Phylogeny of the Madagascan endemic family Didiereaceae

A molecular phylogeny of the Didiereaceae was produced through parsimony analysis of chloroplastrpl16 intron andtrnL-trnF andtrnT-trnL intergenic spacer sequences of all eleven species of the Didiereaceae and several outgroup taxa from the Portulacaceae. Results indicated that: 1) the Didiereaceae were embedded within the Portulacaceae, withCalyptrotheca as the sister group of the family; 2) present generic limits were supported; 3)Alluaudiopsis was the most basal lineage; 4) at least two separate episodes of polyploidization within the genusAlluaudia had occurred, and 5) unusually low amounts of variation were present in rapidly evolving noncoding plastid sequences.     

10种棘豆属植物的trnL-F序列及其分子系统学研究

选择内蒙古27个样地采集的10种棘豆属植物54个单株,提取样品的基因组DNA,对其叶绿体trnL-F序列进行扩增、测序,所得序列利用ClustalX软件进行对位排列,并用MEGA5.0软件采用最大似然法构建系统发育树,以探讨棘豆属的种间关系与系统进化.结果显示:(1)10种棘豆属trnL-F的变异位点54个,信息位点46个,种间碱基差异百分率为1.9％,GC含量变化范围在30.69％～31.50％之间.(2)棘豆属与黄芪属各为一支,自展支持率达99％,支持棘豆属植物为单系起源.(3)系统树中小花棘豆的样本自成一支,为相对独立进化;多叶棘豆、砂珍棘豆和黄毛棘豆的样本相互混杂,表明亲缘关系很近,从而支持《内蒙古植物志》将三者归入真棘豆亚属轮叶棘豆组的观点.(4)刺叶柄棘豆的样本不同样地形成2个分支,对其亚属水平上的分类需进一步探讨.(5)缘毛棘豆与阴山棘豆的样本聚成一支,支持将二者归入矮生棘豆组.研究表明,trnL-F序列可为棘豆属下种间系统发育关系研究提供分子证据.     

A molecular phylogeny of the genus Gagea (Liliaceae) in Germany inferred from non-coding chloroplast and nuclear DNA sequences

The systematics of the mainly yellow flowered Gagea species complex (Liliaceae) has long been considered difficult because only a few phenotypic features within this genus and as a result of hypothesized interspecific hybridisation. A molecular phylogenetic study of seven Gagea species (G. bohemica, G. lutea, G. minima, G. pomeranica, G. pratenis, G. spathacea and G. villosa) from Germany has been undertaken, based on plastid DNA sequences (trnL(UAA)-trnF(GAA), psbA-trnH) and on the nuclear ribosomal internal transcribed spacer (ITS). Sequence divergence within the Gagea species ranges up to 15.5% for psbA-trnH, 22.0% for trnL-trnF and 23.7% for ITS (ITS1 + 5.8S rRNA + ITS2). Two subspecies of Gagea bohemica: G. bohemica subsp. saxatilis and G. bohemica subsp. bohemica are characterized by trnL-trnF data and morphological features. Analysis of the ITS region shows that G. pomeranica represents a hybrid of G. pratensis and G. lutea. Lloydia serotina was initially used as an outgroup species, but it was placed within the investigated Gagea species in the psbA-trnH and the trnL-trnF phylogenetic tree.     

六种沉香属植物叶片解剖结构研究

为比较沉香属不同种植物间的叶片形态解剖特征,将不同来源的六种沉香属植物在海南省兴隆南药园种植,运用石蜡切片法和撕片法对其成熟叶片的解剖特征进行观察,并对叶片的上下表皮,叶脉和叶横切面等12项数量性状进行统计分析。结果表明:六种沉香属植物叶片解剖结构基本一致,均为典型的异面叶,由表皮、叶肉和叶脉组成,表现出典型的旱生形态特点。表皮细胞单层,气孔微下陷,仅分布在下表皮,上下表皮上零星分布着表皮毛。叶肉组织发达,栅栏组织由1~2层排列紧密地圆柱状细胞组成,其间分布着大量的长方晶体,海绵组织内有一层排列较整齐,染色较深的异细胞组成的下皮层。主脉维管束双韧型,呈圆环状,内含大量异细胞。方差分析表明,除栅海比外,叶片厚度、叶脉条数、主脉厚度等其余11项数量指标在六种植物间差异均达到显著水平。聚类分析将这六种植物聚成3类,Aquilaria sinensis(白木香),A.crassna和A.banaensis聚为一类,A.baillonii和A.malaccensis聚为一类;A.yunnanensis(云南沉香)单独为一类。该研究结果为沉香属植物的物种鉴定提供了解剖学依据,同时对沉香属植物合理开发利用具有重要意义。     

