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.     

Phylogenetic relationships in Bulbostylis (Abildgaardieae: Cyperaceae) inferred from nuclear and plastid DNA sequence data

Previous molecular phylogenetic analyses of the family Cyperaceae based on rbcL sequences showed Bulbostylis as paraphyletic, with B. atrosanguinea and B. hispidula forming a clade with Nemum spadiceum. On the contrary, phylogenetic analyses of the tribe Abildgaardieae based on nuclear (ITS ribosomal region) and plastid sequences (trnL-F region) showed Bulbostylis as monophyletic, although they only incorporated four species of Bulbostylis and none of Nemum. In this work, we presented a phylogenetic hypothesis of Bulbostylis based on a comprehensive sampling, including species from different continents for the first time. New sequences of Abildgaardia, Crosslandia, Fimbristylis, and Nemum were included to test the monophyly of Bulbostylis. In total, 84 sequences of both ITS and trnL regions were generated. Analyses were performed using Bayesian inference, maximum likelihood, and parsimony. Ancestral state reconstruction was performed using ML, MCMC, and parsimony methods. In all analyses, Bulbostylis resulted paraphyletic as Nemum atracuminatum is nested within it. Most American species of Bulbostylis grouped together, but relationships amongst them appeared poorly resolved. Ancestral state reconstructions of native distribution suggest an African ancestor of Bulbostylis, with at least three introduction independent events of the species in America. Morphological diagnostic characters such as the ‘style base permanence or detachment from the ripe achene’, and the ‘micromorphological patterns of the achene surface’ are homoplastic in this phylogenetic context, and therefore unsuitable to propose infrageneric groupings within the Bulbostylis.     

Carex, subgenus Carex (Cyperaceae) – A phylogenetic approach using ITS sequences

To evaluate the sectional classification in Carex, subgenus Carex, the ITS region of 117 species belonging to 32 sections was analyzed with Neighbor Joining (NJ) and Markov chain Monte Carlo (MCMC) methods. In our analyses (1) species of subgenus Indocarex appear as a statistically well supported group within subgenus Carex. (2) The representatives of sections Vesicariae, Hirtae, Pseudocypereae, Ceratocystis, Spirostachyae, Bicolores, Paniceae, Trachychlaenae, Scirpinae, Atratae and Albae group in statistically supported clades with higher support in MCMC than in NJ. (3) C. rariflora clusters with representatives of section Limosae, however only weakly supported. (4) Taxa of section Phacocystis are divided in two statistically supported subclusters that are closely related to a core group of section Hymenochlaenae. (5) Species of sections Montanae, Pachystylae, Digitatae, Phacocystis, Rhomboidales, Careyanae and Frigidae are segregated into two or more clusters each. (6) Five species of section Frigidae cluster together, whereas the seven others are in scattered positions. Based on these results, delimitation of sections is discussed.     

Molecular analysis of phylogenetic relationships among Myrmecophytic macaranga species (Euphorbiaceae)

Many species of the paleotropical pioneer tree genus Macaranga Thou. (Euphorbiaceae) live in association with ants. Various types of mutualistic interactions exist, ranging from the attraction of unspecific ant visitors to obligate myrmecophytism. In the latter, nesting space and food bodies are exchanged for protection by highly specific ant partners (mainly species of the myrmicine genus Crematogaster). As a first step toward elucidating the coevolution of ant-plant interactions in the Macaranga-Crematogaster system, we have initiated a molecular investigation of the plant partners' phylogeny. Nuclear ribosomal DNA internal transcribed spacer (ITS) sequences were analyzed for 73 accessions from 47 Macaranga species, representing 17 sections or informally described species groups. Three accessions from the putative sister taxon Mallotus Lour, were included as outgroups. Cladograms of the ITS data revealed Macaranga to be nested within Mallotus. ITS sequences are highly similar within section Pachystemon s.str., suggesting a relatively recent and rapid radiation of obligate myrmecophytes within this section. Forty-three accessions, mainly of ant-inhabited species, were additionally investigated by random amplified polymorphic DNA (RAPD) and microsatellite-primed PCR (MP-PCR) techniques. Phenetic analysis of RAPD and MP-PCR banding profiles generally confirmed the ITS results. Best resolutions for individual clades were obtained when ITS and RAPD/MP-PCR data were combined into a single matrix and analyzed phenetically. The combined analysis suggests multiple (four) rather than a single evolutionary origin of myrmecophytism, at least one reversal from obligate myrmecophytism to nonmyrmecophytism, and one loss of mutualistic specifity.     

