Phylogenetic analysis of Antrodia and related taxa based on partial mitochondrial SSU rDNA sequences

Sequences of mitochondrial SSU rDNA were obtained from six species of Antrodia and related fungal taxa to reveal their phylogenetic relationships. Phylogenetic analysis showed that the species of Antrodia did not cluster into a single clade. Brown rot fungi were separated into two main groups through which Antrodia was dispersed. Antrodia sinuosa, A. serialis, A. heteromorpha and A. malicola clustered with Perenniporia, Fomitopsis, Piptoporus, Daedalea and Melanoporia within one group of brown rot fungi, while A. carbonica and A. vaillantii clustered with Oligoporus, Gloeophyllum and Auriporia within the other group of brown rot fungi, indicating that Antrodia is a heterogeneous genus and that brown rot fungi have evolved convergently. This revised version was published online in June 2006 with corrections to the Cover Date.     

Phylogenetic relationships ofSphaerophoraceae (Ascomycetes) inferred from SSU rDNA sequences

SSU rDNA was sequenced from the lichenized fungiBunodophoron scrobiculatum andLeifidium tenerum (Sphaerophoraceae), andStereocaulon ramulosum andPilophorus acicularis (Stereocaulaceae) and analysed by maximum parsimony with 44 homologous ascomycete sequences in a cladistic study. A small insertion (c. 60 nt.) was found in the sequence ofLeifidium tenerum. Sphaerophoraceae constitutes a strongly supported monophyletic group which groups together withLecanora dispersa and theStereocaulaceae. Together withPorpidia crustulata, this larger group is a sistergroup to thePeltigerineae. This analysis thus supports theLecanorales as monophyletic, includingSphaerophoraceae and thePeltigerineae, but does not provide strong support for this monophyly. The analysis also suggests that the prototunicate ascus in theSphaerophoraceae is a reversion to the plesiomorphic state. Based on morphological, anatomical and chemical reasons,Sphaerophoraceae is proposed to belong to one of the groups presently included in the paraphyletic suborderCladoniineae within theLecanorales.     

Molecular Phylogeny of Conjugating Green Algae (Zygnemophyceae, Streptophyta) Inferred from SSU rDNA Sequence Comparisons

Abstract Nuclear-encoded SSU rDNA sequences have been obtained from 64 strains of conjugating green algae (Zygnemophyceae, Streptophyta, Viridiplantae). Molecular phylogenetic analyses of 90 SSU rDNA sequences of Viridiplantae (inciuding 78 from the Zygnemophyceae) were performed using complex evolutionary models and maximum likelihood, distance, and maximum parsimony methods. The significance of the results was tested by bootstrap analyses, deletion of long-branch taxa, relative rate tests, and Kishino–Hasegawa tests with user-defined trees. All results support the monophyly of the class Zygnemophyceae and of the order Desmidiales. The second order, Zygnematales, forms a series of early-branching clades in paraphyletic succession, with the two traditional families Mesotaeniaceae and Zygnemataceae not recovered as lineages. Instead, a long-branch Spirogyra/Sirogonium clade and the later-diverging Netrium and Roya clades represent independent clades. Within the order Desmidiales, the families Gonatozygaceae and Closteriaceae are monophyletic, whereas the Peniaceae (represented only by Penium margaritaceum) and the Desmidiaceae represent a single weakly supported lineage. Within the Desmidiaceae short internal branches and varying rates of sequence evolution among taxa reduce the phylogenetic resolution significantly. The SSU rDNA-based phylogeny is largely congruent with a published analysis of the rbcL phylogeny of the Zygnemophyceae (McCourt et al. 2000) and is also in general agreement with classification schemes based on cell wall ultrastructure. The extended taxon sampling at the subgenus level provides solid evidence that many genera in the Zygnemophyceae are not monophyletic and that the genus concept in the group needs to be revised.     

