nucleotide substitutions per site for matK is 2.1 times that of rbcL in Cornales. These findings are similar to recent comparisons of matK and rbcL in other dicots. Variable sites of matK are almost evenly distributed among the three codon positions (1.0:1.0:1.3), whereas variable sites of rbcL are mostly at the third position (1.8:1.0 :7.5). Among- lineages rates of nucleotide substitutions in rbcL are basically homogeneous throughout Cornales, but are more heterogeneous in matK.     

Circumscription of the Malvales and relationships to other Rosidae: evidence from rbcL sequence data

The order Malvales remains poorly circumscribed, despite its seemingly indisputable core constituents: Bombacaceae, Malvaceae, Sterculiaceae, and Tiliaceae. We conducted a two-step parsimony analysis on 125 rbcL sequences to clarify the composition of Malvales, to determine the relationships of some controversial families, and to identify the placement of the Malvales within Rosidae. We sampled taxa that have been previously suggested to be within, or close to, Malvales (83 sequences), plus additional rosids (26 sequences) and nonrosid eudicots (16 sequences) to provide a broader framework for the analysis. The resulting trees strongly support the monophyly of the core malvalean families, listed above. In addition, these data serve to identify a broader group of taxa that are closely associated with the core families. This expanded malvalean clade is composed of four major subclades: (1) the core families (Bombacaceae, Malvaceae, Sterculiaceae, Tiliaceae); (2) Bixaceae, Cochlospermaceae, and Sphaerosepalaceae (Rhopalocarpaceae); (3) Thymelaeaceae sensu lato (s.l.); and (4) Cistaceae, Dipterocarpaceae s.l., Sarcolaenaceae (Chlaenaceae), and Muntingia. In addition, Neurada (Neuradaceae or Rosaceae) falls in the expanded malvalean clade but not clearly within any of the four major subclades. This expanded malvalean clade is sister to either the expanded capparalean clade of Rodman et al. or the sapindalean clade of Gadek et al. Members of Elaeocarpaceae, hypothesized by most authors as a sister group to the four core malvalean families, are shown to not fall close to these taxa. Also excluded as members of, or sister groups to, the expanded malvalean clade were the families Aextoxicaceae, Barbeyaceae, Cannabinaceae, Cecropiaceae, Dichapetalaceae, Elaeagnaceae, Euphorbiaceae s.l., Huaceae, Lecythidaceae, Moraceae s.l., Pandaceae, Plagiopteraceae, Rhamnaceae, Scytopetalaceae, Ulmaceae, and Urticaceae.     

RpoA: a useful gene for phylogenetic analysis in diatoms

The aim of this study was to compare the usefulness of two chloroplast-encoded genes (rpoA and rbcL) and the nuclear-encoded small subunit (SSU) ribosomal RNA for reconstructing phylogenetic relationships among diatoms at lower taxonomic levels. To this end, the rpoA and rbcL genes for selected centric and pennate diatoms were sequenced. The new rpoA and rbcL sequences, and an existing nuclear-encoded SSU rRNA data set, were subjected to weighted/unweighted parsimony, maximum likelihood, minimum evolution, and Bayesian analyses. All of the tree-building methods employed showed, based on the support values, that the rpoA gene was the most useful, relative to the rbcL and SSU rRNA genes, in determining phylogenetic relationships among the sampled diatoms. The support values for the relationships among the pennate lineages were, in many instances, greater in the rpoA trees than in the SSU rRNA trees. These results suggest that rpoA might be of value in determining phylogenetic relationships among pennate lineages.     

中国沿海浒苔属rbcL和ITS序列比较及系统进化分析

为阐明中国沿海浒苔的亲缘关系及地理分布特点,采集青岛栈桥、盐城弶港、宁波象山、温州平阳四地浒苔样本,克隆测序得到ITS1、5.8SrDNA和ITS23种不同长度序列片段。四个地区的rbcL目的片段,长度均为1201bp。分析核苷酸差异和遗传距离,采用邻接法建立系统发生树。结果显示,ITS序列进化速率较快,rbcL序列相当保守。ITS区较短,GC含量均在65%以上,5.8SrDNA的CG含量在50%左右,ITS1区的序列差异大于ITS2区。四个地区的浒苔存在一定的地理差异,盐城和青岛的样本间的亲缘关系较近;宁波和温州的样本间的亲缘关系较近。石莼属(Ulva)和浒苔属(Enteromorpha)的物种没有聚成各自独立的分枝,而是相互混合在一起,应是两个亲缘关系相近的属。引起青岛绿潮的海藻很可能是来自盐城海域的Enteromorpha linza或Enteromorpha prolifera。     

Liparis tsii: a new species of Orchidaceae (tribe-Malaxideae) from Guangdong,China with its phylogenetic position

Liparis tsii, a new orchid from Guangdong, China, is described and illustrated. It is compared with its closest allies: L. sasakii Hayata, L. nanlingensis H.Z. Tian & F.W. Xing, L. krameri Franch. & Sav., L. reckoniana T.C. Hsu and L. brunnea Ormerod belonging to section Liparis. Further phylogenetic study based on combined molecular data from nrITS and plastid trnL-F ascertained its phylogenetic position as L. tsii being sister to L. sasakii and L. nanlingensis. A key to identification with the allied species is provided.     