珊瑚菜居群遗传多样性的SRAP分析

利用SRAP对伞形科单种属珊瑚菜7个野生居群和1个栽培居群进行了研究。结果表明:共筛选出8个引物组合,在珊瑚菜8个居群中共扩增出168条条带,其中多态性条带为118条,多态性比率为70.23%;平均每对引物扩增的多态性条带为14.75。各居群之间珊瑚菜遗传相似性系数范围为0.8306~0.9836,遗传距离范围为0.0165~0.1856。聚类分析表明,以相似性系数大于0.8并结合地理分布来看,所研究的野生珊瑚菜居群可以大体分为3类,辽宁大连的野生居群为一类,山东威海—山东青岛的居群为一类,而山东日照—广州深圳之间的为一类。     

A molecular approach to the phylogenetic relationships of the western palaearctic Helicoidea (Gastropoda: Stylommatophora)

Molecular phylogenetic relationships among 45 members of the Helicoidea (Gastropoda: Stylommatophora) were examined using partial mitochondrial 16S rRNA sequences. Phylogenetic relationships were inferred using maximum parsimony, maximum likelihood and Bayesian methods. The reconstructed phylogenies showed a good degree of support for more recent branches, but gave little support to deeper nodes. Mitochondrial rDNA data further confirmed monophyletic status of helicids, recognized monachine hygromiid and bradybaenid clades and resolved a number of relationships in the helicelline hygromiids. With the respect to the latter assemblage, most of the anatomically based groups are confirmed, corroborating the diagnostic value of the dart-sac complex and a close affinity between Ichnusomunda sacchii and species of the genus Cernuella . Nevertheless, some well resolved branches challenge previous systematic arrangements, grouping species previously placed in different arrangements. In particular, support was not found for the monophyly of helicelline hygromiids with pedal penial innervation. Possible explanations for these incongruencies are suggested. 16S sequence data are appropriate for studies of relationships within the different species groups and less so for recovery of more ancient radiations in the Helicoidea. It will be valuable to combine the 16S data with other gene sequences to estimate basal relationships.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 501–512.     

茴芹属16种植物的花粉形态及系统学分析

利用光学显微镜和扫描电镜对茴芹属16种植物的花粉形态进行了观察,其中12种为首次报道。结果表明,茴芹属16种植物花粉大小为（19.75～33.03）μm×（11.52～17.41）μm,极轴与赤道轴的比值（P/E）为1.40～2.28,体积大小指数（P×E）^1/2为16.71～23.97,属于中型花粉,具三孔沟,萌发孔位置为边萌发孔。花粉粒赤道面观有近矩形、赤道收缩形、椭圆形和近菱形等类型,其中近矩形和赤道收缩形占多数;极面观为三角形或三角圆形。扫描电镜下,其外壁表面纹饰赤道面观为脑纹状,极面观近光滑或为穴纹状。在伞形科芹亚科中,茴芹属植物的花粉具有中等进化、比较进化的形态特征。研究认为,花粉形态可为个别物种的分类处理提供孢粉学证据。     

Phylogenetic relationships ofPseudopanax species (Araliaceae) inferred from parsimony analysis of rDNA sequence data and morphology

Sequence data from internal transcribed spacer (ITS) regions of rDNA and data from morphology, cytology and wood anatomy are used to study phylogenetic relationships inPseudopanax. The molecular and non-molecular data are analysed as independent data sets and in combination using parsimony. Results supported the conclusion that the genusPseudopanax is polyphyletic.Pseudopanax species emerge in two major monophyletic groups. The Anomalus group containsPseudopanax anomalus, P. edgerleyi, andP. simplex; these species share a common ancestor withCheirodendron trigynum and more distantly withPseudopanax gunnii. The second major group consists of two smaller groups: the Arboreus group, includingPseudopanax arboreus, P. colensoi, P. kermadecensis, P. laetus, andP. macintyrei, and the Crassifolius/Discolor group, includingP. chathamicus, P. crassifolius, P. discolor, P. ferox, P. gilliesii, P. lessonii, andP. linearis. Meryta species are close relatives of thePseudopanax Arboreus and Crassifolius/Discolor groups.     

