A molecular phylogeny for the large African orchid genus Disa

Phylogenetic relationships were inferred for the African subtribe Disinae (Orchidoideae, Orchidaceae), which include the large genus Disa and the small genus Schizodium. One nuclear (ITS) gene region and two plastid (trnLF and matK) gene regions were sequenced for 136 ingroup, representing 70% of all known Disinae species, as well as for 7 outgroup taxa. The combined data matrix contained 4094 characters and was analysed using parsimony and Bayesian inference. Our results show that the generic status of Schizodium can no longer be supported, as it is deeply embedded within the genus Disa. Furthermore, the currently recognised subgenera do not reflect the phylogenetic relationships and should be rejected. Several of the currently recognised sections are monophyletic, others contain misplaced elements, while some are polyphyletic. Morphological divergence, rather than convergence, has hampered previous attempts at a phylogenetic classification of the Disinae. On the basis of our molecular phylogenetic hypothesis, we propose a monotypic subtribe Disinae and a subdivision of the genus Disa into 18 sections.     

Evidence for two distinctive species of Pseudorchis (Orchidaceae) in Scandinavia.

Reinhammar, L.-G. 1995. Evidence for two distinct species of Pseudorchis (Orchidaceae) in Scandinavia. - Nord. J. Bot. 15: 469–481. Copenhagen. ISSN 0107–055X.
Nordic populations of Pseudorchis albida s.l. were studied for variation in morphological characters. Canonical variates analysis (CVA) arrange populations in two discrete groups, corresponding to P. albida S.S. and P. straminea , respectively. In principal component analysis (PCA) of the total material a small overlap could be seen. However, separate PCA:s on members of the two taxa from the same geographic region show perfect separation. Since the two taxa are distinct in morphology as well as in additional characters, e.g. habitat preference in the area of sympatry, they are best treated as separate species. The generic name Pseudorchis is considered to be validly published and is then preferred over the later Leucorchis . A lectotype is selected for Gymnadenia albida f. subalpina .     

Exploring generic delimitation within the fern family Thelypteridaceae

Thelypteridaceae is one of the largest families of polypodioid ferns. The generic classification of the family is still controversial because of high levels of convergent or parallel evolution of morphological characters and a lack of molecular phylogenetic studies. In the present study, phylogenetic analyses of three chloroplast regions (rbcL, rps4 and trnL-trnF intergenic spacer region) for 115 taxa, representing 27 recognized segregates in the family, were conducted to explore infrafamilial relationships and gain further understanding of generic boundaries. The phylogenetic reconstructions resolved six distinct clades (Clade I-VI) with strong support. Seven genera: Cyclogramma, Macrothelypteris, Oreopteris, Phegopteris, Pseudophegopteris, Stegnogramma, and Thelypteris are recognized from Clades I, II, IV, and V. In Clade III, Metathelypteris was supported as monophyletic, but the other segregates Amauropelta, Coryphopteris, and Parathelypteris were polyphyletic or paraphyletic, preventing clear recognition of generic boundaries within this clade without additional sampling. Considering great morphological homoplasy within Clade VI, a large genus Cyclosorus is recognized to comprise several small recognized segregates. Within this clade, Pronephrium, and Christella were revealed to be polyphyletic, but several Asian-endemic segregates, such as Glaphyropteridopsis, Mesopteris, and Pseudocyclosorus were strongly supported as monophyletic. Analyses of the evolution of morphological character states on the molecular phylogeny showed extremely high levels of homoplastic evolution for many diagnostic characters.     

江西三清山兰科植物区系分析

江西省三清山兰科植物资源丰富,约21属30种,占江西省兰科植物属种的56.76%、38.46%,占中国兰科植物属种的12.28%、2.41%。区内兰科植物生活型以地生兰为主;分布区式样以温带型为主;区系成分分散,缺乏本地特有成分。与各山地的相似性以及属种分布型比较显示,三清山与5山地在属级水平上相似性系数高,兰科植物区系联系比较紧密,从属分布区类型看,三清山、黄山、天目山和庐山以北温带分布为主,井冈山和武夷山以热带亚洲-热带大洋洲为主;在种级水平上相似性系数较低,种分布区类型均以东亚和中国特有分布为主。按生态型划分,地生兰为主,附生兰为辅,三清山和黄山只有两生态类型,武夷山、天目山、井冈山和庐山生态类型齐全。最后,依据"中国物种红色名录"对各山地珍稀濒危保护物种进行归纳统计。     

