Floral ontogeny and systematic position of the Didiereaceae

Floral ontogenetical data from all four genera of the Didiereaceae (s.str.) are presented for the first time. All Didiereaceae s.str. are dioecious, having unisexual flowers with organ rudiments of the opposite sex. Two median bracts followed by a tetramerous perianth (two alternating dimerous ``whorls'), a slightly complex androecium with 6–12 stamens in a single row (on a common ring primordium), four of which mostly alternating with the perianth members, and one basal ovule connecting three free septa at their very base are flower characters in Didiereaceae, supporting phylogenetic analyses based on nucleotide sequence data. Closest relatives are the (formerly) portulacaceous genera Portulacaria (5 stamens alternating with the perianth), Ceraria (5 stamens alternating with the perianth), and Calyptrotheca (many stamens), all with pentamerous perianths, from which the tetramerous perianth in Didiereaceae can be derived. Applequist and Wallace (2003) included these three genera in an expanded family Didiereaceae (with three subfamilies).     

Phylogeny of Rhododendron section Vireya (Ericaceae) based on two non-coding regions of cpDNA

Section Vireya (Blume) Copel.f. is one of the most morphologically diverse groups of the genus Rhododendron. Vireyas have a unique distribution for the genus, being predominantly found throughout the Malesian Archipelago. The alpha taxonomy of section Vireya is relatively well understood and taxa are easily distinguished from other rhododendrons by their general appearance. Defining characteristics of the section the possession of seeds with tailed appendages at both ends, the twisting of capsule valves after opening, placentas that separate as thread-like structures from the central axis as the capsule opens are all subject to exceptions. Phylogenetic analyses of two cpDNA regions, psbA-trnH and trnT-trnL intergenic spacers are reported. The results of each analysis were generally congruent, with clades relating strongly to geographic areas. Section Vireya is monophyletic with the inclusion of at least one species of section Rhododendron. Only two of the seven subsections currently circumscribed are monophyletic: Malayovireya Sleumer and Siphonovireya Sleumer. ``Euvireya', all subsections excluding the paraphyletic subsection Pseudovireya, is monophyletic and includes two major clades, one restricted to eastern Malesia and the other to the western and middle Malesia.     

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.     

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 and evolution of the Macaronesian members of the genus Aichryson (Crassulaceae) inferred from nuclear and chloroplast sequence data

Aichryson is a genus of annual or perennial herbs, comprising approximately 13 species. The genus is nearly endemic to Macaronesia, with the center of diversity on the Canary Islands. Previous studies indicate that Aichryson is monophyletic and sister to a clade comprising two other genera, Monanthes and Aeonium. However, phylogenetic relationships within the genus have yet to be investigated. Phylogenetic relationships were estimated for Aichryson using DNA sequence data from both the nuclear and chloroplast genome. Parsimony analyses were conducted using separate nuclear and chloroplast data sets, as well as a combined data set. These combined analyses provide a well-resolved topology that is used to investigate patterns of evolution within the genus. For example, although typically herbaceous in habit, two members display a woody growth form. Our analyses indicate that woodiness is a derived feature in Aichryson that has arisen once. Furthermore, the data presented suggest that the Aichryson pachycaulon group, a group of five subspecies, are in fact not monophyletic and that a reexamination of classification is necessary. The present study indicates that the biogeographical patterns exhibited by Aichryson appear to be rare, occurring in only one other known genus.The authors would like to thank Susana Fontinha of the Madeiran Botanical Garden for plant material of Madeiran Aichryson; Drs. D. Crawford and J. Archibald, as well as two anonymous reviewers for helpful comments; Eastern Illinois Undergraduate Honors Research Fund, and University of Kansas Plant Biology Research Award. Additional financial support for this work was provided by the Department of Ecology and Evolutionary Biology and the Museum of Natural History and Biodiversity Research Center, University of Kansas and a Kansas NSF EPSCoR First Award (NSF 32171) to MEM.     

Phylogeny ofTyphonium (Araceae) inferred from restriction fragment analysis of chloroplast DNA

The interrelationship of the ten species of the genusTyphonium and related genera in subtribe Arinae of the Araceae was inferred by chloroplast DNA restriction fragment analysis. A total of 42 site mutations were observed and 26 site mutations were shared by two or more species. A majority rule consensus tree was made by performing 100 bootstrap replicates using Wagner Parsimony. Two groups ofTyphonium were recognized significantly as monophyletic groups, i.e. 1)Typhonium larsenii andT. kunmingense, and 2)T. trilobatum, T. blumei andT. flagelliforme.     

