Phylogeny and classification ofFumariaceae, with emphasis onDicentra s. l., based on the plastid generps16 intron

The phylogeny ofFumariaceae, as inferred fromrps16 intron sequences, is compared with morphological data, and nrDNA-ITS. The different data sets are largely congruent and indicate that (1)Dicentra and the tribeCorydaleae as hitherto circumscribed are polyphyletic, (2)Lamprocapnos (=Dicentra spectabilis) is sister group to the rest of subfam.Fumarioideae, (3)Ehrendorferia, gen. nov. (=Dicentra chrysantha andD. ochroleuca) is basal in the latter group, (4) the morphologically aberrantIchtyoselmis, gen. nov. (=Dicentra macrantha) groups withDicentra s. str., (5) the genusCysticapnos should be included in the tribeFumarieae, (6)Dactylicapnos (=Dicentra subg.Dactylicapnos) is sister group toCorydalis, (7) the genusCorydalis is monophyletic, and consists of three subgenera:Chremnocapnos, stat. nov.,Sophorocapnos, stat. nov., andCorydalis. The following new combinations are validated:Ehrendorferia chrysantha, E. ochroleuca, Ichtyoselmis macrantha, andLamprocapnos spectabilis. Dedicated to emer. Univ.-Prof. DrFriedrich Ehrendorfer on the occasion of his 70th birthday     

Phylogenetic analysis of cpDNA restriction sites andrps16 intron sequences reveals relationships among Apiaceae tribes Caucalideae, Scandiceae and related taxa

Evolutionary relationships among members of Apiaceae (Umbelliferae) tribe Caucalideae Spreng. and related taxa were inferred from maximum parsimony analyses of chloroplast DNA restriction sites andrps16 intron sequences and the results compared to an existing phylogeny for the group based on nuclear ribosomal DNA internal transcribed spacer sequences. While these three data sets were not similar in size or composition, the relationships among the shared taxa, with few exceptions, were concordant. Three major lineages are recognized, coinciding with the previously delimited Scandiceae subtribes Daucinae Dumort. (Agrocharis, Ammodaucus, Cuminum, Daucus, Orlaya, Pachyctenium, Pseudorlaya), Torilidinae Dumort. (Astrodaucus, Caucalis, Glochidotheca, Lisaea, Szovitsia, Torilis, Turgenia, Yabea), and Scandicinae Tausch (Anthriscus, Kozlovia, Myrrhis, Osmorhiza, Scandix). Included in Daucinae is representation from tribe Laserpitieae (Laser, Laserpitium, Melanoselinum, Monizia, Polylophium). Daucinae and Torilidinae arise as sister taxa in the chloroplast DNA-based phylogenies, whereas in the ITS trees relationships among the three major lineages are unresolved. Unexpectedly, three species ofFerula ally with Daucinae and Torilidinae. The position ofArtedia is equivocal, occurring either sister to Daucinae in the ITS trees, within Torilidinae in the intron trees, or sister to Torilidinae upon analysis of combined ITS and intron data.Chaetosciadium trichospermum emerges withinTorilis, and is recognized asTorilis trichosperma (L.) Spreng.     

Comparisons of phylogenetic hypotheses among different data sets in dwarf dandelions (Krigia,Asteraceae): Additional information from internal transcribed spacer sequences of nuclear ribosomal DNA