Characterization of Pharyngomonas kirbyi (= "Macropharyngomonas halophila" nomen nudum), a very deep-branching, obligately halophilic heterolobosean flagellate

The tetraflagellate Pharyngomonas is among the most commonly reported morphotypes of halophilic protozoa. We have established two cultures of Pharyngomonas kirbyi, SD1A and AS12B, from 300‰ and 210‰ salinity waters from the USA and Australia, respectively. 18S rRNA gene phylogenies confirm that Pharyngomonas is the same entity as 'Macropharyngomonas' (nomen nudum), and represents the deepest branch in the heterolobosean lineage. Pharyngomonas kirbyi (Strain SD1A) has flattened/discoidal cristae, and lacks conspicuous Golgi dictyosomes. It also has a heterolobosean 'double bikont' flagellar apparatus, with two right roots, each associated with an 'I' fibre and part of a rhizoplast-like complex. One right root splits shortly after its origin, and supplies most of the microtubules that support both the ventral groove, and the sub-anterior cytopharynx. Interestingly, Pharyngomonas has some potentially ancestral features not found in typical Heterolobosea, including elongated left roots associated with multilayered 'C' fibres, orthogonal basal bodies, and a spur structure that might represent a 'B' fibre homolog. Both isolates are obligate halophiles that grow best at 100-200‰ salinity and do not grow below 75‰ salinity. Pharyngomonas is therefore of considerable evolutionary importance, both as a deep-branching, plesiomorphic heterolobosean, and a borderline extreme halophile.     

SSU rDNA phylogeny of cladoniiform lichens

To examine phylogenetic relationships among the "cladoniiform" lichenized fungi, i.e., the families Cladoniaceae, Baeomycetaceae, Icmadophilaceae, Stereocaulaceae, and Siphulaceae, and to provide evidence for the anticipated independent origins of podetia and pseudopodetia, we conducted phylogenetic analyses of SSU (small subunit) rDNA sequences from 39 lichen-forming fungi. These fungi represent all of the major growth forms of lichen associations, fruticose (including "cladoniiform"), foliose, and crustose. Our analysis suggests that lichen-forming fungi with a "cladoniiform" morphology arose multiple times within the ascomycetes. Additionally, each of the other thallus growth forms, crustose, foliose, and fruticose, have originated multiple times. It also seems to be clear that neither all podetiate nor all pseudopodetiate taxa form a monophyletic group. Therefore the term "podetium" should be restricted to homologous structures that are most probably limited to the genera Cladonia, Cladina, Pycnothelia, and allies. The "pseudopodetia" of Stereocaulon (Stereocaulaceae) and Cladia (Cladiaceae) may represent different states of the same homologous character. Our phylogenetic hypothesis supports the monophyletic origin of the order Lecanorales sensu stricto, including representatives of five suborders Cladoniineae, Lecanorineae, Teloschistineae, Agyriineae and Peltigerineae, but excluding representatives of the suborders Acarosporineae (Acarospora schleicheri and Megaspora verrucosa), Pertusariineae (Pertusaria trachythallina), and Umbilicarineae. The suborder Cladoniineae and the family Cladoniaceae both appear to be polyphyletic assemblages.     

Phylogenetic position of Sorogena stoianovitchae and relationships within the class Colpodea (Ciliophora) based on SSU rDNA sequences

The ciliate Sorogena stoianovitchae, which can form a multicellular fruiting body, has been classified based upon its ultrastructure and morphology: the oral and somatic infraciliature of S. stoianovitchae most closely resemble those of members of the order Cyrtolophosidida in the class Colpodea. We characterized the small subunit ribosomal DNA (SSU rDNA) gene sequence from S. stoianovitchae and compared this sequence with those from representatives of all ciliate classes. These analyses placed S. stoianovitchae as either sister to members of the class Nassophorea or Colpodea. In an in-group analysis, including all SSU rDNA sequences from members of the classes Nassophorea and Colpodea and representatives of appropriate outgroups, S. stoianovitchae was always sister to Platyophrya vorax (class Colpodea, order Cyrtolophosidida). However, our analyses failed to support the monophyly of the class Colpodea. Instead, our data suggest that there are essentially three unresolved clades: (1) the class Nassophorea; (2) Bresslaua vorax, Colpoda inflata, Pseudoplatyophrya nana, and Bursaria truncatella (class Colpodea); and (3) P. vorax and S. stoianovitchae (class Colpodea).     