Molecular analyses suggest a need for a significant rearrangement of Rutaceae subfamilies and a minor reassessment of species relationships withinFlindersia

DNA sequencing has been used to construct two molecular phylogenies at the intrafamily and intrageneric level within the Rutaceae. Analysis oftrnL-trnF sequence data for five Rutaceae subfamilies has shown that there is no molecular support for the current subfamily classifications within the Rutaceae. The Dictyolomatoideae and Spathelioideae belong to a clade separate from the clades containing the remaining Rutaceae subfamilies. Rutoideae and Citroideae do not form discrete clades which suggests a reassessment of the subfamily classification is necessary, particularly asRuta falls within the majority Citroideae clade. Flindersioideae forms a clade within the Rutaceae and does not form a separate family or form a clade with Meliaceae.Sequencing of 17Flindersia species produces a similar phylogeny to that proposed by other authors using morphological methods with two exceptions. The molecular phylogeny indicatesF. amboinensis is associated withF. fournieri andF. laevicarpa and, in addition,F. oppositifolia andF. pimenteliana were found to be genetically identical.     

Molecular phylogeny and biogeography of the bipolar Euphrasia (Orobanchaceae): recent radiations in an old genus

Euphrasia includes perennial or annual green parasitic plants, and has a disjunct bipolar distribution except for one transtropical connection across the high mountains of Oceania. The disjunction is coupled with strikingly contrasting patterns of morphological diversity between the southern and northern hemispheres, making it an exciting model to study processes of evolutionary diversification which shaped present floras. We inferred the relationships among 51 species representing 14 of the 15 sections of the genus based on nrDNA ITS and cpDNA trnL intron, trnL-trnF and atpB-rbcL intergenic spacers. Maximum parsimony and Bayesian inference support monophyly of the genus and of several intrageneric groups characterized by morphology, ploidy level, and geographic range. Molecular phylogenetic dating using Bayesian “relaxed” clock methods suggests that the earliest Euphrasia radiations occurred minimum 11–8 Mya with bipolarity being achieved 7–5 Mya. Biogeographic analyses using explicit model-based approach inferred Eurasia as an ancestral area for the genus. The most parsimonious reconstruction found by a dispersal-vicariance analysis requires 17 dispersals to account for the current biogeographic pattern and supports Eurasian origin for Euphrasia. Both long-distance dispersal and across land vicariance can be invoked to explain the diversification in the genus, which experienced rapid radiations driven by new ecological opportunities of the late Pliocene and Pleistocene but also retained a set of local endemic or relict species of an earlier origin.     

Hybrid status of Tibouchina urvilleana Cogn. revealed by ITS sequences of nuclear ribosomal DNA

Tibouchina urvilleana Cogn. is native to southern Brazil and currently cultivated as an important ornamental shrub in frost free areas around the world. Its rapid vegetative growth and sterility suggests that it might be of hybrid origin. In this study, Internal Transcribed Spacer (ITS) of nuclear ribosomal DNA and chloroplast trnL-trnF spacer from T. urvilleana and three other congeneric species were sequenced to test its hybrid status. Cloning sequencing revealed two distinct types of ITS sequences from T. urvilleana, with one type almost identical with Tibouchina aspera. Genetic distance between the two types was much larger than the average interspecific genetic distances calculated from other Tibouchina species. Sequencing of chloroplast trnL-trnF spacer showed that T. urvilleana has identical sequence with T. aspera, but differed from other congeneric species by one nucleotide substitution and two indels. Molecular data demonstrated clearly that T. urvilleana indeed was a hybrid, with T. aspera or closely related species acting as the maternal parent.     

Phylogenetic relationships in the genusStylosanthes (Leguminosae) based upon chloroplast DNA variation

A detailed analysis of chloroplast DNA restriction fragment length variation was undertaken to reconstruct the maternal phylogeny of 18 taxa from both sections of the papilionoid tropical forage legume genusStylosanthes. Data were analysed by means of the computer program PAUP, using an heuristic search with Wagner parsimony. The resulting cladogram dividedStylosanthes into four separate clades, which comprised: (i) theS. guianensis complex and related species (i.e.S. gracilis, S. grandifolia andS. montevidensis); (ii)S. hispida, tetraploidS. hamata s. l.,S. sympodialis, S. humilis, S. leiocarpa, S. angustifolia and certain accesions ofS. scabra; (iii)S. calcicola, S. viscosa, diploidS. hamata s. str., andS. fruticosa, plus accessions ofS. scabra, S. capitata and one accession ofS. grandifolia; and (iv)S. macrocephala and other accessions ofS. capitata not included within clade 3. Results are generally congruent with previously established interspecific relationships and, moreover, enabled identification of putative maternal progenitors for four tetraploid taxa:S. humilis was identified as a likely maternal parent of bothS. sympodialis andS. hamata s. l.,S. viscosa as a maternal parent ofS. scabra, andS. macrocephala as a maternal parent ofS. capitata.     