The internal transcribed spacer (ITS) region of the 18 S–25 S nuclear ribosomal DNA repeat was sequenced from 19 populations of the tribeLactuceae, including all species of dwarf dandelion (Krigia) and five outgroup genera. The incidence of length changes and base substitutions was at least two times higher for ITS 1 than ITS 2. Interspecific sequence divergence withinKrigia averaged 9.62% (1.61%–15.19%) and 4.26% (0%–6.64%) in ITS 1 and ITS 2, respectively. Intergeneric sequence divergence ranged from 15.6% to 44.5% in ITS 1 and from 8.0% to 28.6% in ITS 2. High sequence divergence and homoplasy among genera of tribeLactuceae suggest that the phylogenetic utility of ITS sequence data is limited to interspecific studies or comparisons among closely related genera. Trees generated from ITS sequences are essentially identical to those from restriction site comparisons of the entire nuclear ribosomal (nr) DNA region. The degree of tree resolution differed depending on how gaps were treated in phylogenetic analyses. The ITS trees were congruent with the chloroplast DNA and morphological phylogenies in three major ways: 1) the sister group relationship betweenKrigia andPyrrhopappus; 2) the recognition of two monophyletic sections,Krigia andCymbia, in genusKrigia; and 3) the monophyly of theK. occidentalis-K. cespitosa clade in sect.Cymbia. However, the two nrDNA-based trees are not congruent with morphology/chloroplast DNA-based trees for the interspecific relationships in sect.Krigia. An average of 22.5% incongruence was observed among fourKrigia data sets. The relatively high degree of incongruence among data sets is due primarily to conflict between trees based on nrDNA and morphological/cpDNA data. The incongruence is probably due to the concerted evolution of nrDNA repeating units. The results fromKrigia and theLactuceae suggest that nrDNA data may have limited utility in phylogenetic studies of plants, especially in groups which exhibit high levels of sequence divergence. Our combined phylogenetic analysis as a total evidence shows the least conflict to each of the individual data sets.     

Phylogenetic analysis of the subfamily Alpinioideae (Zingiberaceae), particularly Etlingera Giseke, based on nuclear and plastid DNA

Parsimony analyses based on DNA sequence data of the plastid group II intron rps16 and the internal transcribed spacer (ITS) were performed in order to examine the relationship of the pantropical subfamily Alpinioideae in Zingiberaceae (Zingiberales). Special emphasis was given to the large genus Etlingera placed in the tribe Alpinieae. A total of 50 taxa were included in the analysis. The strict consensus tree obtained by combining all data (280 parsimony informative characters of ITS, rps16, and coded indels) is well resolved with strongly supported clades. The subfamily Alpinioideae (excluding Pommereschea and Rhynchanthus) is strongly supported as monophyletic. The basal part of the tree is unresolved but a clade containing the derived genera of Alpinieae (Geocharis, Amomum, Hornstedtia, and Etlingera) is strongly supported. The establishment of Etlingera as the inclusive name for Achasma, Geanthus, and Nicolaia is also strongly supported: Etlingera is monophyletic with Hornstedtia as sister group.     

Phylogenetic relationships betweenVicia faba (Fabaceae) and related species inferred from chloroplasttrnL sequences

The chloroplasttrnL intron from 46 differentVicia accessions, representing five of the nine sections of the genusVicia subg.Vicia sensuMaxted (1991a) were amplified by the Polymerase Chain Reaction (PCR) using oligonucleotide primers homologous to conserved regions intrnL. The products fell into two distinct groups; those of approximately 250 nt and those of around 450 nt in length. Of these, products from 17 differentVicia species were cloned and their nucleotide sequences determined. Multiple alignments were assembled and phylogenetic trees constructed by the weighted least-squares distance method. ALathyrus latifolius trnL intron sequence was used as an outgroup. The resulting trees clearly group and separate the sectt.Narbonensis, Bithynica andFaba species but were less able to distinguish species from sectt.Hypechusa andPeregrinae. Based on these sequence data,V. faba appears to be more distant from sect.Narbonensis than sectt.Hypechusa andPeregrinae. The results are in general agreement with a recent treatment ofVicia subg.Vicia (Maxted 1993) and lend further support to placingV. faba in the monospecific sect.Faba.     

Serologische Untersuchungen zur Gliederung derBrassicaceae

The serological investigations support the opinion ofJanchen (1942) to combine the generaBunias, Isatis, andSisymbrium in the tribeSisymbrieae; Cheiranthus, Erysimum, andMatthiola in the tribeHesperideae; andBrassica, Crambe, Sinapis, andSuccowia in the tribeBrassiceae. They further underline the central position of theSisymbrieae and the isolated position of theHeliophileae. In accordance withEigner (1973) theBrassiceae are placed closer to theSisymbrieae than inJanchen; the same holds for thePringleeae. No serological justification could be found to uniteArabis andBarbarea in the tribeArabideae, andAlyssum andLunaria in theAlysseae. From the antigen-systems used among the representatives ofJanchen's Lepidieae the generaLepidium andNeslia show remarkable correspondence both toCamelina andThlaspi, but not toCochlearia which appears distant fromCamelina andThlaspi also.

Teil 1/Part 1.     