Phylogenetic analysis of Leucojum and Galanthus (Amaryllidaceae) based on plastid matK and nuclear ribosomal spacer (ITS) DNA sequences and morphology

Phylogenetic analyses of the monocotyledonous genera Leucojum and Galanthus (Amaryllidaceae, Asparagales), using plastid (trnL-F and matK) and largely non-coding nuclear ribosomal (ITS) DNA sequences show the two to be closely related to Lapiedra, Narcissus, Vagaria, Pancratium and Sternbergia. We compare the results obtained with a combined parsimony analysis of these nucleotide sequences with that of a matrix of morphological characters. The sampling included all species of Leucojum and most species of Galanthus (representing all series and subseries of the genus) and used as outgroup the above mentioned genera of Amaryllidaceae shown to be close relatives. The plastid, nuclear and morphological data were analysed independently and in combination, showing that the boundaries between the two genera are not appropriate. Galanthus is monophyletic but embedded in Leucojum. On the basis of chromosome numbers and floral characters Leucojum has been previously divided into four subgenera, which have been accepted as genera by some authors. In our phylogenetic analyses (separate as well as combined), Leucojum species are separated in two primary clades corresponding to L. subgenera Ruminia + Acis and L. Leucojum + Aerosperma. The taxonomic implications of this pattern are discussed, and an alternative classification is proposed. Finally, biogeographic relationships of species of both Leucojum and Galanthus are discussed, emphasising the possible origin of the narrowly distributed taxa of Leucojum relative to the widespread species.     

Phylogenetic relationships within Pappophoreae s.l. (Poaceae: Chloridoideae): Additional evidence based on ITS and trnL-F sequence data

Historically, Pappophoreae included the genera Cottea, Enneapogon, Kaokochloa, Pappophorum and Schmidtia. Some authors consider this tribe as a well-supported monophyletic group; while other evidences reveals Pappophoreae as polyphyletic, with Pappophorum separated from the rest of the tribe. When the latter happens, it can form a clade with Tridens flavus. Molecular phylogenetic analyses of the subfamily Chloridoideae have included few species of Pappophoreae; therefore, further research involving more representatives of this tribe is needed. With the aim of providing new evidence to help clarify the phylogenetic position of Pappophorum and its relationships with other genera of the tribe and the subfamily Chloridoideae, eight new sequences of ITS and trnL-F regions of Pappophoreae species were generated. These sequences were analyzed together with other available sequence data obtained from GenBank, using maximum parsimony and Bayesian inference, for individual (trnL-F or ITS) or combined trnL-F/ITS data sets. All analyses reveal that Pappophoreae is polyphyletic, with Pappophorum separated from the rest of the tribe forming a well-supported clade sister to Tridens flavus.     

两栖蓼的分子系统学研究

两栖蓼是一种水陆两栖植物,植株在不同生态环境下外部形态差异较大,同时两栖蓼的系统位置存在争议,被归入春蓼组(sect.Persicaria)或提升为两栖蓼组(sect.Amphibium)。该文选取两栖蓼及春蓼组植物12种,以及刺蓼组、头状蓼组、神血宁组、拳参组、萹蓄组和外类群掌叶大黄共23种植物进行研究。植物总DNA的提取采用改进的CTAB法,所测序列以及从Genbank数据库下载的序列,以掌叶大黄为外类群,采用最大简约法和贝叶斯法对核糖体ITS序列和叶绿体trn L-F序列进行了系统发育分析。ITS序列对位排列的长度为735 bp,包括489个可变位点,272个位点是信息位点。简约法得到9个简约树,步长为1 084,CI指数为0.680,RI指数为0.614。trn L-F序列对位排列的长度为1 121 bp,包括427个可变位点,239个位点是信息位点。简约法寻找到9个简约树,步长为551(CI=0.911,RI=0.910)。贝叶斯法和简约法得到的树基本一致。分子序列分析结果显示,trn L-F序列树类似于ITS序列树。ITS序列构建的发育树上,两栖蓼与刺蓼组植物、春蓼组其他植物形成3个并列的分支;在trn L-F序列树上,两栖蓼则与其他春蓼组植物形成两个并列的分支。由此可见,两栖蓼与春蓼组其他植物的亲缘关系较远,成一独立的分支。两个分子证据支持将两栖蓼提升为两栖蓼组的处理意见。此外,两栖蓼的花粉具散沟,与典型的春蓼组的具散孔花粉不一致。再加上两栖蓼水陆两栖的特性,因此支持把两栖蓼提升为两栖蓼组的观点。两栖蓼组的界定为多年生草本,水陆两栖,根状茎横生,生于水中茎漂浮,叶长圆形或椭圆形,生于陆地茎直立,叶披针形或长圆状披针形,托叶鞘为筒状、薄膜质,总状花序穗状,瘦果近圆形,花粉具散沟。     