Monoxenic cultivation of the anaerobic amoeboflagellate Psalteriomonas lanterna and isolation of the methanogenic endosymbiont

Abstract The endosymbiont of the anaerobic amoeboflagellate Psalteriomonas lanterna was isolated and identified as Methanobacterium formicicum , a H₂/CO₂- and formate-utilizing methanogen. A monoxenic culture of P. lanterna was established in a complex liquid medium with Pseudomonas fluorescenss as food bacterium.     

Phylogenetic position of the enigmatic myxomycete genus Kelleromyxa revealed by SSU rDNA sequences

The coprophilous myxomycete Kelleromyxa fimicola (Dearn. & Bisby) Eliasson was first described in 1929 as Licea fimicola Dearn. & Bisby. Based on the superficial resemblance of its sporocarps to those of Licea biforis, the species was placed within the Liceales, an order assigned by molecular phylogenies to the bright-spored clade of myxomycetes. However, detailed studies of the morphology and life cycle of K. fimicola revealed several characters of the dark-spored order Physarales. To elucidate the systematic position of Kelleromyxa, we obtained three partial and one complete sequence of the SSU rDNA, which demonstrated a clear relationship of K. fimicola to the order Physarales. However, the obtained sequences are not closely related to any of the two known families of Physarales, supporting the erection of a monotypic family for this species. Along with morphological observations, our data support the exclusion of K. fimicola from the order Liceales and placement among the order Physarales within the dark-spored clade of myxomycetes.     

Phylogenetic relationships among Thunnus species inferred from rDNA ITS1 sequence

Intra and interspecific nucleotide sequence variation of rDNA first internal transcribed spacer (ITS1) was analysed using all eight species of the genus Thunnus plus two out‐group species within the same family, skipjack tuna Katsuwonus pelamis and striped bonito Sarda orientalis . Intraspecific nucleotide sequence variation in ITS1, including intra‐genomic variation, was low, ranging from 0·003 to 0·014 [Kimura's two parameter distance (K2P)], whereas variation between species within the genus Thunnus ranged from 0·009 to 0·05. The Atlantic and Pacific northern bluefin tunas Thunnus thynnus thynnus and Thunnus thynnus orientalis , recently proposed to be distinct species, were found to share nearly identical ITS1 sequences (mean K2P = 0·006) well within the range of intraspecific variation. The northern bluefin tuna appeared to be a sister group to albacore Thunnus alalunga , with all other Thunnus species in a distinct clade. The ITS1 phylogeny was consistent with mtDNA phylogeny in clustering the three tropical Thunnus species ( T. albacares , T. atlanticus and T. tonggol ). Southern bluefin Thunnus maccoyii and bigeye Thunnus obesus tunas showed a closer affinity to this tropical tuna group than to the northern bluefin tuna and albacore. The molecular data supported mitochondrial introgression between species and contradicted morphological subdivision of the genus into two subgenera Neothunnus and Thunnus .     

Phylogenetic relationships of Palaeacanthocephala (Acanthocephala) inferred from SSU and LSU rDNA gene sequences

The Palaeacanthocephala is traditionally represented by 2 orders, Echinorhynchida and Polymorphida, with 10 and 3 families, respectively. To test the monophyly of the class, these 2 orders, and certain families, phylogenies were inferred using nuclear small-subunit (SSU) and large-subunit (LSU) ribosomal DNA sequences obtained for 29 species representing 10 families, 2 other classes of acanthocephalans, and 3 rotifer outgroups. Phylogenetic relationships were inferred by analyzing combined SSU and LSU sequences using maximum parsimony (MP) and maximum likelihood (ML) methods. Parsimony and ML trees inferred from combined analysis of these rDNA data strongly supported monophyly of Palaeacanthocephala and provided good resolution among species. Neither Polymorphida nor Echinorhynchida was monophyletic. Gorgorhynchoides bullocki (Echinorhynchida) was nested within the 6 species representing Polymorphida, and this clade was nested within species representing Echinorhynchida. Three of 4 palaeacanthocephalan families that could be evaluated were not monophyletic, and this finding was strongly supported. These results indicate that the family level classification of palaeacanthocephalans, which is mainly based on combinations of shared characters (not shared derived characters), needs to be reevaluated with respect to comprehensively sampled phylogenetic hypotheses.     

