Systematics of Amaryllidaceae based on cladistic analysis of plastid sequence data

Cladistic analyses of plastid DNA sequences rbcL and trnL-F are presented separately and combined for 48 genera of Amaryllidaceae and 29 genera of related asparagalean families. The combined analysis is the most highly resolved of the three and provides good support for the monophyly of Amaryllidaceae and indicates Agapanthaceae as its sister family. Alliaceae are in turn sister to the Amaryllidaceae/Agapanthaceae clade. The origins of the family appear to be western Gondwanaland (Africa), and infrafamilial relationships are resolved along biogeographic lines. Tribe Amaryllideae, primarily South African, is sister to the rest of Amaryllidaceae; this tribe is supported by numerous morphological synapomorphies as well. The remaining two African tribes of the family, Haemantheae and Cyrtantheae, are well supported, but their position relative to the Australasian Calostemmateae and a large clade comprising the Eurasian and American genera, is not yet clear. The Eurasian and American elements of the family are each monophyletic sister clades. Internal resolution of the Eurasian clade only partially supports currently accepted tribal concepts, and few conclusions can be drawn on the relationships of the genera based on these data. A monophyletic Lycorideae (Central and East Asian) is weakly supported. Galanthus and Leucojum (Galantheae pro parte) are supported as sister genera by the bootstrap. The American clade shows a higher degree of internal resolution. Hippeastreae (minus Griffinia and Worsleya) are well supported, and Zephyranthinae are resolved as a distinct subtribe. An Andean clade marked by a chromosome number of 2n = 46 (and derivatives thereof) is resolved with weak support. The plastid DNA phylogenies are discussed in the context of biogeography and character evolution in the family.     

基于rbcL和matK序列探讨马鞭草科部分植物的系统学位置

为探究适用于马鞭草科植物的DNA条形码及该类群的系统分类关系,对豆腐柴(Premna microphylla)的叶绿体基因ycf6-psbM、trnV-atpE、rbcL、trnL-F、psbM-trnD、atpB-rbcL、trnC-ycf6、trnH-psbA、rpl36-infA-rps8和核基因ITS序列进行了PCR扩增和测序,结果表明仅rbcL、trnl-F、trnH-psbA序列的PCR扩增以及测序效果较好,而ITS不能得到明显的扩增条带,ycf6-psbM不能成功测序,其它序列存在有部分双峰或噪值高等问题。根据DNA条形码标准,rbcL序列是所有测试条码中相对最适合的。应用rbcL和matK序列对马鞭草科(Verbenaceae)豆腐柴属、牡荆属(Vitex L.)、马鞭草属(Verbena L.)和大青属(Clerodendrum L.)等4属与唇形科宝盖草属(Lamium L.)、水苏属(Stachys L.)、鼠尾草属(Salvia L.)和香科科属(Teucrium L.)等4属的分类和系统发育关系进行分析,以紫草科Lithospermum multiflorum L.为外群,最大简约法对2个片段的单独和联合矩阵分别构建系统发育树。豆腐柴属和大青属应从马鞭草科划入唇形科,马鞭草属仍归于马鞭草科,而牡荆属的系统学位置还需更多的证据。     

Phylogeny and classification of Ranunculales: Evidence from four molecular loci and morphological data

Previous phylogenetic analyses of Ranunculales, which have mostly been focused on an individual family and were based on molecular data alone, have recovered three main clades within the order. However, support for relationships among these three clades was weak. Earlier hypotheses were often hampered by limited taxon sampling; to date less than one-tenth of the genera in the order have been sampled. In this study, we used a greatly enlarged taxon sampling (105 species, representing 99 genera of all seven families in the order). Our study is, furthermore, the first to employ morphology (65 characters) in combination with sequence data from four genomic regions, including plastid rbcL, matK and trnL-F, and nuclear ribosomal 26S rDNA to reconstruct phylogenetic relationships within Ranunculales. Maximum parsimony and Bayesian inference were performed on the individual and combined data sets. Our analyses concur with those of previous studies, but in most cases provide stronger support and better resolution for relationships among the three main clades retrieved. The first, comprised solely of the monogeneric family Eupteleaceae, is the earliest-diverging lineage. The second clade is composed exclusively of taxa of Papaveraceae, which is sister to the third clade, the core Ranunculales, comprising the other five families of the order. Circaeasteraceae and Lardizabalaceae form a strongly supported clade. Pteridophyllum is supported as sister to Hypecoum, contradicting the viewpoint that the former is the earliest-diverging genus in Papaveraceae. Glaucidium is basalmost in Ranunculaceae. Within this phylogenetic framework, the evolution of selected characters is inferred and diagnostic morphological characters at different taxonomic levels are identified and discussed. Based on both morphological and molecular evidence, a classification outline for Ranunculales is presented, including the proposal of two new subfamilies, Menispermoideae and Tinosporoideae in Menispermaceae and a new tribe, Callianthemeae, for the genus Callianthemum (Ranunculaceae).     

