Phylogenetic analysis of the generaCladonia andCladina (Cladoniaceae, lichenizedAscomycota)

A cladistic analysis of 44 species of the generaCladina andCladonia is presented.Pycnothelia papillaria, Cladia aggregata andC. retipora were used as outgroup taxa. The consensus of all equally parsimonious trees suggests a common ancestral origin for species inCladonia andCladina while the generaPycnothelia andCladia cluster outside this group. The results do not support distinction ofCladina at genus level although it is distinguished as a monophyletic group but within the genusCladonia. The current sectional division ofCladonia is not supported. SectionsCocciferae andHelopodium are best supported but even these groups as currently delimited seem to in include elements that are more closely related to species of the other sections, e.g.C. carneola of sect.Cocciferae andC. pityrophylla of sect.Helopodium. Sections such asUnciales andPerviae seem to be artificial assemblages. In general the evolutionary scheme of the genus seems to be more complicated than revealed by the current sectional division.     

Phylogenetic affiliations ofRhodoferax fermentans and related species of phototrophic bacteria as determined by automated 16S rDNA sequencing

16S rDNA sequences of strains ofRhodoferax fermentans were analyzed and compared with those of species of the generaRubrivivax andRhodocyclus. Approximately 1.5-kb fragments of 16S rDNA from crude cell lysates were amplified by the polymerase chain reaction (PCR) and sequenced directly by usingTth DNA polymerase with the linear PCR sequencing protocol, followed by on-line detection with an automated laser fluorescent DNA sequencer. Pairwise sequence comparisons and distance matrix tree analysis showed thatRhodoferax fermentans, Rubrivivax gelatinosus, andRhodocyclus species belong to three separate lineages within the beta subclass of theProteobacteria, thereby confirming the phylogenetic validity of the genusRhodoferax, as well as of the generaRubrivivax andRhodocyclus.     

Phylogenetic placement of the basidiomycetous yeastsKondoa malvinella andRhodosporidium dacryoidum,and the anamorphic yeastSympodiomycopsis paphiopedili by means of 18S rRNA gene sequence analysis

The 18S ribosomal RNA gene sequences of the basidiomycetous yeastsKondoa malvinella andRhodosporidium dacryoidum, and an anamorphic yeastSympodiomycopsis paphiopedili were determined. The 18S rRNA gene ofR. dacryodium IAM 13522 (ex type) revealed the presence of an intron-like region with a length of 404 nucleotides, which is presumably assigned to a group I intron. The phylogenetic tree, including 34 published reference sequences, was inferred from 1493 sites which could be unambiguously aligned. The molecular phylogeny, using the ascomycetes as an outgroup, divided the basidiomycetes into three major lineages. The first lineage was composed of the smut fungi (Ustilaginales), represented byUstilago maydis, U. hordei, andTilletia caries, includingS. paphiopedili. The second lineage included the type species of teliospore-forming yeast generaLeucosporidium, Rhodosporidium, andSporidiobolus, and the generaErythrobasidium andKondoa, both previously included in the Filobasidiaceae.Rhodosporidium dacryodium showed a close relationship withE. hasegawianum, which was backed by a high bootstrap support. The rust fungiCronartium ribicola andPeridermium harknessii were also included in this lineage. The last lineage was formed by the filobasidiaceous yeasts,Cystofilobasidium capitatum, Mrakia frigida, Filobasidium floriforme, andFilobasidiella neoformans, and the anamorphic yeastsBullera alba (the anamorph ofBulleromyces albus) andTrichosporon cutaneum. Members ofTremella and selected hymenomycetous genera were also included in this lineage.The nucleotide sequence data reported in this paper will appear in the GSDB, DDBJ, EMBL and NCBI nucleotide sequence databases with the following accession numbers D13459 (Rhodosporidium dacryodium), D13776 (Kondoa malvinella), and D14006 (Sympodiomycopsis paphiopedili).     