Phylogenetic Relationships of Scenedesmus and Scenedesmus-like Coccoid Green Algae as Inferred from ITS-2 rDNA Sequence Comparisons

Abstract: Analyses of ITS-2 ribosomal DNA from Scenedesmus and Scenedesmus-like strains showed that this molecule is well suited for resolving evolutionary relationships at various taxo-nomic levels. The analyses clearly suggested the separation of the investigated strains into two groups which corresponded to the "subgenera" Desmodesmus and Scenedesmus/Acutodesmus . No clear distinction between Acutodesmus and Scenedesmus was seen. It is proposed to regard both groups as distinct genera, Desmodesmus gen. nov. and Scenedesmus sensu strictu , and to merge Acutodesmus into Scenedesmus . Monophyly of both genera, Scenedesmus and Desmodesmus , is further supported by certain secondary structure features of ITS-2. The relationships resolved by the ITS-2 analyses are congruent with findings from cell wall ultrastructure, but not with those from other morphological features such as cell wall surface structures or cell shape. Didymocystis inermis and Dicloster acuatus , though somewhat similar in vegetative cell morphology to species of Scenedesmus and Desmodesmus , were seen as members of independent genera because of substantial differences in primary structure and length variations in ITS-2 when compared with each other and the latter two genera.     

The Phylogeny of the Families Lecanoraceae and Bacidiaceae (Lichenized Ascomycota) Inferred from Nuclear SSU rDNA Sequences

Abstract: The phylogeny of the families Lecanoraceae and Bacidiaceae (Lecanorales, Ascomycota) was investigated using 29 nuclear small subunit ribosomal DNA sequences, 9 of which were newly determined. The data set contained 368 variable characters, 234 of which were parsimony-informative. Phylogenetic estimations were performed with maximum parsimony and maximum likelihood optimality criteria. In the most parsimonious and most likely reconstructions, the Bacidiaceae sensu Hafellner 1988 forms a monophyletic group and the Lecanoraceae sensu Hafellner a paraphyletic group. The genera Tephromela and Scoliciosporum appear to belong outside these families. However, the hypothesis that the Lecanoraceae sensu Hafellner is monophyletic cannot be rejected, as indicated by a Kishino-Hasegawa test. Three hypotheses were rejected by Kishino-Hasegawa tests, viz. (1) that the Lecanoraceae and Bacidiaceae together form a monophyletic group; (2) that both the Lecanoraceae (incl. Scoliciosporum ) and Bacidiaceae (incl. Tephromela ) are monophyletic; and (3) that the ascus apex anatomy reflects phylogeny. The suborder Lecanorineae is paraphyletic unless the Stereocaulaceae and Cladoniaceae are included. One or both of the Bacidia and Lecanora types of ascus have probably evolved at least twice.     

Two Anaerobic Ciliates (Ciliophora,Armophorea) from China: Morphology and SSU rDNA Sequence,with Report of a New Species,Metopus paravestitus nov. spec

The morphology and phylogeny of two metopid ciliates, collected from anaerobic habitats in China, were investigated using live observation, protargol staining method, and SSU rDNA sequencing. The new species Metopus paravestitus nov. spec. can be distinguished by a combination of the following features: oblong cell with densely arranged ectobiotic prokaryotes perpendicular to cell surface, filiform intracytoplasmic structures packed in the anterior portion of the cell. Our work also demonstrates the wide geographical distribution of Metopus es (Müller, 1776) Lauterborn, 1916. The order Metopida is consistently depicted as a paraphylum in SSU rDNA phylogeny. Metopus paravestitus nov. spec. is closely related to its marine congeners than to freshwater forms. The present study confirms once again the non-monophyly of the genus Metopus and genus Metopidae.     