The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications

Whether the Amborella/Amborella-Nymphaeales or the grass lineage diverged first within the angiosperms has recently been debated. Central to this issue has been focused on the artifacts that might result from sampling only grasses within the monocots. We therefore sequenced the entire chloroplast genome (cpDNA) of Phalaenopsis aphrodite, Taiwan moth orchid. The cpDNA is a circular molecule of 148,964 bp with a comparatively short single-copy region (11,543 bp) due to the unusual loss and truncation/scattered deletion of certain ndh subunits. An open reading frame, orf91, located in the complementary strand of the rrn23 was reported for the first time. A comparison of nucleotide substitutions between P. aphrodite and the grasses indicates that only the plastid expression genes have a strong positive correlation between nonsynonymous (Ka) and synonymous (Ks) substitutions per site, providing evidence for a generation time effect, mainly across these genes. Among the intron-containing protein-coding genes of the sampled monocots, the Ks of the genes are significantly correlated to transitional substitutions of their introns. We compiled a concatenated 61 protein-coding gene alignment for the available 20 cpDNAs of vascular plants and analyzed the data set using Bayesian inference, maximum parsimony, and neighbor-joining (NJ) methods. The analyses yielded robust support for the Amborella/Amborella-Nymphaeales-basal hypothesis and for the orchid and grasses together being a monophyletic group nested within the remaining angiosperms. However, the NJ analysis using Ka, the first two codon positions, or amino acid sequences, respectively, supports the monocots-basal hypothesis. We demonstrated that these conflicting angiosperm phylogenies are most probably linked to the transitional sites at all codon positions, especially at the third one where the strong base-composition bias and saturation effect take place.     

Subsidiary cells in the Orchidaceae: their general distribution with special reference to development in the Oncidieae

Subsidiary cell formation in leaves of the Oncidieae begins with the production of a trapezoid cell on each side of the guard cell mother cell. The trapezoid cells are formed by oblique divisions in the tiles of cells next to the tile of cells containing the guard cell mother cell. The trapezoid cell usually divides unequally to form a subsidiary cell and a derivative cell. The subsidiary cell is smaller and next to the guard cell mother cell. The derivative cell enlarges and is often indistinguishable from the other epidermal cells. Rarely, polar subsidiary cells are also formed. In very rare cases the smaller of the division products of the trapezoid cell divides to form two subsidiary cells next to each guard cell. Subsidiary cells have been found in all tribes of the epidendroid and vandoid groups, all neottoid tribes examined except the Orchideae, and the subfamily Cypripedioideae. The absence of subsidiary cells in primitive genera of the epidendroid tribes and the presence of subsidiary cells in the most advanced genera of the epidendroid and vandoid groups supports the hypothesis that the presence of subsidiary cells is an advanced condition in the Orchidaceae.     

A phylogeny of the chloroplast gene rbcL in the Leguminosae: taxonomic correlations and insights into the evolution of nodulation

Phylogenetic analysis of the chloroplast-encoded rbcL gene in Leguminosae are consistent with previous hypotheses in suggesting that the family as a whole is monophyletic, but that only two of its three subfamilies are natural. The earliest dichotomies in the family appear to have involved tribes Cercideae or Cassieae (subtribe Dialiinae), followed by Detarieae/ Macrolobieae, all of which are members of subfamily Caesalpinioideae. The remainder of the family is divided into two clades: (1) Mimosoideae and the caesalpinioid tribes Caeasalpinieae and Cassieae (subtribes Ceratoniinae and Cassiinae); (2) Papilionoideae. Basal groups within Papilionoideae are, as expected, elements of the grade tribes Sophoreae and Swartzieae. Major clades within Papilionoideae include: (1) a Genistoid Alliance comprising Genisteae, Crotalarieae, Podalyrieae, Thermopsideae, Euchresteae, and also some Sophoreae; (2) a clade marked by the absence of one copy of the chloroplast inverted repeat, with which are associated Robinieae. Loteae, and some Sophoreae; (3) Phaseoleae, Desmodieae. Psoraleeae, and most Millettieae, a group also marked by presence of pseudoracemose inflorescences; and (4) a well-supported clade comprising Aeschynomeneae, Adesmieae, and some Dalbergieae. Nodulation is most parsimoniously optimized on the rbcL strict consensus tree as three parallel gains, occurring in Papilionoideae, the caesalpioioid ancestors of Mimosoideae, and in the genus Chamaecrista (Caesalpinieae: Cassieae).     