Molecular phylogeny of Armillaria from the Patagonian Andes

A number of species in the plant pathogen genus Armillaria are known from South America where they cause root rot disease on a wide variety of hosts. Knowledge pertaining to phylogenetic relationships of these species with those of other Armillaria species is almost non-existent. In addition, very few cultures representing these species are available, making DNA-based phylogenetic analyses impossible. The aim of this study was to characterise a collection of Armillaria isolates from the Patagonian Andes using DNA sequences and to determine their phylogenetic relationships with other Armillaria species. DNA sequences were obtained from the internal transcribed regions (ITS1, 5.8S and ITS4) and ribosomal large subunit (LSU) gene and used in phylogenetic analyses. Phylogenetic trees generated from the sequences separated the Armillaria isolates into four lineages. Lineages I and II represented A. novae-zelandiae and A. luteobubalina, respectively. Isolates belonging to A. novae-zelandiae from Malaysia, New Zealand, Australia and South America showed considerable intra-clade sub-structure. Lineages III and IV are probably distinct species and are most closely related to A. hinnulea and an unnamed species isolated from New Zealand and Kenya. This is the first comprehensive study of the phylogenetic relationships of Armillaria species from Patagonia and it provides a foundation for future research in this region.     

The phylogenetic utility of chloroplast and nuclear DNA markers and the phylogeny of the Rubiaceae tribe Spermacoceae

The phylogenetic utility of chloroplast (atpB-rbcL, petD, rps16, trnL-F) and nuclear (ETS, ITS) DNA regions was investigated for the tribe Spermacoceae of the coffee family (Rubiaceae). ITS was, despite often raised cautions of its utility at higher taxonomic levels, shown to provide the highest number of parsimony informative characters, in partitioned Bayesian analyses it yielded the fewest trees in the 95% credible set, it resolved the highest proportion of well resolved clades, and was the most accurate region as measured by the partition metric and the proportion of correctly resolved clades (well supported clades retrieved from a combined analysis regarded as “true”). For Hedyotis, the nuclear 5S-NTS was shown to be potentially as useful as ITS, despite its shorter sequence length. The chloroplast region being the most phylogenetically informative was the petD group II intron.We also present a phylogeny of Spermacoceae based on a Bayesian analysis of the four chloroplast regions, ITS, and ETS combined. Spermacoceae are shown to be monophyletic. Clades supported by high posterior probabilities are discussed, especially in respect to the current generic classification. Notably, Oldenlandia is polyphyletic, the two subgenera of Kohautia are not sister taxa, and Hedyotis should be treated in a narrow sense to include only Asian species.     

Genotypic and phenotypic diversity of cyanobacteria assigned to the genus <Emphasis Type="Italic">Phormidium</Emphasis> (Oscillatoriales) from different habitats and geographical sites

In this study, 30 strains of filamentous, non-heterocystous cyanobacteria from different habitats and different geographical regions assigned to diverse oscillatorian genera but here collectively referred to as members of the Phormidium group have been characterized using a polyphasic approach by comparing phenotypic and molecular characteristics. The phenotypic analysis dealt with cell and filament morphology, ultrastructure, phycoerythrin content, and complementary chromatic adaptation. The molecular phylogenetic analyses were based on sequences of the 16S rRNA gene and the adjacent intergenic transcribed spacer (ITS). The sequences were located on multiple branches of the inferred cyanobacterial 16S rRNA tree. For some, but not all, strains with identical 16S rDNA sequences, a higher level of discrimination was achieved by analyses of the less conserved ITS sequences. As shown for other cyanobacteria, no correlation was found between position of the strains in the phylogenetic tree and their geographic origin. Genetically similar strains originated from distant sites while other strains isolated from the same sampling site were in different phylogenetic clusters. Also the presence of phycoerythrin was not correlated with the strains’ position in the phylogenetic trees. In contrast, there was some correlation among inferred phylogenetic relationship, original environmental habitat, and morphology. Closely related strains came from similar ecosystems and shared the same morphological and ultrastructural features. Nevertheless, structural properties are insufficient in themselves for identification at the genus or species level since some phylogenetically distant members also showed similar morphological traits. Our results reconfirm that the Phormidium group is not phylogenetically coherent and requires revision.     