Evaluation of random amplified polymorphic DNA for species identification and phylogenetic analysis inStylosanthes (Fabaceae)

Random amplified polymorphic DNA (RAPD) was assessed for its suitability as a tool to be used in the identification of taxa from the genusStylosanthes (Fabaceae, Papilionoideae, Aeschynomeneae). Five random primers were used to fingerprint accessions from seven species in the genus, and generated RAPD profiles that were species-specific. Data were used to examine evolutionary relationships between taxa, employing both clustering and ordination techniques, and the results were compared with those from a previous cladistic analysis of chloroplast DNA (cpDNA) restriction fragments. Both multivariate approaches indicated relationships that were generally similar to those obtained by RFLP analysis of cpDNA. However, while cluster analysis grouped together all accessions within species, ordination placed certain accessions ofS. humilis, S. macrocephala andS. capitata into separate groups. Experiments to test the assumed homology of comigrating RAPDs estimated 85.7% homology for accessions within species, and 53.8% homology for accessions between species. The value of RAPD data in systematics is discussed.     

Molecular phylogeny and systematics of the Lilium carniolicum group (Liliaceae) based on nuclear ITS sequences

The Lilium carniolicum group consists of several taxonomically dubious taxa endemic to the European flora. Internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA (nrDNA) were used to clarify both the delineation of, and relationships among, taxa in the group as well as to provide insight on the phylogenetic position of the group within the genus. Maximum parsimony, maximum likelihood and Bayesian analyses were in general agreement, with all taxa in the group being very closely related, and the entire group being monophyletic. L. pyrenaicum and L. pomponium are placed at the basal position in the group, while L. chalcedonicum is shown to be more closely related to L. carniolicum than previously thought. Our analyses suggested that L. albanicum and L. jankae are distinct from L. carniolicum, while no evidence was found to support the same separation for L. bosniacum.     

A new species of Cymopterus (Apiaceae) from the Rocky Mountain region, U.S.A.

Cymopterus constancei is described as new from mostly western portions of Wyoming, Colorado, and New Mexico and from eastern Utah and Arizona. It has been confused withC. bulbosus A. Nelson but differs in several features of its bractlets, phenology, and habitat. The novelty is among the earliest of the native flora to bloom and is quite uniform morphologically. The number of collections encountered exceeds 200, a fourfold increase, in the past 22 years.     

Molecular phylogenetic analysis ofChrysosplenium (Saxifragaceae) in Japan

The phylogeny of Japanese species ofChrysosplenium (Saxifragaceae) was examined using variation in DNA sequences. Sequences ofrbcL andmatK genes were compared for their feasibility for reconstructing the phylogeny ofChrysosplenium, and thematK sequences was found to give greater resolution. All but one of the 17 Japanese species have been examined formatK gene sequences and phylogenetic analysis of these data resulted in eight most parsimonious trees of 390 steps and a consistency index (Cl) of 0.823. The molecular phylogeny obtained was generally in agreement with Hara's (1957) classification based upon phenotypic similarity, although a conclusion needs extensive examination of the genus on a world-wide level. Using the phylogenetic data, character evolution was examined, especially in the characters traditionally used for grouping infrageneric taxa. Differentiation of opposite and alternate phyllotaxis appears to have occurred only once in the course of evolution ofChrysosplenium.     

Cytotaxonomic analysis of the Himalayan species of the genusTorilis (Apiaceae)

Chromosome studies of four HimalayanTorilis species reveal a remarkable interand intraspecific differentiation of chromosome numbers and karyotypes:T. arvensis (2n = 12),T. leptophylla (2n = 12),T. Stocksiana (2n = 36) andT. japonica (2n = 16). Base numbers inTorilis are x = 6, 8, 9 and 11.     

A pair of species of Tauschia Schltdl. (Umbelliferae/Apiaceae) from Mexico

Two species of Tauschia—T. spellenbergii from Chihuahua and T. beruloides from Michoacán and México—are described as new.     

A phylogenetic analysis of the aureoidSenecio (Asteraceae) complex based on ITS sequence data

The internal transcribed spacer region of the 18S–25S nuclear ribosomal DNA repeat was sequenced from 28 populations of the aureoidSenecio complex as well as two populations from the Lugentes group and one from the Tephroseroid group. Divergence levels for populations within the aureoid complex are very low (0.0 to 4.1%). Phylogenetic trees generated from the sequence data provide no support for the recognition of Aurei, Tomentosi and Lobati subgroups within the aureoid complex. With two Lugentes and one Tephroseroid species as outgroups,Senecio glabellus is the sister group of the rest of the aureoids. The high level of divergence between the aureoids and the three outgroup species indicates that the Lugentes and the Tephroseroids may not be closely related to the aureoids.     