Phylogenetic analyses of anatomical and nuclear SSU rDNA sequence data indicate that the Dasyaceae and Delesseriaceae (Ceramiales,Rhodophyta) are polyphyletic

The aim of the current investigation was to test the general convention that the Dasyaceae, Delesseriaceae and Rhodomelaceae are all monophyletic families of the red algal order Ceramiales. Phylogenetic relationships among 45 ceramialean taxa were determined, including eight ceramiacean, 18 dasyacean, nine delesseriacean and eight rhodomelacean species, plus two of uncertain ceramialean affinities, based on 34 anatomical characters and nuclear small subunit (SSU) rDNA sequences. Results from our ‘total-evidence’ approach were consistent with the notion that the Dasyaceae, Delesseriaceae and Rhodomelaceae have evolved from a common ancestor within a paraphyletic Ceramiaceae. Our data indicate, however, that the Rhodomelaceae alone is monophyletic at the family level, with both the Dasyaceae and Delesseriaceae polyphyletic. In particular we resolved two independent and well-supported lineages for the included Dasyaceae, viz., a Dasya group and a Heterosiphonia group, which were as distinct from one another as they were from the Rhodomelaceae and the various lineages of Delesseriaceae. The molecular data alone were equivocal on the issue of monophyly of the Dasyaceae. We therefore advocate conservative taxonomic revisions as an interim step towards eventual resolution of familial-level taxonomy in the Ceramiales. Based on our results, the Heterosiphonioideae H.-G. Choi, Kraft, I.K. Lee et G.W. Saunders subfam. nov. is proposed for Heterosiphonia and five closely related genera, and the Dasyoideae Schmitz et Falkenberg is emended for the remaining taxa. Although the Dasyoideae is a natural group, it is in need of a thorough systematic reinvestigation at the generic level. Our analyses indicate that the genus Dasya is polyphyletic or paraphyletic in excluding Dasysiphonia, Eupogodon and Rhodoptilum and that Heterosiphonia japonica also has affinities to this group, taxonomic issues that will be addressed in detail elsewhere.     

Evolution of Filamentous Ascomycetes Inferred from LSU rDNA Sequence Data

Abstract: The nuclear LSU rRNA gene was examined in order to evaluate the current phylogeny of ascomycetes, which is mainly based on nuclear SSU rRNA data. Partial LSU rRNA gene sequences of 19 ascomycetes were determined and aligned with the corresponding sequences of 13 other ascomycetes retrieved from Genbank, including all classes traditionally distinguished and most of the recently accepted classes. The classification based on SSU rDNA data and morphological characters is supported, while the traditional classification and classifications based on the ascus type are rejected. Ascomycetes with perithecia and cleistothecia form monophyletic groups, while the discomycetes are a paraphyletic assemblage. The Pezizales are basal to all other filamentous ascomycetes. The monophyly of Loculoascomycetes is uncertain. The results of the LSU rDNA analysis agree with those of the SSU rDNA and RPB2 gene analyses, suggesting that most classes circumscribed in the filamentous ascomycetes are monophyletic. The branching order and relationships among these classes, however, cannot be elucidated with any of these data sets.     

杉科、柏科的系统发生分析——来自28S rDNA序列分析的证据

对杉科（Taxodiaceae）与柏科（Cupressaceae s.s.）的28S rRNA基因的部分序列（约630 bp）进行PCR扩增、序列测定和系统发生关系分析,用简约法和邻接法构建的系统发生树基本一致。结果表明,杉科与柏科构成一个单系群,支持将杉科、柏科（Sciadopitys除外）合并为一个科——广义柏科（Cupressaceae sensu lato）的观点。在广义柏科中,Taiwania、Athrotaxis分别形成一支系;Metasequoia、Sequoia、Sequoiadendron关系较近,聚成一支系; Taxodium、Glyptostrobus、Cryptomeria聚成一支系;柏科聚成一支系。这一分析结果与叶绿体基因序列的分析结果相吻合,但是由于28S rRNA基因的进化速率较慢,尚不能分辨上述各个支系之间的系统演化关系。 Abstract:DNA sequences from 28S rDNA were used to assess relationships between and within traditional Taxodiaceae and Cupressaceae s.s.The MP tree and NJ tree generally are similar to one another.The results show that Taxodiaceae and Cupressaceae s.s.form a monophyletic conifer lineage excluding Sciadopitys.In the Taxodiaceae-Cupressaceae s.s.monophyletic group,the Taxodiaceae is paraphyletic.Taxodium,Glyptostrobus and Cryptomeria forming a clade(Taxodioideae),in which Glyptostrobus and Taxodium are closely related and sister to Cryptomeria;Sequoia,Sequoiadendron and Metasequoia are closely related to each other,forming another clade (Sequoioideae),in which Sequoia and Sequoiadendron are closely related and sister to Metasequoia;the seven genera of Cupressaceae s.s.are found to be closely related to form a monophyletic lineage (Cupressoideae).These results are basically similar to analyses from chloroplast gene data.But the relationships among Taiwania,Sequoioideae,Taxodioideae,and Cupressoideae remain unclear because of the slow evolution rate of 28S rDNA,which might best be answered by sequencing more rapidly evolving nuclear genes.     