基于5个基因片段的野胡麻属系统位置研究

对单种属野胡麻属(原隶属于广义玄参科)及其可能近缘类群广泛取样,选择合适外类群,通过对4个叶绿体基因联合数据(trnL-F、rps16、rbcL、rps2)、核基因ITS片段、叶绿体基因与核基因ITS片段联合数据,进行最大简约法和贝叶斯法分析,探讨野胡麻属在科级系统位置及其与近缘类群系统发育关系。结果表明,所有系统树都支持野胡麻属先和肉果草属构成姐妹群关系,叶绿体基因联合系统树支持率分别为97%[Bootstrap(BS)]和100%[Posterior probability(PP)];ITS系统树支持率分别为99%(BS)和100%(PP);叶绿体基因和ITS联合系统树支持率均为100%(BS和PP)。野胡麻属、肉果草属与通泉草属一起构成一单系群,叶绿体基因联合系统树、ITS系统树、叶绿体基因和ITS联合系统树的支持率均为100%(BS和PP)。形态学证据也支持野胡麻属、肉果草属和通泉草属这3个属的近缘关系。本研究结果支持单种属野胡麻属隶属于透骨草科的通泉草亚科,与肉果草属亲缘关系最近,这两个属进而与通泉草属近缘,可能隶属于通泉草属内,与岩白翠亲缘关系较近,也可能与通泉草属互为姐妹群关系。     

基于ITS和trnL-F以及rps4基因片段的 粗疣藓属分类学地位研究

选择粗疣藓属及相关属样本作为内群,油藓属样本作为外群,选取核基因ITS片段以及叶绿体基因trnL-F和rps4片段进行PCR扩增、测序,运用贝叶斯推论(BI)、最大似然法(ML)和最大简约法(MP)构建分子系统发育树,以明确粗疣藓属的分类学地位。结果表明:(1)用于分子系统分析的基因序列共有1 744个位点,其中747个位点属于核基因片段,997个位点属于叶绿体基因片段。(2)3种系统发育树拓扑结构基本一致,都显示粗疣藓属与毛锦藓科成员聚成一支,支持粗疣藓属应隶属于毛锦藓科的观点。(3)小粗疣藓和粗疣藓的种间界限模糊。(4)小鼠尾藓属的3个种与棉藓属成员聚成一支,支持将其归入棉藓科的观点。     

Phylogenetic analysis ofIridaceae with parsimony and distance methods using the plastid generps4

A molecular phylogeny of the familyIridaceae based on the plastid generps4 was obtained using both parsimony and distance methods. Thirty-four species were examined together with eight outgroup species. Results show that theIridaceae are monophyletic, and thatIsophysis is likely to be the earliest emerging genus. SubfamilyIxioideae plus the generaAristea andNivenia form a strongly supported clade. Within subfam.Iridoideae, the tribeIrideae includes the genusBobartia (of disputed position), and the tribeMariceae includesCypella. The division ofIridoideae into tribes is consistent with their geographical distribution.     

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.     

Molecular phylogenetic analyses reveal a close relationship between powdery mildew fungi on some tropical trees and Erysiphe alphitoides, an oak powdery mildew

To investigate the phylogenetic relationships among the powdery mildew fungi of some economically important tropical trees belonging to Oidium subgenus Pseudoidium, we conducted molecular phylogenetic analyses using 30 DNA sequences of the rDNA internal transcribed spacer (ITS) regions and 26 sequences of the domains D1 and D2 of the 28S rDNA obtained from the powdery mildews on Hevea brasiliensis (para rubber tree), Anacardium occidentale (cashew), Bixa orellana, Citrus spp., Mangifera indica (mango), and Acacia spp. The results indicate that the powdery mildew fungi isolated from these tropical trees are closely related to one another. These powdery mildews are also closely related to E. alphitoides (including Erysiphe sp. on Quercus phillyraeoides). Because of the obligate biotrophic nature of the powdery mildew fungi, the relationship between powdery mildews and their host plants is conservative. However, the present study suggests that a particular powdery mildew species has expanded its host ranges on a wide range of the tropical trees. This article also suggests that a powdery mildew fungus distributed in temperate regions of the Northern Hemisphere expanded its host ranges onto tropical plants and may be a good example of how geographical and host range expansion has occurred in the Erysiphales.     