An analysis of interspecific hybrids and phylogenetic implications inCucumis (Cucurbitaceae)

Investigations on interspecific crossability in 8Cucumis species (2n = 24) and chromosome pairing and pollen fertility of their hybrids from 15 combinations have been utilized for tracing the phylogenetic relationships among these taxa and factors responsible for their differentiation. A collective evaluation of data suggests that there are three broad groups of species, one of the spiny fruited interfertile species, whose hybrids show varying degree of chromosome associations and low to high pollen fertility; the second of species with non-spiny fruits, which are completely incompatible with the former but weakly compatible with the cultivated species,C. melo L. to produce partly developed seeds, and the third group ofC. metuliferus E. Mey. exSchrad. andC. melo and its different botanical varieties. The species with spiny fruits can be further divided based on karyomorphological similarities and/or on relative genomic affinity, indicated by chromosome pairing and hybrid pollen fertility.Cytogenetics inCucumis III.     

中国伞形科矮泽芹属植物叶表皮形态特征的研究

利用光学显微镜、扫描电镜对伞形科矮泽芹属8种植物叶表皮形态进行观察与研究。结果表明:(1)矮泽芹属8种植物上下表皮细胞均为不规则形或规则多边形,垂周壁为近平直状或波状,上表皮细胞长宽比在1.3~2.4之间,下表皮细胞长宽比在1.5~2.5之间;在近轴面,有细叶矮泽芹、聂拉木矮泽芹和绿花矮泽芹3种植物没有气孔器的存在,其余物种气孔密度在20~74个/mm2之间,气孔指数为6.0%~17.7%;在远轴面,所有物种都具有丰富的气孔器,气孔密度为100~183个/mm2,气孔指数为16.1%~23.6%。(2)聚类分析结果显示,矮泽芹、大苞矮泽芹、粗棱矮泽芹为类群Ⅰ,鹤庆矮泽芹为类群Ⅱ,聂拉木矮泽芹、细叶矮泽芹、绿花矮泽芹为类群Ⅲ,松潘矮泽芹则单独聚为类群Ⅳ;聚类分析结果大体上支持形态学分类的结果。(3)叶表皮形态特征对于区分矮泽芹属不同物种具有十分重要的分类学价值。     

An attempt to clarify taxonomic relationships in ``Verwandtschaftskreis der Gattung Ligusticum' (Umbelliferae-Apioideae) by molecular analysis

Relationships among the taxa of Umbelliferae, presumably close to Ligusticum and Selinum were investigated by two independent molecular taxonomic methods. 134 ITS 1-2 sequences were analyzed (29 new and 2 reinvestigated species) and immunochemical comparison of storage seed proteins for 38 species of Apioideae of Ligusticum affinity was performed, eight reference systems (antisera) were used. Both approaches yield similar results, showing the extremely polyphyletic nature of this group and some large genera (Ligusticum s.l., Selinum s.l., Pachypleurum) in the Umbelliferae. The independent status of the genera Magadania, Sphaenolobium, Arafoe, Lomatocarpa, Dimorphosciadium and some other segregates of Ligusticum, Cnidium and Selinum have been confirmed, but Cnidium proved to be unnatural even as currently circumscribed. In the group of East Asian taxa the genera Oreocome, Ligusticopsis, Cortia and Cortiella appeared to be closely related. Haplosphaera was shown to be a genus of Hansenia-Notopterygium group.     

Identification of apomorphies and the role of groundpatterns in molecular systematics

Putative apomorphic character states are the only relevant phylogenetic signal contained in sets of sequence data. Using the sequence position as a character, a way to identify putative apomorphies prior to phylogenetic analysis is proposed. It is shown that distance-matrix methods use trivial characters. The concept of the asymmetrical split is presented for determination of character polarity. It is furthermore argued that groundpatterns (node sequences) should be reconstructed prior to the study of relationships between taxa of high phylogenetic age. The 'evolutionary noise'contained in groundpatterns can be illustrated with a network of distances using a split-decomposition analysis.