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.     

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.     

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。     

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.     

缘管浒苔Rubisco酶大亚基基因编码序列rbcL克隆及分析

主要对缘管浒苔光合作用第一关键酶Rubisco大亚基基因(rbcL)进行了克隆分离.首先通过PCR特异性扩增叶绿体基因编码的缘管浒苔大亚基编码序列rbcL部分基因序列(1035 bp).依据基因步移原理,首次克隆得到缘管浒苔rbcL5'上游非翻译区序列(224 bp).据推测,rbcL 5'上游非翻译区序列存在类似原核生物的启动子元件-10区(TAAAAT)和-35区(TTGAAA).此外,依据3'-RACE(cDNA末端快速扩增技术)原理,克隆得到缘管浒苔rbcL3'末端cDNA序列(579 bp).     

Molecular Phylogeny of the Suborder Leucodontineae (Musci; Leucodontales) Inferred from rbcL Sequence Data

rbcL sequence data (1324 bp on average). Our analyses indicate (1) that Antitrichia is distantly related to the other members of Leucodontaceae and should be excluded from the family, (2) that Cryphaeaceae form a monophyletic clade, not with Anomodontaceae and Leptodontaceae, but with Leucodontaceae, refuting the placement of Leucodontaceae and Cryphaeaceae in different superfamilies, (3) that Forsstroemia, variously classified in Leucodontaceae, Cryphaeaceae or Leptodontaceae, forms a monophyletic clade with Neckera (Neckeraceae), and (4) that the presumed monophyly of Anomodon and that of Anomodontaceae are not supported. Received 18 September 1999/ Accepted in revised form 27 December 1999     

基于nrDNAITS序列数据的兰属系统发育关系的初步分析(英)

现存的兰属分类系统是基于宏观形态学性状、尤其是花粉块的数目以及唇瓣与蕊柱的愈合程度而建立的。兰属因此而划分为 3个亚属 :兰亚属 (subgenusCymbidium) ,大花亚属 (subgenusCyperorchis)和建兰亚属 (subgenusJensoa)。本文运用PCR扩增和直接测序的方法分析兰属 (Cymbidium) 2 7种、3个栽培品种以及 3个外类群的核DNAITS区段序列。通过最简约性分析产生的ITS系统发育树表明 ,兰属的 3个亚属均可能为不自然的类群。大花亚属表现为一复系群 ,兰亚属的冬凤兰 (C .dayanum )隐藏于其中 ;建兰亚属为一并系群 ,它的成员之一兔耳兰(C .lancifolium)偏离出去而成为兰属一最基部的分支 ;兰亚属为一复系群 ,它分为几支而分别与另两个亚属组合在一起。由于兰属ITS序列位点变异率较低 ,最简约性分析产生的几支主要分支均得不到Bootstrap分析的高度支持 ,各亚属内组之间的关系也不明确。研究兰属的系统发育关系还需要新的数据。     

Higher level relationships of Apiales (Apiaceae and Araliaceae) based on phylogenetic analysis of rbcL sequences

The two families of the order Apiales (Apiaceae and Araliaceae) represent a classic example of the difficulty in understanding evolutionary relationships between tropical-temperate family pairs. In Apiales, this problem is further compounded by phylogenetic confusion at almost every taxonomic level, including ordinal, interfamilial, and infrafamilial, due largely to difficulties in understanding trends in morphological evolution. Phylogenetic analyses of rbcL sequences were employed to resolve relationships at the ordinal and familial levels. The results of the ordinal analysis confirm the placement of Apiales in an expanded subclass Asteridae as the sister group to Pittosporaceae, and refute the traditional alliance of Apiales with Cornales and Rosidae. This study has also resolved relationships of a number of enigmatic genera, suggesting, for example, that Melanophylla, Aralidium, Griselinia, and Toricellia are close relatives of Apiales. Clarification of phylogenetic relationships has concomitantly provided insights into trends of morphological evolution, and suggests that the ancestral apialean taxon was probably bicarpellate, simple-leaved, woody, and paleotropical. Phylogenetic analysis at the family level suggests that apiaceous subfamily Hydrocotyloideae, often envisioned as an intermediate group between Apiaceae and Araliaceae, is polyphyletic, with some hydrocotyloids closely allied with Araliaceae rather than Apiaceae. With the exception of some hydrocotyloids, Apiaceae appear to be monophyletic. The relationship between Apiaceae and Araliaceae remains problematic. Although the shortest rbcL trees suggest that Apiaceae are derived from within a paraphyletic Araliaceae, this result is only weakly supported.     