Correlation between pollen morphology and pollination mechanisms in the Hydrocharitaceae

The pollen morphology of 11 genera and 11 species of the Hydrocharitaceae and one species of the Najadaceae was studied using scanning and transmission electron microscopies, and the exine structures and sculptures are discussed in relation to pollination mechanisms and the molecular phylogeny. The pollen grains of the Hydrocharitaceae are spherical, inaperturate, and form monads or tetrads, while those of the Najadaceae are elliptical, inaperturate, and form monads. The entomophilous genera Egeria, Blyxa, Ottelia, Stratiotes, and Hydrocharis share pollen grains that have projections like spines or bacula. The anemophilous genus Limnobium has reticulate pollen grains. The hypohydrophilous genera Thalassia and Najas are characterized by pollen grains with reduced exine structures. The pollen-epihydrophilous genera Elodea and Hydrilla have tightly arranged small spinous pollen grains, and the male flower-epihydrophilous genera Enhalus and Vallisneria have reduced reticulate or gemmate exines. Character state reconstruction of the exine structures and sculptures using a molecular phylogenetic tree suggests that variation in the exine is generally correlated with the pollination mechanism; the selective pressures acting on the pollination mechanisms have reduced the exine structure in hypohydrophilous plants and resulted in various exine sculptures that are adapted to the different pollination mechanisms in entomophilous, anemophilous, and pollen-epihydrophilous plants.     

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 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.     

The generic classification of Fayum anthropoidea

The early anthropoid species initially described asAegyptopithecus zeuxis Simons, 1965, from the Oligocene of Egypt, although retained by many authors in the monotypic genusAegyptopithecus, has been lumped by others into the genusPropliopithecus. Similarly, the species originally described asParapithecus grangeri Simons, 1974, has been ranked by some authors in a monotypic genusSimonsius, while others retain it inParapithecus. Criteria to be considered in resolving these taxonomic debates are (1) the adequacy and consistency of proposed morphological differences between species; (2) analogy with the degree of morphological variation tolerated within extant genera; and (3) nomenclatural conservatism. A philosophy that would require strict monophyletic classification is of insufficient practical value for assessing the validity of Fayum genera. Characters cited as distinguishing vetweenAegyptopithecus andPropliopithecus, and betweenSimonsius andParapithecus, are reviewed and evaluated. The results indicate thatA. zeuxis is generically distinct from species ofPropliopithecus, based on differences in the crown structure and proportions of the molars.Pa. grangeri cannot be shown to differ at the generic level from the type and only known specimen ofPa. fraasi, thus establishing Simonsius as a junior synonym ofParapithecus.     

LOLA ZRREGULARIS (CHLOROPHYTA-CLADOPHORACEAE): A NEW SPECIES FROM THE ROSS SEA,ANTARCTICA1

A small, loose lying, unbranched, filamentous alga from the Ross Sea, Antarctica, is described as a new species, Lola irregularis. The genus Lola is closely related to the genera Hormiscia, Rhizoclonium, and Chaetomorpha in the family Cladophoraceae. A key to all known species of Lola is included. This is the first record of a species of Lola south of the Antarctic convergence.     

Phylogeny ofRubiaceae-Rubieae inferred from the sequence of a cpDNA intergene region

A phylogenetic analysis of 25 species, representing eight genera of theRubieae tribe (Rubiaceae), has been made using the DNA sequence of the chloroplastatp B-rbc L intergene region. Six tropical genera from other tribes ofRubiaceae have been used as outgroups. Whatever the method of analysis (distance, parsimony or maximum likelihood), five groups are clearly separated and described as informal clades. Their relative relationships are not clearly resolved by the parsimony analysis, resulting in eight equally parsimonious trees, 327 steps long, with a consistency index (CI) of 0.749 (excluding uninformative sites). TheRubieae tribe appears monophyletic from the data available. Some new and partly unexpected phylogenetic relationships are suggested. The genusRubia forms a separate clade and appears to be the relatively advanced sister group of the remaining taxa. TheSherardia clade also includes the generaCrucianella andPhuopsis. Galium sect.Aparinoides appears closely attached to theAsperula sect.Glabella clade. The remaining taxa ofGalium are paraphyletic:Galium sect.Platygalium (in theCruciata clade) is linked to the advanced generaCruciata andValantia; the more apomorphic groups ofGalium form theGalium sect.Galium clade, including the perennial sectionsGalium, Leiogalium, andLeptogalium as well as the annual (and possibly polyphyletic) sect.Kolgyda.     