Phylogeny of gymnosperms inferred fromrbcL gene sequences

Partial nucleotide sequences of the large subunit of ribulose-1,5-bisphosphate carboxylase (rubisco) gene (1333 base pairs: about 90% of the gene) from several seed plants were determined. Phylogenetic trees based on amino acid sequences were inferred by using the neighbor joining and maximum likelihood methods. The results indicate (1) monophyly of gnetum group (Ephedra, Gnetum, Welwitschia), (2) monophyly of extant gymnosperms containing gnetum group, which contradicts the results of morphological data.     

Extensive length variation in the cpDNA trnT-trnF region of hemiparasitic Pedicularis and its phylogenetic implications

The cpDNA trnT-trnF region, a molecular marker widely used in the phylogenetic reconstruction at lower taxonomic levels, is relatively conserved in size and structure. In this region single length variation over 100 bp is much less common than small deletion for congeneric species of angiosperms. Here we examined evolutionary patterns of the trnT-trnF region in 43 species of Pedicularis, a species-rich genus with adaptive radiation. Four independent large deletions, varying from 203 to 297 bp in length, were detected from nine species of the genus, which might result from slipped-strand mispairing. These deletions occurred in different locations of the cpDNA region and in different clades of the phylogenetic tree, indicating that the deletion of large cpDNA fragments may be very frequent in the hemiparasitic lineage of the family Orobanchaceae. Parsimony analyses showed that section Cyathophora of Pedicularis, endemic to the Sino-Himalayan region, was a strongly supported monophyletic group. This section could have a recent origin followed by rapid radiation, considering that it is characterized by a large deletion in the trnT-trnF region and a relatively low interspecific sequence divergence.     

Phylogeny of the Calliergonaceae (Bryophyta) based on molecular and morphological data

Phylogeny of the Calliergonaceae is reconstructed based on nuclear and chloroplast sequence data, and morphology. Depending on treatment of insertions and deletions, the total number of informative characters was 194 or 163. The study yielded good support for two major clades, one with Hamatocaulis, Scorpidium, and possibly Hygrohypnum ochraceum (Wils.) Loeske, and one with Calliergon, Loeskypnum, Straminergon, and Warnstorfia. Inclusion of H. ochraceum in the ingroup increased tree length, markedly decreased consistency and retention indices, and decreased support for the structure of the Hamatocaulis-Scorpidium clade, and its position within the family is challenged. When H. ochraceum was excluded, good support is found for the genera Hamatocaulis and Scorpidium. Within the other major subclade the monophyly of a clade with Loeskypnum, Straminergon, and Warnstorfia, of a portion of Calliergon, and of Warnstorfia fluitans plus W. pseudostraminea are well supported.     

The position ofCastrilanthemum Vogt & Oberprieler and the phylogeny of Mediterranean Anthemideae (Compositae) as inferred from nrDNA ITS and cpDNAtrnL/trnF IGS sequence variation

Sequences of the nrDNA internal transcribed spacer (ITS) region and the cpDNAtrnL/trnF intergenic spacer (IGS) region were analysed for 41 Mediterranean and Eurasian representatives of the Anthemideae (Compositae) to ascertain the systematic position of the unispecific genusCastrilanthemum Vogt & Oberprieler and to study the phylogeny of the Anthemideae in the Mediterranean region. Both markers consistently point to the close relationship ofCastrilanthemum with the W Mediterranean generaLeucanthemopsis (Giroux) Heywood andProlongoa Boiss., forming a strongly supported monophyletic group (theLeucanthemopsis-group which also comprises the unispecific genusHymenostemma (Kunze) Willk.). Results also demonstrate that subtribes Achilleinae, Leucantheminae, and Matricariinae sensu Bremer & Humphries are non-monophyletic. Besides results from sequence variation, a marked 5bp-deletion intrnL/trnF IGS divides all these subtribes into more basal subgroups which are related to each other and to the large Eurasian generaTanacetum L. andAnthemis L., and a monophyletic group of closely related and more advanced subgroups which also contain the monophyletic Chrysantheminae sensu Bremer & Humphries. For this second group a W Mediterranean centre of diversification is suggested, however, its sister-group relationships within the basal grade of generic groups remain unclear.     