Phylogenetic relationships within the New World subfamily Larreoideae (Zygophyllaceae) confirm polyphyly of the disjunct genus Bulnesia

The Larreoideae subfamily is the major representative of the family Zygophyllaceae in South America, where several of its members are common to dominant in arid regions of the Southern Cone. However, there are currently no phylogenetic analyses of the subfamily that may help to understand its origin and diversification. Additionally, there are taxonomic discrepancies around Bulnesia Gay (1845), one of its more important genera. Accordingly, we performed a phylogenetic analysis combining chloroplast (rbcL and trnL-F) and nuclear (ITS) DNA sequences. Bayesian and Parsimony analyses were performed to highlight the intergeneric relationships within Larreoideae. All genera with the exception of Bulnesia are monophyletic and we propose to redefine Bulnesia, dividing it in two genera. Furthermore, other taxonomic issues of the remaining genera are solved. This study represents the first approximation to clarify the phylogenetic relationships amongst all Larreoideae genera, producing a phylogenetic framework that can be used in future macro-ecological studies.     

Investigation of the Presence of Phenolic Compounds in Monocotyledonous Cell Walls, using UV Fluorescence Microscopy

Harris and Hartley (1976, 1980) demonstrated the presence offerulic acid in cell walls of certain monocotyledons using UVfluorescence microscopy (fluorescing green after treatment withammonium hydroxide solution). The presence or absence of thistype of fluorescence is apparently critical in higher levelsystematics of monocotyledons. In order to evaluate the significanceof this character, cell wall fluorescence was investigated ina range of monocotyledon species, particularly the AustralianXanthorrhoeaceae sensu lato (Bedford et al., 1986), which werenot investigated in earlier studies. This family is widely regardedas polyphyletic and was divided into several families by Dahlgren,Clifford and Yeo (1985). Some of its constituent genera, suchas Dasypogon, Kingia and Calectasia, have been linked with bothcommelinoid and non-commelinoid monocotyledons, and are of obscureaffinity. Some genera of Xanthorrhoeaceae sensu lato (Baxteria,Calectasia, Dasypogon and Kingia) show this type of green cellwall fluorescence and may therefore be more closely linked withthe commelinoid monocotyledons, rather than the Lilianae-Asparagales,as previously placed (Dahlgren et al., 1985).Copyright 1994,1999 Academic Press Asparagales, Dasypogonaceae, fluorescence, Hanguana, monocotyledons, systematics, Xanthorrhoeaceae     

A global plastid phylogeny of the fern genus Asplenium (Aspleniaceae)

The infrageneric relationships and taxonomy of the largest fern genus, Asplenium (Aspleniaceae), have remained poorly understood. Previous studies have focused mainly on specific species complexes involving a few or dozens of species only, or have achieved a large taxon sampling but only one plastid marker was used. In the present study, DNA sequences from six plastid markers (atpB, rbcL, rps4, rps4-trnS, trnL and trnL-F) of 1030 accessions (616 of them newly sequenced here) representing c. 420 species of Asplenium (60% of estimated species diversity), 16 species of Hymenasplenium, three Diplaziopsidaceae, and four Rhachidosoraceae were used to produce the largest genus-level phylogeny yet for ferns. Our major results include: (i) Asplenium as broadly circumscribed is monophyletic based on our inclusion of representatives of 32 of 38 named segregate genera; (ii) 11 major clades in Asplenium are identified, and their relationships are mostly well-resolved and strongly supported; (iii) numerous species, unsampled in previous studies, suggest new relationships and numerous cryptic species and species complexes in Asplenium; and (iv) the accrued molecular evidence provides an essential foundation for further investigations of complex patterns of geographical diversification, speciation and reticulate evolution in this family.     