Molecular phylogeny of the genus<Emphasis Type="Italic">Hypericum</Emphasis> (Hypericaceae) from Korea and Japan: evidence from nuclear rDNA ITS sequence data

As part of our ongoing phylogenetic study of genusHypericum, nuclear ribosomal DNA internal transcribed spacer sequences were analyzed for 36 species ofHypericum as ingroup and two species ofThornea as outgroup. This sampling included most of the previously described species from both Korea and Japan. The ITS phylogeny suggested that the surveyedHypericum species belong to a monophyletic section,Trigynobrathys, and a polyphyletic section,Hypericum. In addition, two monotypic sections,Sampsonia andRoscyna, were identified. Members of sectionHypericum occur in four different lineages worldwide, which imply at least four independent origins. The Korean and Japanese species of sectionHypericum form a monophyletic group, except forH. vulcanicum. Instead, that particular species belongs to a distinct monophyletic group withH. scoreri andH. formosa from other geographic areas, and is a sister to sectionTrigynobrathys. The Korean and Japanese species of sectionTrigynobrathys show a monophyletic origin.H. sampsonii is now recognized as a distinct section rather than being a member of sectionsHypericum orDrosocarpium, as had been indicated previously. Our results differ somewhat from those of recent morphological and cytological studies. The phylogenetic relationships among Korean and Japanese species have now been mostly resolved via ITS phylogeny.     

Interspecific relationship of ten European orchid species as revealed by enzyme electrophoresis

Ten species of orchid plants belonging to the generaOrchis (7),Dactylorhiza (2), andGymnadenia (1) were analyzed by enzyme electrophoresis. Each species can be identified by a combination of enzyme bands different from those of all other species examined. The electrophoretic data were used for the construction of phenetic and phylogenetic trees with the help of computer programs. The trees were almost identical regardless which method was used. Our results differ considerably from a classification based on morphological evidence. The electrophoretic data indicate that the genusOrchis is not a monophyletic group.     

Molecular phylogeny ofSalicaceae and closely relatedFlacourtiaceae: Evidence from 5.8 S, ITS 1 and ITS 2 of the rDNA

A ribosomal DNA region, including the entire 5.8S RNA gene and the internal transcribed spacers ITS 1 and ITS 2, was used for studying the phylogeny ofSalicaceae and the relationship betweenSalicaceae andFlacourtiaceae. The length of the ITS regions withinSalicaceae andFlacourtiaceae was similar to that found in other angiosperms. The GC content of both ITS regions was high, varying 62.7-72.2%. The most parsimonious tree clusters the wind-pollinatedChosenia bracteosa among theSalix species, suggesting that it should be included in the genusSalix. The grouping withinSalix leaves subg.Salix as paraphyletic, for which reason the subgeneric division is questionable.Populus was monophyletic and formed a sister group toSalix. The interspecific variation of the ITS sequences was very small inSalicaceae, which is in contradiction to the age of the group according to the evidence from fossil data.Idesia polycarpa fromFlacourtiaceae shows great sequence similarity withSalicaceae, but the analysis of 5.8S rDNA supports monophyly of the four species ofFlacourtiaceae sampled for this study.     