九子母属的系统位置：来自叶绿体rbcL序列及核核糖体ITS序列的证据

九子母属Dobinea Buch-Ham.ex D.Don是一个东亚特有属,包含贡山九子母D.vulgaris Buch-Ham.ex D.Don和羊角天麻D.delavayi(Baill.)Baill.两种,主要分布于中国两南地区.有关九子母属的系统位置长期存在争议,小同的学者曾将其归入漆树科Anacardiaceae、无忠子科sapindaceae和九子母科Podoaceae.本文基于rbcL和ITs探讨了其系统位置,结果表明,九子母属的两个种自成单系,并且是漆树科的成员.     

The questionable affinities of Corsia (Corsiaceae): evidence from floral anatomy and pollen morphology

The floral anatomy and pollen morphology of Corsia are described in the context of its systematic relationships. Flowers of Corsia are epigynous, lack septal nectaries and possess a large labellum formed from the outer median tepal (sepal). The labellum is highly vascularized and has a prominent outgrowth (callus) that is apparently nectiiferous in some species of section Sessilis , although not in section Unguiculatis . The six fertile stamens are proximally fused to the style, forming a gynostemium. This combination of labellum and gynostemium is otherwise found only in Orchidaceae (Asparagales), but the orchid labellum is formed from the opposite median inner tepal, and is therefore not homologous with that of Corsia . The three genera of Corsiaceae ( Corsia , Arachnitis and Corsiopsis ) are markedly different in some respects; e.g. only Corsia has a gynostemium. However, they share a unique synapomorphy in the presence of a labellum formed from the outer median tepal (sepal). Corsia and Arachnitis are also similar in pollen sexine sculpturing. Among other putative relatives, the range of morphological similarities between Corsia and Campynemataceae (Liliales) tends to support recent preliminary inferences from molecular data that they are closely related, but a relationship with Thismia (Dioscoreales) cannot be discounted. Both Campynemataceae and Thismia share similarities with Corsia , including epigyny, absence of septal nectaries, presence of tepal nectaries, and pollen morphology. © 2002 Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 138 , 315–324.     

Molecular phylogenetics of Diseae (Orchidaceae): a contribution from nuclear ribosomal ITS sequences

We present here the first molecular phylogeny of tribe Diseae (Orchidoideae: Orchidaceae). Nuclear ribosomal ITS1, 5.8S rDNA, and ITS2 sequences were compared for 30 Diseae, 20 Orchideae, and four Cranichideae and Diurideae outgroups. ITS - rDNA sequences exhibited a transition:transversion ratio of 1.3 and extensive ITS length polymorphism. Phylogenetic analyses using maximum parsimony identified seven major core orchidoid groups. The branching order of the five Diseae and two Orchideae clades was weakly supported but indicated paraphyly of Diseae, with Disperis sister to the rest, followed by successive divergence of Brownleea, Disinae, Coryciinae sensu stricto (s.s.), Satyriinae, and terminated by Orchidinae plus Habenariinae. Within the monophyletic Disinae, Herschelia and Monadenia were nested within a paraphyletic Disa and clustered with D. sect. Micranthae. Within monophyletic Satyriinae, Satyridium rostratum plus Satyrium bicallosum was sister to the rest of Satyrium, and then Satyrium nepalense plus S. odorum was distinct from a cluster of six species. Coryciinae are paraphyletic because Disperis is sister to all other core orchidoids. Coryciinae s.s. are sister to Satyriinae plus Orchideae, with Pterygodium nested within Corycium. Maximum likelihood analysis supported possible affinities among Disinae, Brownleeinae, and Coryciinae but did not support monophyly of Diseae or an affinity between Disinae and Satyriinae. Morphological characters are fully congruent with the well-supported groups identified in the ITS phylogeny.     

基于叶绿体基因rbcL和psbA-trnH间区探讨石杉科植物系统关系

关于石杉科Huperziaceae植物的分类,一直存在一些争议。在旧的分类体系中石杉科植物被包含在一个混合的石松科Lycopodiaceae和多谱系的石松属Lycopodium中。本文利用叶绿体rbcL基因和psbA-trnH基因间区序列探讨石杉科植物的系统位置及石杉科内部的分类关系,用最大简约法和邻接法对自测序列结合由GenBank下载的rbcL及psbA-trnH基因间区序列进行系统发育分析。结果显示,石杉科与Phylloglossum属关系较近,与石松科关系较疏远。在石杉科中热带石杉属Huperzia植物和马尾杉属Phlegmariurus植物的关系要比它们与其他石杉属植物更近。所以,我们的rbcL基因数据不支持秦仁昌关于石杉科分为石杉属和马尾杉属的分类处理。但是,因为我们的psbA-trnH序列没有包括热带种类,对石杉属植物和马尾杉属植物的关系无验证。因此需要更多的样品和序列数据进一步探讨石杉科的演化关系。     