Phylogenetic position of the southern African members of the tribe Psoraleeae based on molecular and morphological data

The tribe Psoraleeae (Leguminosae subfamily Papilionoideae) comprises 185 species in nine genera that have a nearly worldwide distribution, occurring predominantly in Mediterranean regions. About 60% of the species belong to the genera, Otholobium C.H.Stirt. and Psoralea L., which have a centre of diversity in the Cape Floristic Region of South Africa. Since previous molecular studies have sampled only a few species of the tribe from this region, this study sought to determine the phylogenetic position of the southern African genera and to test whether they are monophyletic. Phylogenetic relationships were reconstructed using DNA sequence data (trnL-F, rpoB-trnC and ITS) and seven morphological characters, which diagnose the two southern African genera. The data were analysed using the parsimony method. There was strong support for the Psoraleeae as a clade, but most of the nodes within the large genera were poorly supported. The southern African species of Psoralea and Otholobium together formed a strongly supported clade. This clade was sister to the genus Hoita Rydb., but without support. However, the Psoralea species were nested within the southern African Otholobium. Additionally, some South American species that are currently recognised as Otholobium were resolved in a clade distinct from the southern African species, making Otholobium polyphyletic. Morphological characters that separate Otholobium and Psoralea are discussed. Finally, the southern African genera as currently circumscribed are not monophyletic. However, further investigations using more informative DNA loci are required to validate this observation. Furthermore, the taxonomic placement of the South American species needs to be reviewed.     

Phylogeny of Cyperaceae Based on DNA Sequence Data: Current Progress and Future Prospects

In the last decade, efforts to reconstruct suprageneric phylogeny of the Cyperaceae have intensified. We present an analysis of 262 taxa representing 93 genera in 15 tribes, sequenced for the plastid rbcL and trnL-F (intron and intergenic spacer). Cyperaceae are monophyletic and resolved into two clades, here recognised as Mapanioideae and Cyperoideae, and the overall topology is similar to results from previous studies. Within Cyperoideae, Trilepideae are sister to rest of taxa whereas Cryptangieae, Bisboeckelerieae and Sclerieae are resolved within Schoeneae. Cladium and Rhynchospora (and Pleurostachys) are resolved into clades sister to the rest of Schoeneae, lending support to the recognition of these taxa in separate tribes. However, we retain these taxa in Schoeneae pending broader sampling of the group. The phylogenetic position of 40 species in 21 genera is presented in this study for the first time, elucidating their position in Abildgaardieae (Trachystylis), Cryptangieae (Didymiandrum, Exochogyne), Cypereae (Androtrichum, Volkiella), Eleocharideae (Chillania), and Schoeneae (Calyptrocarya, Morelotia). More sampling effort (more taxa and the use of more rapidly evolving markers) is needed to resolve relationships in Fuireneae and Schoeneae.     

Paraphyly of Cyrtomium (Dryopteridaceae): evidence from rbcL and trnL-F sequence data

Cyrtomium is an Asiatic genus characterized by anastomosing veins with included veinlets, and comprises about 40 species. We sequenced rbcL and trnL-F sequences of 19 species of Cyrtomium and eight species from related genera in order to elucidate a molecular phylogeny of the genus using maximum-parsimony methods. The phylogenetic trees did not agree with traditional classifications. Cyrtomium was resolved as paraphyletic, and a clade including subseries Balansana of Cyrtomium, Cyrtogonellum, Polystichum subacutidens and Cyrtomidictyum (the BCPC clade) and a second one containing Cyrtomium sensu stricto were monophyletic. The results also implied that: (1) C. uniseriale was synonymous with C. balansae; (2) C. falcatum was likely the female parent of C. devexiscapulae; and (3) based on the rbcL and trnL-F sequence data, C. nephrolepioides and C. grossum were the female parents of C. shingianum and C. chingianum, respectively, although other evidence is needed for the confirmation of this hypothesis.     

Molecular phylogenetics of Ruscaceae sensu lato and related families (Asparagales) based on plastid and nuclear DNA sequences

Background

Previous phylogenetics studies of Asparagales, although extensive and generally well supported, have left several sets of taxa unclearly placed and have not addressed all relationships within certain clades thoroughly (some clades were relatively sparsely sampled). One of the most important of these is sampling within and placement of Nolinoideae (Ruscaceae s.l.) of Asparagaceae sensu Angiosperm Phylogeny Group (APG) III, which subfamily includes taxa previously referred to Convallariaceae, Dracaenaaceae, Eriospermaceae, Nolinaceae and Ruscaceae.