Archiascomycetes: detection of a major new lineage within the Ascomycota

For phylogenetic analysis of the higher fungi, we sequenced the nuclear small subunit rRNA (18S rRNA) gene fromTaphrina populina, the type species of the genusTaphrina, andProtomyces lactucae-debilis. The molecular phylogeny inferred from these 2 sequences and 75 sequences from the DNA data bank divided the Ascomycota into three major lineages: the hemiascomycetes, the euascomycetes, and the archiascomycetes, newly described herein. The former two lineages are monophyletic, whereas the archiascomycetes, which originated first and are comprised ofTaphrina, Protomyces, Saitoella, Schizosaccharomyces, andPneumocystis, may not be monophyletic. Among the archiascomycetes, theTaphrina/Protomyces branch is monophyletic. Confirmation of the archiascomycetes as a monophyletic taxonomic class will require comparison of additional genetically defined characters.This work was supported in part by grants 05454030 from the Ministry of Education, Science, and Culture of Japan (to J. S.) and 4369 from the Japan Society for the Promotion of Science Fellowship Programs (to H. N.).     

Chemotaxonomic studies onArachniodes (Dryopteridaceae) II. Phloroglucinol derivatives and taxonomic evaluation

Seven species ofArachniodes from Japan and the Philippines were examined for phloroglucinol derivatives and glandularity of rhizome and petiole bases. For comparison 3 species ofDryopteris, 2 species ofNothoperanema, 3 species ofPolystichum, 1 species ofAcrophorus and 2 species ofCtenitis were investigated as well. Phloroglucinol derivatives were detected for the first time in the following taxa:Arachniodes assamica, A. cavalerii, A. tripinnata, A. yasu-inouei, Dryopteris pulvinulifera, D. cochleata, Polystichum rigens, Acrophorus nodosus, Ctenitis setosa andC. subglandulosa. The phloroglucinols ofDryopteris, Arachniodes andPolystichum are structurally related in agreement with the taxonomic relationships of these genera. On the other hand, the less related generaAcrophorus andCtenitis contain several unknown phloroglucinols not identical with those occurring in the former genera. The phloroglucinol containing species ofArachniodes, Polystichum, Acrophorus andCtenitis contain external glands, whereasDryopteris pulvinulifera andD. cochleata have both internal and external glands. The species of the genusNothoperanema seem to completely lack phloroglucinols and glands. The phloroglucinol composition of most taxa investigated is almost constant except for that inArachnoides amabilis and its varieties,A. aristata (A. exilis) andPolystichum tsus-simense. These species show varying phloroglucinol spectra in materials collected from different geographical sources.     

LOLA IRREGULARIS (CHLOROPHYTA-CLADOPHORACEAE) : A NEW SPECIES FROM THE ROSS SEA,ANTARCTICA1

A small, loose lying, unbranched, filamentous alga from the Ross Sea, Antarctica, is described as a new species, Lola irregularis. The genus Lola is closely related to the genera Hormiscia, Rhizoclonium, and Chaetomorpha in the family Cladophoraceae. A key to all known species of Lola is included. This is the first record of a species of Lola south of the Antarctic convergence.     

Synonomy of the yeast generaHansenula andPichia demonstrated through comparisons of deoxyribonucleic acid relatedness

The relationship between the generaHansenula andPichia was examined through comparisons of DNA relatedness among phenotypically similar species.Hansenula minuta andPichia lindneri showed 75% DNA base sequence complementarity. In other comparisons,H. nonfermentans was found to share nearly 50% of its DNA sequences with bothH. minuta andP. lindneri. Because of the high degree of relatedness observed, it is proposed that ability to assimilate nitrate, the sole distinction betweenHansenula andPichia, is of insufficient taxonomic value for the reliable separation of either species or genera. Hat-spored species ofHansenula H. et P. Sydow 1919 are being transferred toPichia Hansen 1904. Species ofHansenula andPichia with Saturn-shaped ascospores will be transferred to the genusWilliopsis. The mention of firm names or trade products does not imply that they are endorsed or recommended by the U.S. Department of Agriculture over other firms or similar products not mentioned.     