Phylogeny of the family hydrocharitaceae inferred fromrbcL andmatK gene sequence data

The family Hydrocharitaceae, with 15 genera and ca. 80 species, shows a remarkable morphological diversity which presumably developed as an adaptation to their aquatic habitat. This is particularly true in the case of the many different kinds of pollination mechanisms. To gather more basic information regarding the adaptive evolution of Hydrocharitaceae, we have carried out a phylogenetic analysis based on the sequences of therbcL andmatK. Our resulting neighbor-joining distance tree provides the following insights: (1) none of the previous classification systems were supported by molecular phylogenetic tree; (2) Najas (Najadaceae), which has never been included in Hydrocharitaceae except in Shaffer-Fehre's (1991) system based on seed coat structures, is an ingroup of Hydrocharitaceae; (3) Limnocharitaceae and Alismataceae are sister groups of Hydrocharitaceae; (4) the three marine genera,Halophila, Enhalus andThalassia, are monophyletic; and (5) a peculiar pollination mechanism specific to Hydrocharitaceae (Hydrocharitaceae-epihydrophily), underwent a parallel evolution.     

A phylogenetic study of the palm family (Palmae) based on chloroplast DNA sequences from thetrnL —trnF region

Phylogenies of the palm family based on DNA sequences from thetrnL —trnF region of the chloroplast genome are presented. Although the region is highly conserved in palms and relatively few sites in the aligned data matrix are parsimony informative, a variety of relationships among members of the family are revealed by the analyses, some of which are congruent with the current classification of the palms, and others which are not. However, consensus trees contain high levels of ambiguosity, partly due to the inadequate numbers of informative characters in the dataset. Additional data are required before well resolved palm phylogenies can be generated.     

Phylogeny of the genera Trichophyton using mitochondrial DNA analysis

Diversity of mitochondrial DNA (mtDNA) was investigated in 92 Trichophyton rubrum strains, 2 T. mentagrophytes var. mentagrophytes, 2 T. m. vor. interdigitale, 2 T. m. var. goetzii, 1 T. m. var. erinacei, 2 T. quinckeanum, 2 T. schoenleinii, 1 T. tonsurans, 2 T. verrucosum var. album, 2 T. v. var. discoides, 1 T. violaceum var. violaceum, 1 Arthroderma benhamiae, and 1 A. vanbreuseghemii using endonucleases, Hae III, Msp I, Hind III, Xba I, and Bgl II. Trichophyton species were divided into 7 groups, and a phylogenetic tree was produced based on sequence divergence within mtDNA. The following results were obtained: (1) T. rubrum was divided into 2 groups Type I and Type II, and was suggested to be a complex. (2) A. benhamiae was closely related to T. m. var. erinacei. (3) T. rubrum Type II, T. tonsurans, and A. vanbreuseghemii showed identical restriction profiles, and were suggested to be closely related to each other or identical. (4) T. quinckeanum and T. schoenlenii showed identical restriction profiles, which differed slightly from those of A. vanbreuseghemii. (5) mtDNA analysis was useful in identifying pleomorphic strains.     

TrnL-trnF sequence data imply paraphyly of Aquilaria and Gyrinops (Thymelaeaceae) and provide new perspectives for agarwood identification

The genera Aquilaria and Gyrinops (Thymelaeaceae, Malvales) are well known for the production of agarwood which is a highly wanted forest product of substantial economic value. The taxonomic status of Aquilaria and Gyrinops as separate genera is doubted as they are only distinguished by the number of stamens. We investigated their status by conducting phylogenetic analyses of DNA sequences from the plastid trnL-trnF spacer. Control of international trade of agarwood is currently hampered by the failure of traditional methods such as microscopy to identify samples to species level. We therefore evaluated the potential of molecular identification of agarwood by searching for species- and region-specific plastid DNA polymorphisms. DNA sequences were obtained from 31 Thymelaeaceae accessions encompassing 20 different species in six genera. Aquilaria and Gyrinops appear to be paraphyletic. Success in sequencing wood samples demonstrates that molecular markers provide new perspectives for agarwood identification.