Molecular systematics of genus Bulbophyllum (Orchidaceae) in Peninsular Malaysia based on combined nuclear and plastid DNA sequences

Phylogenetic relationships were inferred for representative Bulbophyllum species of 13 sections from subtribe Bulbophyllinae (Epidendroideae, Orchidaceae) in Peninsular Malaysia. The combined data matrix consists of sequences from ITS nuclear gene region and trnL-F, matK, and rbcL plastid gene regions with 3114 characters. Molecular data were analysed using parsimony and Bayesian inference. The results show that several recognized sections are monophyletic. Section Hirtula with paraphyletic status must split up and section Desmosanthes contain misplaced elements. Furthermore, generic status of Cirrhopetalum and Epicrianthes cannot be supported, because they are deeply embedded within the genus Bulbophyllum. Section Desmosanthes is recognized as the closest group to section Cirrhopetalum; therefore, they can be merged in some aspects.     

Incorporating gaps as phylogenetic characters across eight DNA regions: ramifications for North American Psoraleeae (Leguminosae)

The impact of including insertion/deletion events as phylogenetic characters was explored within North American Psoraleeae (Leguminosae). This comprehensive analysis of the impact of gap character incorporation spanned four different indel coding schemes, gaps coded as missing characters, simple binary characters, multi-state characters, and as a 5th state, across two optimality criteria: maximum parsimony and Bayesian Inference. Two nuclear (ITS and Waxy) and six chloroplast (trnS/G, trnL/F, trnK, matK, trnD/T, and rpoB-trnC) DNA regions were sequenced from 43 species of North American Psoraleeae as the foundation of the study. Our results suggest that gaps can provide a substantial percentage of informative characters and can increase phylogenetic resolution and nodal branch support. Phylogenetic signal within indels was higher in chloroplast regions relative to nuclear regions, demonstrating their inclusion as especially important in chloroplast-based phylogenetic studies. Phylogenetic analysis of generic relationships within Psoraleeae is largely congruent with that proposed by Grimes (1990) with a few exceptions. New World species are supported as a monophyletic group. Our analyses suggest that Otholobium may need to be split into two genera and that Psoralidium is polyphyletic and will require movement of Psoralidium tenuiflorum to Pediomelum.     

Phylogenetic position of Apostasia and Neuwiedia (Orchidaceae)

JUDD, W. S., STERN, W. L. & CHEADLE, V. I. 1993. Phylogenetic position of Apostasia and Neuwiedia (Orchidaceae). Cladistic analyses of the phylogenetic relationships of selected orchid taxa were conducted in order to assess the phylogenetic position of Apostasia and Neuwiedia (Orchidaceae: Apostasioideae). These analyses employed newly available anatomical characters, along with several morphological features that had been used in recent phylogenetic analyses of Orchidaceae. Our analyses indicate that Apostasia is more closely related to Neuwiedia than it is to Cypripedioideae. The two genera comprise an apostasiad clade; this clade is the sister-group to a clade including Cypripedioideae and monandrous orchids. The apostasiad clade is diagnosed by the derived features of operculate pollen colpi, Apostasia-type seeds, and vessel members with simple perforation plates. Of these, the presence of simple perforation plates is considered to be the most significant phylogenetically. Therefore, the apostasiads should not be considered ancestral to the remaining orchid groups. Vessel members of the monandrous orchids, as well as the cypripediads, are multiperforate–the hypothesized ancestral state based on the condition in Hypoxidaceae.     

EXISTENCE OF TWO STOMATAL SHAPES IN THE GENUS DENDROBIUM (ORCHIDACEAE) AND ITS SYSTEMATIC SIGNIFICANCE

On the basis of the shape and size of the outer stomatal ledge, 153 species of the genus Dendrobium (Orchidaceae) were divided into three groups, i.e., species group I, species group II, and section Grastidium. Student's t-test and principal components analysis using seven stomatal characters suggest that the first two groups are quite distinct from each other. The values for section Grastidium, however, are scattered and indicative of heterogeneity. Our data suggest a high probability that species groups I and II are monophyletic sister groups. However, section Grastidium, in which stomatal diversification has occurred, may be para- or polyphyletic relative to the genus Dendrobium.     