Molecular phylogenetic study of the basidiomycetous anamorphic yeast genusTrichosporon and related taxa based on small subunit ribosomal DNA sequences

Small subunit ribosomal DNA sequences of all species of the basidiomycetous anamorphic yeast genusTrichosporon were determined, and phylogenetic trees were constructed by the neighbor-joining and maximum likelihood methods. The sequence data showed that, with the exception ofT. pullulans, the genus is monophyletic, although its members have two different major ubiquinones, Q9 and Q10. The genus can be divided phylogenetically into three major clusters. Species with Q10 as the major ubiquinone constitute a single cluster, while those with Q9 form two clusters.Trichosporon pullulans was phylogenetically distinct from other taxa of the genus. It is located in a cluster containingCystofilobasidium capitatum, Mrakía frigida, Xanthophyllomyces dendrorhous and three species ofUdeniomyces. This result sugests thatT. pullulans does not belong to the genusTrichosporon.     

Phylogenetic Relationships among the Major Lineages of the Birds-of-Paradise (Paradisaeidae) Using Mitochondrial DNA Gene Sequences

Complete mitochondrial cytochromebgene sequences were determined from 12 species of the Australo-Papuan birds-of-paradise (Paradisaeidae) representing 9 genera. Phylogenetic analysis of these and 5 previously published sequences reveals a radiation of the main paradisaeinine lineages that took place over a relatively short evolutionary time scale. The core paradisaeinines are resolved as the monophyletic sister-group to the crow-like manucodines. The genusParotiais basal to other paradisaeinines and is not closely related to the morphologically similar generaPtilorisandLophorina.Three major clades within the paradisaeinine ingroup include: (1)CicinnurusandDiphyllodes,(2)PtilorisandLophorina,and (3) the genusParadisaea.The monotypic genusSeleucidisis apparently closely related to clades (1) and (2). Cytochromebsequences did not provide evidence for the monophyly of the sicklebill generaEpimachusandDrepanornis.The paradisaeid tree is characterized by short internodal distances. Thus, some clades cannot be strongly resolved by cytochromebsequences alone.     

Fungi in sediments of the sea of Japan and their biologically active metabolites

The most abundant marine fungi encountered in various regions of the Sea of Japan belong to the generaPenicillium, Aspergillus, Wardomyces, Trichoderma, Chrysosporium, andChaetomium. Facultative marine fungi of the generaScytalidium, Verticillium, andOidiodendron and obligate marine fungi of the genusDendryphiella are much less abundant. The composition of marine sediments and the anthropogenic load on them were found to influence the abundance and species diversity of fungi, as well as the occurrence of fungal strains producing hemolytically active substances. The biodiversity of mycobiota and the abundance of hemotoxin-producing fungi in marine sediments may be used to evaluate the anthropogenic load on marine biocenoses. Hemolytic compounds were produced by 57% of the fungi isolated from marine sediments. The hemolytic activity ofChaetomium spiculipilium was revealed in the fraction of the culture liquid containing extracellular fatty acids and pigments. The fatty acid composition of this marine fungus was determined.     

Nutritional physiology of type isolates of currently accepted species ofExophiala andPhaeococcomyces

Nutritional physiological and tolerance tests were performed for all type strains of species currently classified in the black yeast generaExophiala andPhaeococcomyces, including some additional type strains of taxa recently reidentified asExophiala species. Most describedExophiala species can be distinguished by physiological characters.Exophiala jeanselmei with its varieties, andE. castellanii should all be retained as separate taxa. The pairs of strainsMycotorula schawii/Exophiala dermatitidis, Hormodendrum negronii/Exophiala jeanselmei var.lecaniicorni andSporotrichum gougerotii/Torula bergeri were found to be conspecific. Phenetic analyses of physiological data support the identity ofPhaeococcomyces exophialae as a yeast-like synanamorph ofExophiala spinifera. The taxonomic positions of the generaNadsoniella, Phaeoannellomyces andWangiella are discussed. The generaExophiala andPhaeococcomyces are unrelated.