Molecular phylogeny of onygenalean fungi based on small subunit ribosomal DNA (SSU rDNA) sequences

Phylogenetic analysis of nucleotide data from small subunit ribosomal DNA (SSU rDNA) sequences (ca. 1685 bp.) was performed on 19 taxa of the Onygenales and three related mitosporic fungi. Phylogenetic trees were constructed by the neighbor-joining method with the sequence data of related taxa obtained from DNA databases. The species in the Onygenales form two clusters and seven subclusters, and the tree topology reflects the traditional classification by Currah (1985) with some exceptions. The Myxotrichaceae is placed in the different lineage, separate from other plectomycetous taxa and among the Leotiales and the Erysiphales. Furthermore, two separate lineages in the Myxotrichaceae were found. Tree topology suggested the Onygenaceae is polyphyletic and composed of three subgroups; 1) most members of Onygenaceae, 2)Spiromastix warcupii, and 3) pathogenic dimorphic fungi classified inAjellomyces.     

SSU rDNA sequence support for a close relationship between the elaphomycetales and the Eurotiales and Onygenales

Based on parsimony analyses of eight new SSU rDNA sequences and 24 homologous sequences retrieved from the DNA databases, we suggest a possible phylogenetic relationship of Elaphomycetales with Eurotiales and Onygenales. Our three includedElaphomyces sequences strongly cluster together (bootstrap value 100%) within a monophyletic group (100%) of Elaphomycetales, Eurotiales, and Onygenales. Earlier reports that another cleistothecial lineage (Erysiphe) is related to Leotiales, are supported by our discovery that also another cleistothecial species,Amylocarpus encephaloides, shows affinity to Leotiales. Ascosphaeraceae and Eremascaceae are possibly better accommodated in Onygenales. We describe a new DNA extraction method in which sonication is used to disrupt thick-walled spores. It is useful for both fresh and dried fungal material.     

Phylogenetic affinities of an enigmatic nannoplankton,Braarudosphaera bigelowii based on the SSU rDNA sequences

The phylogenetic position of an enigmatic calcareous nannoplankton Braarudosphaera bigelowii, whose taxonomic position has long been questioned, was investigated using molecular genetic methods. The SSU rDNA sequences of B. bigelowii were obtained using a single cell PCR technique independently from two single cells isolated from field samples. A BLAST search revealed that the SSU rDNA of B. bigelowii was most similar to those of the division Haptophyta. Subsequent phylogenetic analyses showed that B. bigelowii was included in a clade comprising members of the orders Isochrysidales and Coccolithales, the genus Chrysoculter and two unidentified haptophytes. Morphometric measurements of extant B. bigelowii populations were made to obtain precise information on their intraspecific size variation. The results showed that these populations could be subdivided into a small form (< 2.4 μm), an intermediate form A (4.0–5.3 μm), and an intermediate form B (5.3–7.2 μm), although the borders of the latter two forms overlapped. The SSU rDNA sequences showed the presence of 10-bp substitutions plus six insertions/deletions between specimens of intermediate forms A and B. The levels of DNA variation between them suggested that these two forms are genetically distinct from each other.