Evidence for the Polyphyly of Haworthia (Asphodelaceae Subfamily Alooideae; Asparagales) Inferred from Nucleotide Sequences of rbcL, matK, ITS1 and Genomic Fingerprinting with ISSR-PCR

Abstract: Four molecular markers have been studied to examine the phylogenetic position of the South African plant genus Haworthia Duval within the succulent Asphodelaceae. Sequence data of the chloroplast genes mat K and rbc L were compared to the nuclear markers ITS1 and ISSR (Inter Simple Sequence Repeat) analysis. Both lines of molecular data, chloroplast and nuclear DNA, indicate that Haworthia is polyphyletic, forming two distinct clades. Most taxa previously combined as Haworthia subgenus Haworthia branch off early in the alooid chloroplast trees forming a strongly monophyletic group, whereas subgenus Hexangulares forms a polyphyletic assemblage comprising other alooid genera. The nuclear markers ITS1 and ISSR fingerprinting support the two groups as distinctly different, therefore confirming the division seen in chloroplast DNA. The practical implication is that the generic concept of Haworthia may have to be restricted to H. subgenus Haworthia or alternatively, that the groups of Haworthia be treated as infrageneric taxa within a broadened (Linnaean) concept of Aloe.     

Phylogenetic significance of morphological characters in the tropical Hypotrachyna clade of parmelioid lichens (Parmeliaceae, Ascomycota)

Lichen-forming ascomycetes exhibit often complex morphologies of the vegetative thallus that are usually not found in non-lichenized fungi. This includes the thallus organization and appendical structures associated with the main thallus, such as cilia and rhizines. Such morphological characters are widely employed in the taxonomy of parmelioid lichens, especially at generic level. Within parmelioid lichens, several monophyletic groups can be distinguished, the Hypotrachyna clade being one of them, which includes mostly tropical taxa. In this first molecular study focused specifically on the Hypotrachyna clade, we used maximum parsimony and Bayesian analyses of a combined data set of nuclear ITS and mitochondrial SSU rDNA sequences to (1) test the monophyly of genera presently accepted within the clade and (2) evaluate the phylogenetic value of the morphological characters used to circumscribe genera in parmelioid lichens. Out of the 89 mtSSU and 88 nuITS sequences included in the present study, 121 sequences were newly obtained. Our results show that the taxa within the clade fall into two major groups and that the genus Hypotrachyna is polyphyletic. Everniastrum and Parmelinopsis are nested within Hypotrachyna sensu stricto, the latter being also polyphyletic. Bulbothrix is paraphyletic with Parmelinella nested within and is basal to the second major Hypotrachyna clade. Monophylies of Bulbothrix and Hypotrachyna are significantly rejected. The phylogenetic analysis demonstrates that morphological characters currently used to circumscribe genera in parmelioid lichens, such as cortical anatomy, lobe configuration, cilia, and rhizines have been overestimated and have only minor value in identifying monophyletic groups.     

POLLEN MORPHOLOGY OF THE CHLORAEINAE (ORCHIDACEAE: DIURIDEAE) AND RELATED SUBTRIBES

Pollen organization and morphology of the South American Chloraeinae (Orchidaceae) was examined by scanning electron microscopy and compared with that of the remainder of the otherwise Australasian Diurideae. All five genera of the Chloraeinae, Bipinnula, Chloraea, Codonorchis, Gavilea, and Geoblasta, and at least one genus from each of the other subtribes were sampled. The Australasian Diurideae are diverse in pollen organization and morphology. The two genera of the Acianthinae, Corybas and Acianthus, have very different pollen and their classification is questioned. Monad pollen organization of Pterostylis (Pterostylidinae) is reinterpreted as primitive and not secondarily derived. Pollen of the Chloraeinae is uniform in exine morphology and organization. Most species sampled have reticulate pollen which tends to be foveolate distally. The basic pollen unit of all Chloraeinae is the tetrad, except Codonorchis which possesses monads. Pollen morphology and organization of the Chloraeinae is most similar to the Caladeniinae, which supports the contention that the Chloraeinae including Codonorchis should be retained in the Diurideae.     