基于ITS和trnL-trnF序列的草木樨种群遗传多样性研究

以白花草木樨(Melilotus alba)和黄花草木樨(Melilotus officinalis)18个地理种群植物为材料,用ITS序列和trnL-trnF序列研究了2种草木樨不同种群间的遗传多样性。结果表明:(1)trnL-trnF序列对位后长度为459bp,其中包括6个变异位点,6个简约信息位点,G+C含量为33.1%;ITS序列对位后长度为714bp,其中包括5个变异位点,3个简约信息位点,G+C含量为48.9%。(2)在基于trnL-trnF序列构建的系统发育树中,2种草木樨能够形成单系分支,说明trnL-trnF序列在草木樨中的鉴别能力较强。(3)单倍型多样性以及核苷酸多样性分析表明,黄花草木樨的遗传多样性高于白花草木樨。     

Phylogenetics of Quiinaceae (Malpighiales): evidence from trnL-trnF sequence data and morphology

We present the first parsimony analyses of the Neotropical family Quiinaceae using nucleotide sequence data from the non-coding trnL intron and trnL-trnF intergenic spacer of the plastid genome, analysed separately as well as in combination with morphology. Both molecules and combined data recover Quiinaceae as a well-supported monophyletic group. Quiinaceae form a polytomy together with their potential sister groups, the monophyletic Ochnaceae s.str. and the monotypic Medusagynaceae from the Seychelles in the Indian Ocean. Froesia is resolved as sister to the rest of the family. Other members of the family, Lacunaria, Quiina, and Touroulia, are all recovered as monophyletic despite the inclusion of strikingly distinctive representatives (L. oppositifolia and Q. pteridophylla). Relationships among the last three genera, however, are yet uncertain. Optimising characters of breeding system onto the molecular phylogeny reveals that bisexual flowers (Froesia) are the ancestral state in Quiinaceae, whereas androdioecy (Quiina, Touroulia) and dioecy (Lacunaria) are derived breeding systems.     

Reassessing the relationships between Gordoniaand Polyspora (Theaceae) based on the combined analyses of molecular data from the nuclear, plastid and mitochondrial genomes

The combined analyses, based on ITS, trnL-F and matR DNA sequence data respectively from the nuclear, plastid and mitochondrial genomes, reveal that Gordonia is not a monophyletic group, and on the contrary, distributed in two major lineages in Theaceae. The only North American species, G. lasianthus, is located in Gordonieae together with Schima and Franklinia, whereas the Chinese Gordonia species are positioned in Theeae together with Camellia, Pyrenaria s.l. and Apterosperma. This result, to great extent, supports the viewpoints of separating the North American and Asiatic Gordonia species into two different genera, Gordonia s.str. and Polyspora, respectively.The study was partially supported by funds from a project of the Provincial Natural Sciences Foundation Committee of Yunnan, P. R. China (97C039Q), the special support grants from The Chinese Academy of Sciences for biotaxonomy and floristics.     