Methods

A phylogenetic analysis of a combined data set for 126 taxa of Ruscaceae s.l. and related groups in Asparagales based on three nuclear and plastid DNA coding genes, 18S rDNA (1796 bp), rbcL (1338 bp) and matK (1668 bp), representing a total of approx. 4·8 kb is presented. Parsimony and Bayesian inference analyses were conducted to elucidate relationships of Ruscaceae s.l. and related groups, and parsimony bootstrap analysis was performed to assess support of clades.

Key Results

The combination of the three genes results in the most highly resolved and strongly supported topology yet obtained for Asparagales including Ruscaceae s.l. Asparagales relationships are nearly congruent with previous combined gene analyses, which were reflected in the APG III classification. Parsimony and Bayesian analyses yield identical relationships except for some slight variation among the core asparagoid families, which nevertheless form a strongly supported group in both types of analyses. In core asparagoids, five major clades are identified: (1) Alliaceae s.l. (sensu APG III, Amarylidaceae–Agapanthaceae–Alliaceae); (2) Asparagaceae–Laxmanniaceae–Ruscaceae s.l.; (3) Themidaceae; (4) Hyacinthaceae; (5) Anemarrhenaceae–Behniaceae–Herreriaceae–Agavaceae (clades 2–5 collectively Asparagaceae s.l. sensu APG III). The position of Aphyllanthes is labile, but it is sister to Themidaceae in the combined maximum-parsimony tree and sister to Anemarrhenaceae in the Bayesian analysis. The highly supported clade of Xanthorrhoeaceae s.l. (sensu APG III, including Asphodelaceae and Hemerocallidaceae) is sister to the core asparagoids. Ruscaceae s.l. are a well-supported group. Asparagaceae s.s. are sister to Ruscaceae s.l., even though the clade of the two families is weakly supported; Laxmanniaceae are strongly supported as sister to Ruscaceae s.l. and Asparagaceae. Ruscaceae s.l. include six principal clades that often reflect previously named groups: (1) tribe Polygonateae (excluding Disporopsis); (2) tribe Ophiopogoneae; (3) tribe Convallarieae (excluding Theropogon); (4) Ruscaceae s.s. + Dracaenaceae + Theropogon + Disporopsis + Comospermum; (5) Nolinaceae, (6) Eriospermum.

Conclusions

The analyses here were largely conducted with new data collected for the same loci as in previous studies, but in this case from different species/DNA accessions and greater sampling in many cases than in previously published analyses; nonetheless, the results largely mirror those of previously conducted studies. This demonstrates the robustness of these results and answers questions often raised about reproducibility of DNA results, given the often sparse sampling of taxa in some studies, particularly the earliest ones. The results also provide a clear set of patterns on which to base a new classification of the subfamilies of Asparagaceae s.l., particularly Ruscaceae s.l. (= Nolinoideae of Asparagaceae s.l.), and examine other putatively important characters of Asparagales.     

Phylogenetic relationships among genera of Massonieae (Hyacinthaceae) inferred from plastid DNA and seed morphology

The tribe Massonieae Baker (Hyacinthaceae-Hyacinthoideae) presently consists of about 19 genera and 230 species distributed from Africa (south of the Sahara) to Madagascar and India. Based on atpB and trnL-F DNA sequences the tribe is monophyletic only when the genus Pseudoprospero is excluded from Massonieae. In most trnL-F trees, this genus occupies a basal position within subfamily Hyacinthoideae and is sister to the rest of the subfamily. Molecular data suggest that the remaining genera of Massonieae do not share common ancestry with the Eurasian/North-African tribe Hyacintheae Dumort. (Scilla, Hyacinthus and allies), and thus a narrow concept of the essentially Eurasian genus Scilla is supported. Members of well-supported clades in Massonieae usually show similarities in seed characteristics as determined by scanning electron microscopy. Phylogenetic position and seed morphology indicate that Massonia angustifolia and M. zeyheri do not belong to the genus Massonia but fall into a clade together with Daubenya, Androsiphon and Amphisiphon. The genus Whiteheadia appears paraphyletic in the 50% majority rule trnL-F tree and occupies a basal position next to Massonia. However, in the strict consensus tree neither monophyly nor polyphyly can be excluded for this genus. Seed appendages are documented for members of the genera Ledebouria and Lachenalia. Within the genera of Massonieae there is a tendency towards bending of the seed axis. This phenomenon is most obvious within the genus Lachenalia. Delimitation of genera based on seed morphology largely agrees with the results of molecular studies. Correlation between number, size and color of seeds, geographical distribution and phylogenetic position of the genera are discussed. Electronic Publication     

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.     