Phylogeny of the plant bug subfamily Mirinae (Hemiptera: Heteroptera: Cimicomorpha: Miridae) based on total evidence analysis

The first comprehensive phylogenetic analyses of the most diverse subfamily of plant bugs, Mirinae, is presented in this study, for 110 representative taxa based on total evidence analysis. A total of 85 morphological characters and 3898 bp of mitochondrial (16S, COI) and nuclear (18S, 28S) sequences were analysed for each partitioned and combined dataset based on parsimony, maximum likelihood and Bayesian inference. Major results obtained in this study include monophyly of the tribe Mecistoscelini. The largest tribe, Mirini, was recovered as polyphyletic, and Stenodemini was recovered as paraphyletic. The clade of Stenodemini + Mecistoscelini is the sister group of the remaining Mirinae. The monophyly of two complexes composed of superficially similar genera were tested; the Lygus complex was recovered as nonmonophyletic, and the Adelphocoris–Creontiades–Megacoelum complex was confirmed to be monophyletic. The generic relationships of the main clades within each tribe based on the phylogeny, as well as their supported morphological characters, are discussed.     

分支系统学当前的理论和方法概述及华东地区山胡椒属十二个种的分支系统学研究

本文概述了当前分支系统学研究中涉及的主要理论和方法,包括性状的选取、性状状态和极性的确定、数据矩阵的分析计算、结果分支图的处理、分支图可靠性的评价及分支图的应用。本文同时以华东地区樟科山胡椒属Linderal2个种的分支系统学研究为例,讨论了用形态性状进行分支系统学研究中可能遇到的问题,也揭示了一些分支系统学与传统的系统学在应用性状推导进化关系上的不同点。对这12个种的分支系统学研究得出了一些不同于传统系统学方法所推测的山胡椒属内的系统发育关系,如分支系统学研究显示山胡椒组和球果组很近缘。在严格一致性分支图上,杯托组的黑壳楠和江浙山胡椒分别位于最原始和最进化的分支,表明这个组是复系类群。分支图也显示山胡椒组可能是复系类群。     

Phylogenetic relationships in the Marcetia alliance (Melastomeae,Melastomataceae) and implications for generic circumscription

The Marcetia alliance of Melastomataceae is an exclusively Neotropical group that includes at least 12 genera of mostly herbs and subshrubs, occurring in the cerrado of central Brazil and savannas of the Amazon region and Guayana highlands. This study aimed to test the monophyly of genera in the Marcetia alliance, evaluate their phylogenetic relationships and generic boundaries, and investigate morphological characters as potential synapomorphies for delimiting clades or genera. We used nuclear (ITS, ETS) and plastid (accD‐psaI, atpH‐atpF, trnS‐trnG) DNA sequences of 107 terminals in 12 genera from the alliance. Aciotis, Fritzschia, Marcetia and Siphanthera were shown to be monophyletic and supported by molecular and morphological characters. Other genera with variable morphology and wider distributions, such as Acisanthera, Comolia, Ernestia and Macairea, were recovered as paraphyletic or polyphyletic. Most morphological characters analysed were found to be homoplastic, but when combined they are potentially useful for the diagnosis of genera and infrageneric groups. This study represents a major step in understanding internal relationships and provides the basis for a revision of the generic classification in the Marcetia alliance.     

A Review of Current Theories and Methods in Cladistics and a Cladistic Study of Twelve Lindera Species in Eastern China

Cladistics has become a widely used method for phylogenetic reconstruction．Because of rapid improvement Of cladistic theories and methodologies,and application of new data,especially,molecular data,it is becoming realistic to reconstruct phylogenies of organisms,and to establish natural classifications based on these phylogenies．This paper reviews some current cladistic theories and methods in a practical way,such as choosing characters,defining character states,polarizing characters,analyzing data matrices, calculating consensus cladograms,choosing among multiple equally most parsimonious cladograms,estimating reliability of cladograms,and applying cladograms to classification, character evolution,and biogeography． Based on 36 morphological characters．a parsimony analysis of 12 species representing six sections in subgenus Lindera and an outgroup species from subgenus lteodaphne of the genus Lindera(Lauraceae)was conducted．The results suggest a close relationship between section Lindera and section Sphaerocarpae,which is different from the previous phylogenetic hypothesis within the genus．In the strict consensus cladogram,two species,L．megaphylla and L.chienii,from section Cupuliformes are in the most primitive and the most advanced clades respectively,indicating that the section is polyphyletic．The cladogram also suggests that section Lindera be a polyphyletic group．     

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.