Phylogenetic relationships in Peniocereus (Cactaceae) inferred from plastid DNA sequence data

The phylogenetic relationships of Peniocereus (Cactaceae) species were studied using parsimony analyses of DNA sequence data. The plastid rpl16 and trnL-F regions were sequenced for 98 taxa including 17 species of Peniocereus, representatives from all genera of tribe Pachycereeae, four genera of tribe Hylocereeae, as well as from three additional outgroup genera of tribes Calymmantheae, Notocacteae, and Trichocereeae. Phylogenetic analyses support neither the monophyly of Peniocereus as currently circumscribed, nor the monophyly of tribe Pachycereeae since species of Peniocereus subgenus Pseudoacanthocereus are embedded within tribe Hylocereeae. Furthermore, these results show that the eight species of Peniocereus subgenus Peniocereus (Peniocereus sensu stricto) form a well-supported clade within subtribe Pachycereinae; P. serpentinus is also a member of this subtribe, but is sister to Bergerocactus. Moreover, Nyctocereus should be resurrected as a monotypic genus. Species of Peniocereus subgenus Pseudoacanthocereus are positioned among species of Acanthocereus within tribe Hylocereeae, indicating that they may be better classified within that genus. A number of morphological and anatomical characters, especially related to the presence or absence of dimorphic branches, are discussed to support these relationships.     

Phylogenetic relationships in Blumea (Asteraceae: Inuleae) as evidenced by molecular and morphological data

The present study, based on sequences of cpDNA (trnL-F & psbA-trnH) and nrDNA (ITS) and morphology, examined the evolutionary relationships in Blumea and its position among related genera. The results confirmed that the closest relatives of Blumea are Caesulia, Duhaldea and Pentanema p.p., and showed that the monotypic genera Blumeopsis and Merrittia are nested within Blumea. In Blumea s.l., two major, well-supported clades were recognised and a single species, the widespread Blumea balsamifera, that could not be placed with certainty relative to the two main clades. The two main clades differ in habit, ecology and distribution. The Blumea densiflora clade contains shrubs and subshrubs of evergreen forests, distributed from continental Asia to New Guinea and Polynesia, whereas the Blumea lacera clade is a widespread paleotropical group that comprises mostly annual, weedy herbs of open forests and fields.     

Phylogenetic relationships and taxonomy of subfamily Zygophylloideae (Zygophyllaceae) based on molecular and morphological data

Phylogenetic analysis of noncoding trnL plastid DNA sequences and morphological data for 43 species of Zygophylloideae, representing most of the morphological and geographical variation in the subfamily, indicates that the currently recognised genera Augea (monotypic, southern Africa), Tetraena (monotypic, China), and Fagonia (c. 30 species, widespread), are embedded in Zygophyllum (c. 150 species, widespread). A generic classification based on six monophyletic and morphologically distinctive entities is proposed: Roepera with c. 60 species in Australia and southern Africa, Zygophyllum with c. 50 species in Asia, Tetraena with c. 40 species in Africa and Asia, Augea with a single species in southern Africa, Melocarpum with two species in the Horn of Africa region, and Fagonia with c. 30 species in both the Old and the New World. Scanning electron microscopy studies of testa structure provided important characters for the delimitation of some genera. New combinations (61) are made in Roepera, a resurrected genus originally described from Australia, one new name is proposed in Zygophyllum, 35 new combinations are made in Tetraena, and two new combinations are made in Melocarpum (previously Zygophyllum sect. Melocarpum).     

Phylogenetic patterns in the fleshy-fruited Myrtaceae – preliminary molecular evidence

A phylogenetic study of selected fleshy-fruited genera of the Myrtaceae was conducted using sequences from the ITS region of nuclear DNA and the psbA-trnH region of plastid DNA. Studies to date have suggested that the fleshy-fruited state has arisen on several occasions in the Myrtaceae. The previously accepted and predominantly Neotropical tribe Myrteae has traditionally been divided into three groups, the subtribes Myrtinae, Eugeniinae and Myrciinae. This subtribal arrangement is analysed in detail here for the first time. The monophyly of the tribe and subtribes are tested and relationships of the genera within them, in particular those of the Myrciinae and anomalous genera sometimes associated with it, are discussed. Combined analyses of these two DNA regions revealed 40 shortest trees, all of which resolve Myrteae (excluding the Acmena group) as monophyletic. Myrciinae appears to be monophyletic whereas Myrtinae and Eugeniinae appear polyphyletic. The phylogenetic positions and relationships of the anomalous genera Myrceugenia, Luma and Blepharocalyx are unclear, but Myrceugenia is never included within the Myrciinae s.str. A Myrciinae s.str. clade emerges within which Myrcia, Calyptranthes and Marlierea appear polyphyletic. Clades emerge, however, that may reflect some natural groupings within the subtribe.We thank David Simpson, Lazlo Csiba, Edith Kapinos and many others from Kew for invaluable advice and support. It would not have been possible to collect the Brazilian samples without the patience and careful guidance of Dr. Vinicius C. Souza, Fiorella F. Mazine (Universidade de São Paulo, ESALQ), Professor Gert Hatschbach, Joel M. de Silva (Museu Botânico Municipal, Curitiba) and many others from the ESA and MBM herbaria. Thanks also to Les Landrum, Andrew Salywon, Marcos Sobral and an anonymous reviewer for helpful comments at different stages of this work. British Airways are gratefully acknowledged for providing a flight to Brazil under their Community and Conservation programme.     