Taxonomic Study of Korean <Emphasis Type="Italic">Scirpus</Emphasis> L. s.l. (Cyperaceae) II: Pattern of Phenotypic Evolution Inferred from Molecular Phylogeny

Scirpus L. s.l. is well known as one of the polyphyletic groups in Cyperaceae. Recent molecular phylogenetic studies clearly suggested that Scirpus s.l. should be separated into several independent genera. In this study, we intend to present the morphological variations and patterns of phenotypic evolution based on molecular phylogeny of Korean Scirpus s.l. Five genera, including 21 taxa from Korean Scirpus s.l., were examined: three species of Bolboschoenus, three species of Schoenoplectus, eight species of Schoenoplectiella including one hybrid, five species of Scirpus, and two species of Trichophorum. For morphological analyses, 23 and 48 characters were selected from vegetative and reproductive organs, respectively. Molecular phylogeny was inferred from a nuclear ribosomal internal transcribed spacer, the chloroplast rbcL gene, and the chloroplast trnL-F region. Distinct characteristics and quantitative variation was presented for identification of the five genera and their species. A pronounced pattern of morphological character change was reduction, although many other character states seem to be homoplastic. We suggest that the reduction of phenotypic characteristics has been expressed in terms of condensation of internodes, reduction of leaf blade, and simplification of inflorescence among five genera of Korean Scirpus s.l.     

Phylogeny of Caragana (Fabaceae) based on DNA sequence data from rbcL, trnS–trnG, and ITS

Phylogenetic relationships of 48 species of Caragana (Fabaceae: tribe Hedysareae) and one representative each of Astragalus, Calophaca, Halimodendron, and Hedysarum are estimated from DNA sequences of the rbcL gene, trnS–trnG intron and spacer, and ITS region. At least one representative of all five sections and 12 series within Caragana are included. Analyses yielded strongly supported clades corresponding to sections Caragana, Bracteolatae, and Frutescentes. The species of section Jubatae are distributed among three strongly supported clades, i.e., one with the species of section Bracteolatae, another with two species of section Spinosae, and a third as sister to section Frutescentes. All but the last of these six clades are corroborated by at least one unambiguously traced morphological character. The placement of the other four species of section Spinosae are not well supported and lack unambiguous morphological synapomorphies, and the samples of Calophaca and Halimodendron nest within Caragana with weak support.     

Phylogenetics of <Emphasis Type="Italic">Cucumis</Emphasis> (Cucurbitaceae): Cucumber (<Emphasis Type="Italic">C. sativus</Emphasis>) belongs in an Asian/Australian clade far from melon (<Emphasis Type="Italic">C. melo</Emphasis>)

Background  

Melon, Cucumis melo, and cucumber, C. sativus, are among the most widely cultivated crops worldwide. Cucumis, as traditionally conceived, is geographically centered in Africa, with C. sativus and C. hystrix thought to be the only Cucumis species in Asia. This taxonomy forms the basis for all ongoing Cucumis breeding and genomics efforts. We tested relationships among Cucumis and related genera based on DNA sequences from chloroplast gene, intron, and spacer regions (rbcL, matK, rpl20-rps12, trnL, and trnL-F), adding nuclear internal transcribed spacer sequences to resolve relationships within Cucumis.     

Molecular characterization of endangered endemic plant Aloe pseudorubroviolacea using chloroplast matK and plastid rbcL gene

An endangered and rare species Aloe pseudorubroviolacea from the plant family Asphodelaceae which is presently recorded as endangered in Saudi Arabia collected from Al-Baha region of Saudi Arabia its GPS Latitude and Longitude coordinates 19.8345, 41.5481. The chloroplast matK and rbcL gene was considered in this study based on molecular identification the size is about 571 and 664 bp respectively. From the sequence analysis the gene matK and rbcL confirm that this species is very much closely related with A. rubroviolacea and also inter related with the species Astroloba rubriflora, Chrysopogon gryllus, Chortolirion angolense shows about 98.7% sequence homology. The partial matK and rbcL gene sequence discriminate Aloe pseudorubroviolacea from the closely related plant species, A. rubroviolacea. The gene sequence of rbcL discriminates the species from Chrysopogon gryllus and Chortolirion angolense, demonstrates the nucleotide variations in 3 different sites (623C/T; 653C/T; 700C/A). This study showed that matK and rbcL sequence region of chloroplast gene used to authenticate the samples of A. pseudorubroviolacea and which provide to help in correct identification and conservation process of this medicinally valuable endangered plant species.