Systematics of the Dactylorhiza euxina/incarnata/maculata polyploid complex (Orchidaceae) in Turkey: evidence from allozyme data

 Material of Dactylorhiza were sampled from 49 localities in Turkey and investigated for allozyme variation at ten loci (nine enzyme systems). Among diploids, the Anatolian D. osmanica and D. umbrosa were allozymically variable, but not distinct from each other or from D. incarnata. Dactylorhiza saccifera contained the same alleles as the European D. fuchsii. Dactylorhiza iberica and D. euxina were distinct from each other and the other diploids. On basis of allozyme patterns three distinct allotetraploid genotypes were distinguished, and each of them could be treated as a separate species. Dactylorhiza nieschalkiorum is similar to European allotetraploids, and may have arisen from hybridization between D. incarnata s.l. and D. saccifera. Dactylorhiza urvilleana may have arisen from parents related to present-day D. saccifera and D. euxina, but it also contains additional alleles that have not been found in any of the diploids investigated. A third allotetraploid known from four populations in the Ardahan and Kars provinces of north-eastern Turkey combines the allozyme patterns found in material of D. incarnata s.l. from the same area with those from D. euxina. It is here described for the first time as D. armeniaca. Received November 14, 2000 Accepted June 20, 2001     

Shifting ditypic site analysis: Heuristics for expanding the phylogenetic range of nucleotide sequences in Sankoff analyses

Summary We describe and illustrate a simple heuristic approach to the Sankoff methods for construction of parsimonious evolutionary trees from nucleotide sequence data. The procedure is intended to permit more valid inferences, particularly from relatively short sequences, concerning relationships among taxa separated for long time intervals. The procedure is based on the freat variability of evolutionary plasticity among sites in the molecules and removes from consideration the more highly variable sites. Editing is accomplished after classifying sites in carefully aligned arrays of sequences. Only “ditypic sites,” i.e., sites observed in only two evolutionary states within the array, are used in making phylogenetic inferences. This strategy makes possible the construction of good approximations to the most parsimonious Steiner strees, by means of efficient programs that require “dense species arrays,” i.e., species sets that differ from each other by relatively small numbers of differences in conservative sites. The technique is illustrated with 5S and 5.8S rRNA sequence data from published catalogs.     

Nujiangia (Orchidaceae: Orchideae): A new genus from the Himalayas

The phylogenetic positions of the enigmatic “wildcard” taxon,Habenaria griffithii,were inferred from molecular data and morphological evidence.Morphologically,H.griffithii is quite “isolated” in Habena...     

Coelonin,A 9,10-dihydrophenanthrene from the orchids Coelogyne ochracea and Coelogyne elata

2,7-Dihydroxy-4-methoxy-9,10-dihydrophenanthrene was isolated and identified from the whole plant of Coelogyne ochracea and C. elata.     

A scaleless scale worm: Molecular evidence for the phylogenetic placement of Pisione remota (Pisionidae, Annelida)

Pisionidae is a group of interstitial worms whose phylogentic affinities have been enigmatic. They have been allied to different Phyllodocida taxa. Although originally associated with Glyceridae and Phyllodocidae, they are more recently considered to be related to scale worms. Scale worms are a well-defined taxon, Aphroditiformia, within Annelida due to the unique possession of dorsal scales called elytra. Pisionidae lack elytra but they have been grouped with scale worms because they possess two pairs of jaws with venom glands, also found in Glyceridae. Determining the phylogenetic position of Pisionidae is important for understanding if features such as elytra and venomous jaws are evolutionarily labile in annelid history. Therefore, we explored 18S rDNA and Cytochrome c Oxidase subunit I data from several Aphroditiformia, Pisionidae, and other Phyllodocida to determine the phylogenetic placement of Pisionidae. Maximum likelihood and Bayesian inference of separate and combined data sets were conducted. All analyses support a derived position of Pisionidae within Aphroditiformia, close to Pholoidae and Sigalionidae. The loss of elytra in Pisionidae is probably due to adaptation for interstitial life. Furthermore, the results reject a monophyletic Aphroditoidea comprising Acoetidae, Aphroditidae, Eulepethidae and Polynoidae. Thus, the possession of only simple chaetae is either symplesiomorphic or convergent.