Molecular characterization of reciprocal crosses of Aerides vandarum and Vanda stangeana (Orchidaceae) at the protocorm stage

Aerides vandarum and Vanda stangeana are two rare and endangered vandaceous orchids with immense floricultural traits. The intergeneric hybrids were synthesized by performing reciprocal crosses between them. In vitro germination response of the immature hybrid embryos was found to be best on half-strength Murashige and Skoog medium supplemented with 20% (v/v) coconut water/liquid endosperm from tender coconut. Determination of hybridity was made as early as the immature seeds or embryos germinated in vitro, using randomly amplified polymorphic DNA (RAPD) markers. Out of 15 arbitrarily chosen decamer RAPD primers, two were found to be useful in amplification of polymorphic bands specific to the parental species and their presence in the reciprocal crosses. However, a decisive profile that can identify the reciprocal crosses could not be provided by RAPD. Amplification of the trnL-F non-coding regions of chloroplast DNA of the parent species and hybrids aided easy identification of the reciprocal crosses from the fact that maternal inheritance of chloroplast DNA held true for these intergeneric hybrids. Subsequent restriction digestion of the polymerase chain reaction (PCR) amplified trnL-F non-coding regions of chloroplast DNA also consolidated the finding. Such PCR-based molecular markers could be used for early determination of hybridity and easy identification of the reciprocal crosses.     

A Preliminary Molecular Phylogeny of the Rhynchosporeae (Cyperaceae)

The tribe Rhynchosporeae comprises the genera Rhynchospora and Pleurostachys and has never been studied using molecular techniques. The objective of this study was to use an analysis of trnL-F sequences to evaluate the hypothesized taxonomic divisions within the Rhynchosporeae including the monophyly of the genera and the soundness of the subgenera and sections. A total of 44 ingroup species were studied, 41 of Rhynchospora representing 22 of Kükenthal’s 28 sections, and three of Pleurostachys. Five outgroup species from other genera were also included. The cladistic analysis of 50 trnL intron and trnL-F intergenic spacer sequences resulted in 16 trees and a strict consensus tree. The Rhynchosporeae form two well-supported primary clades with several well-supported smaller clades, many of which agree with previously hypothesized sections. Pleurostachys is embedded within the second primary clade.     

Molecular phylogeny and systematics of Genista (Leguminosae) and related genera based on nucleotide sequences of nrDNA (ITS region) and cpDNA (trnL-trnF intergenic spacer)

Phylogenetic relationships of Genista and related genera (Teline, Chamaespartium, Pterospartum, Echinospartum, Ulex, Stauracanthus and Retama) were assessed by the analysis of sequences of the nrDNA internal transcribed spacer (ITS region), and the cpDNA trnL-trnF intergenic spacer. The tree obtained by combining both sets of data indicates the existence of three lines of diversification within Genista, that correspond to three subgenera: Genista, Phyllobotrys and Spartocarpus, however, each of these lineages encompass also species of the related genera Echinospartum, Teline, Retama, Chamaespartium, Pterospartum, Ulex, Stauracanthus. The molecular data do not support division of these subgenera into taxonomical units at the sectional level; only sections Genista and Spartocarpus are monophyletic groups. The sequences of both regions are also informative at the specific level, grouping morphologically related species (e.g. the G. cinerea aggregate). The molecular data have also helped to clarify the position of taxa whose relationships were not well established (e.g. G. valdes-bermejoi). The relationships of related genera that belong to the Genista lines of diversification have also been investigated. Echinospartum splits into two separate clades matching the separation of two ecological and caryological differentiated groups. Teline also forms two groups, both placed near to Genista subgenus Genista, but that separated from the main core of the group. Retama, morphologically well differentiated from Genista, is close to Genista subgenus Spartocarpus. Chamaespartium and Pterospartum do not form a monophyletic group. Chamaespartium is closer to Genista subgenus Genista, whereas Pterospartum stands close to: 1) Genista subgenus Spartocarpus (particularly, sect. Cephalospartum); and 2) the Ulex-Stauracanthus clade (a terminal derivative of Genista subgenus Spartocarpus). Cases of incongruence (e.g. Echinospartum, Chamaespartium, Teline) between the trees obtained from the two molecular markers, may be indicating hybridisation and/or introgression between different lines of Genisteae.     