Phylogenetic relationships ofMicrosphaera andErysiphe sectionErysiphe (powdery mildews) inferred from the rDNA ITS sequences

The genusMicrosphaera has been considered to be derived from sectionErysiphe of the genusErysiphe by a single event. Cleistothecial appendages are the most distinct difference between the two genera and have an important role for overwintering. To understand the phylogenetic relationship betweenErysiphe sectionErysiphe andMicrosphaera more precisely, phylogenetic trees were constructed using the nucleotide sequences of the rDNA ITS region from 11Erysiphe (sectionErysiphe) and 16Microsphaera taxa. The phylogenetic trees indicated the close relationship between the two genera. However, the generaErysiphe (sectionErysiphe) andMicrosphaera did not group into separate monophyletic lineages; instead, they formed several small clusters that were mixed together. This result suggests that the differentiations of the genera occurred two or more times independently. This also supports the idea that appendage morphology does not always accurately reflect the phylogeny of the powdery mildews because the morphology of appendages may evolve convergently under the selection pressure of their particular biotopes (host plants). Contribution No. 144 from the Laboratory of Plant Pathology, Mie University.     

Phylogenetics of the slipper orchids (Cypripedioideae, Orchidaceae): Nuclear rDNA ITS sequences

Cypripedioideae (Orchidaceae) have been the subject of numerous taxonomic treatments with conflicting interpretations of relationships among the five genera and the 150–170 species. We have produced nuclear ribosomal ITS nucleotide sequences for nearly 100 slipper orchid species and used parsimony analysis to investigate their relationships. Our results demonstrate that each genus, as currently circumscribed, is monophyletic (Mexipedium andSelenipedium being represented by a single taxon). LikerbcL data, ITS sequences placeMexipedium sister toPhragmipedium. Relationships at the sectional level inPaphiopedilum are largely as described byCribb. However, the division ofPaphiopedilum into subgg.Brachypetalum andPaphiopedilum is not supported; subg.Brachypetalum is paraphyletic to subg.Paphiopedilum. Phragmipedium species are divided into the same three major clades as in the taxonomic scheme ofMcCook. The plicate-leaved genera,Cypripedium andSelenipedium, are successive sister groups to the rest of the subfamily, confirming generally held opinions that they display plesiomorphic characters compared to the conduplicate-leaved genera. A survey of karyotypes in the context of the ITS tree reveals a general trend toward increased chromosome number, probably brought about by centric fission. These data also accord with a previously suggested biogeographic hypothesis of a widespread Northern Hemisphere distribution, followed by range fragmentation due to Miocene cooling.     

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。     

Dioecy inMikania (Compositae:Eupatorieae)

For the first time dioecy inMikania and in the tribeEupatorieae is described and discussed. The condition is known only in members of theMikania swartziana Griseb. complex, a group of eight species, all endemic to the Greater Antillean Islands of Cuba, Hispaniola, and Jamaica.     

Genotypic and phenotypic analysis of strains assigned to the widespread cyanobacterial morphospecies <Emphasis Type="Italic">Phormidium </Emphasis><Emphasis Type="Italic">autumnale</Emphasis> (Oscillatoriales)

In this study, ten cyanobacterial strains assigned to the oscillatorian species Phormidium autumnale have been characterized using a polyphasic approach by comparing phenotypic and molecular characteristics. The phenotypic analysis dealt with cell and filament morphology, ultrastructure, and pigment content. The molecular phylogenetic analyses were based on sequences of the 16S rRNA gene and the adjacent intergenic transcribed spacer (ITS). The strains were quite homogenous in their morphologic features. Their thylakoids showed a stacked or fascicular pattern. Some, but not all strains contained phycoerythrin. Only one strain (P. autumnale UTCC 476) deviated significantly in its phenotype by lacking a calyptra. In neighbour-joining and maximum Parsimony trees most 16S rRNA sequences were located on a single well-defined branch, which, however, also harboured sequences assigned to other cyanobacterial genera. Two strains (P. autumnale UTCC 476 and P. autumnale UTEX 1580) were found on distant branches. The presence of phycoerythrin was not correlated with the strains’ position in the phylogenetic trees. Our results reconfirm that the morphospecies P. autumnale and the Phormidium group in general are not phylogenetically coherent and require revision. However, as indicated by sequence similarities most of the strains assigned to P. autumnale except P. autumnale UTCC 476 and P. autumnale UTEX 1580 are phylogenetically related and might belong to a single genus.