Polyphyly of Limoniastrum (Plumbaginaceae): evidence from DNA sequences of plastid rbcL, trnL intron and trnL-F intergene spacer

Phylogenetic relationships of Limoniastrum and other genera of subfamily Staticoideae (Plumb-aginaceae) were studied using parsimony analysis of the plastid gene rbc L, the intron of trn L and the intergene spacer of trnL-trn F. Our analysis showed that Limoniastrum was polyphyletic. Limoniastrum ifniense , in both rbc L and combined data analyses, is sister to Armeria and Psylliostachys , whereas in the trn L-F (intron and spacer combined) analysis it is sister to a clade composed of Acantholimon, Dictyolimon and the remaining species of Limoniastrum . In all analyses, the five remaining species of Limoniastrum (excluding Limoniatrum ifniense ) formed a clade with two groups of species: L. monopetalum+L. guyonianum and those sometimes considered as the segregate genus Bubania ( L.feei, L. weygandiorum and L. rechingeri ). Levels of sequence divergence among these three groups of Limoniatrum were greater than for other well supported genera in the family and, in combination with morphological differences and paucity of synapomorphies, led us to conclude that separate generic status for each of the three clades is warranted.     

Three new species of Liparis s.l. (Orchidaceae: Malaxideae) from Southwest China based on morphological characters and phylogenetic evidence

Liparis aureolabella and L. mengziensis, two new species from the karst region of southwestern China, and L. bingzhongluoensis, a new species from montane region in Yunnan, are described and illustrated. L. aureolabella is easily distinguished from its relatives by having abaxially purple leave with purple reticulate veins prominent adaxially, a lip auriculate at base, and falcate-lanceolate pollinia. Liparis mengziensis is closely related to L. petiolata and L. auriculata, but differs from them by having an ovate to broadly ovate leaf, purple lip and apex connate along the margins. Liparis bingzhongluoensis is similar to Liparis nanlingensis, but the new species is characterized by having a lip with two transparent ridges on its disc, longitudinally concave basal callus and triangular column wings. Phylogenetic analyses based on nuclear ribosomal ITS and plastid matK sequences showed that L. aureolabella and L. mengziensis are nested with L. petiolata or L. auriculata in a monophyletic clade. L. bingzhongluoensis is sister to a clade formed by L. nanlingensis, L. tsii, L. sasakii and L. krameri. Moreover, morphological comparisons strongly support that the three species as separated species newly to science.     

Phylogeny of genera of Prasinophyceae and Pedinophyceae (Chlorophyta) deduced from molecular analysis of the rbcL gene

A molecular approach was used to study the phylogeny of 12 genera of Prasinophyceae and two genera of Pedinophyceae (Chlorophyta). The study was based on maximum likelihood and LogDet transformation analyses of a 1094-basepair fragment of the large subunit of ribulose-l,5-bisphosphate carboxylase/oxygenase (rbcL), a chloroplast-encoded gene. With the inclusion of homologous sequences from two cyanobacteria (Anabaena PCC 7120 and Anacystis nidulans (Richter) Drout et Daily) and a prochlorophyte(Prochlorothrix hollandica Burger-Wiersma, Stal et Mur), the maximum likelihood reconstructions suggested that species referred to the family Mamiellaceae are secondarily reduced forms rather than the most ancestral eukaryotic green plants. The systematic position of Micromonas pusilla (Butcher) Manton et Parke based on morphology is ambiguous, but the rbcL-based inferences indicated that it is related to the Mamiellaceae. In spite of being morphologically very different, Pycnococcus and Pseudoscourfieldia appear to be closely related, and it is suggested that Pseudoscourfieldia be included in the family Pycnococcaceae. The phylogenetic framework when based on first and second codon positions identifies the Mamiellaceae, Pycnococcaceae, Halosphaer-aceae, and Mesostigmataceae as monophyletic families, whereas the Chlorodendraceae appears to be of polyphyletic origin. However, this branching pattern was not confirmed by bootstrap analyses. The analysts based on a LogDet transformation matrix also supported the close relationship among species belonging to the Mamiellaceae (including Micromonas pusiila) and that the pedinophytes form a separate group. The branching pattern among most of the prasinophyte genera was not resolved giving a tree topology similar to those obtained in the bootstrap analyses. A relative rate test showed that the rbcL gene in the Pedinophyceae has evolved at a slower speed relative to that in the Prasinophyceae.