The use of a non-coding region of chloroplast DNA in phylogenetic studies of the subtribeSonchinae (Asteraceae:Lactuceae)

The systematic utility of sequences from a non-coding region of chloroplast DNA (cpDNA) betweenpsbA andtrnH^(GUG) was examined by assessing phylogenetic relationships in subtribeSonchinae (Asteraceae:Lactuceae). Primers constructed against highly conserved regions of tRNA genes were used for PCR amplification and sequencing. ThepsbA-trnH intergenic spacer contains several insertions and deletions (indels) inSonchinae with the length varying from 385 to 450 bp. Sequence divergence ranges from 0.00% to 7.54% withinSonchinae, with an average of 2.4%. Average sequence divergence inSonchus subg.Sonchus is 2.0%, while the mean for subg.Dendrosonchus and its close relatives in Macaronesia (the woodySonchus alliance) is 1.0%. Our results suggest that this region does not evolve rapidly enough to resolve relationships among closely related genera or insular endemics in theAsteraceae. The phylogenetic utility ofpsbA-trnH sequences of the non-coding cpDNA was compared to sequences from the ITS region of nuclear ribosomal DNA. The results suggest that ITS sequences evolve nearly four times faster thanpsbA-trnH intergenic spacer sequences. Furthermore, the ITS sequences provide more variable and phylogenetically informative sites and generate more highly resolved trees with more strongly supported clades, and thus are more suitable for phylogenetic comparisons at lower taxonomic levels than thepsbA-trnH intergenic chloroplast sequences.     

Phylogeny of Castanea (Fagaceae) based on chloroplast trnT-L-F sequence data

Species in the genus Castanea are widely distributed in the deciduous forests of the Northern Hemisphere from Asia to Europe and North America. They show floristic similarity but differences in chestnut blight resistance especially among eastern Asian and eastern North American species. Phylogenetic analyses were conducted in this study using sequences of three chloroplast noncoding trnT-L-F regions. The trnT-L region was found to be the most variable and informative region. The highest proportion of parsimony informative sites, more and larger indels, and higher pairwise distances between taxa were obtained at trnT-L than at the other two regions. The high A+T values (74.5%) in the Castanea trnT-L region may explain the high proportion of transversions found in this region where as comparatively lower A+T values were found in the trnL intron (68.35%) and trnL-F spacer (70.07%) with relatively balanced numbers of transitions and transversions. The genus Castanea is supported as a monophyletic clade, while the section Eucastanon is paraphyletic. C. crenata is the most basal clade and sister to the remainder of the genus. The three Chinese species of Castanea are supported as a single monophyletic clade, whose sister group contains the North American and European species. There is consistent but weak support for a sister–group relationship between the North American species and European species.     

A review of chemistry,quality and analysis of infected agarwood tree (<Emphasis Type="Italic">Aquilaria</Emphasis> sp.)

Agarwood is a valuable oleoresin obtained from wounded tree of various genus of Thymelaeaceae family especially from Aquilaria species. Agarwood is regarded as most treasured non-timber forest product used in fragrances as well as medicines. Quality of agarwood plays an important role to define its commercial value. Different countries use different grading pattern to define the quality of agarwood. More than 250 compounds have been identified so far, mostly sesquiterpenoids, chromones and volatile aromatic compounds. GC–MS is the considered as a best method for the identification of chemical profile of the agarwood by various authors. Present review discusses the various methods used to determine quality of agarwood and chemical constituents of infected agarwood tree.