Towards a subordinal classification of the Pezizales (Ascomycota): phylogenetic analyses of SSU rDNA sequences.

Phylogenetic analyses of partial SSU rDNA sequences from representatives of 36 pezizales associated genera are presented, including new sequences from 28 species: Aleuria aurantiaca, Ascodesmis sphaerospora, Boudiera acanthospora, Caloscypha fulgens, Cheilymenia stercorea, Cookeina sulcipes, Desmazierella acicola, Geopyxis carbonaria, Hydnotrya tulasnei, Iodophanus carneus, Microstoma protracta, Otidea leporina, Paurocotylis pila, Peziza succosa and P vesiculosa (the type species of the family Pezizaceae and the order Pezizales), Pyronema domesticum, Pulvinula archeri, Saccobolus sp., Sarcoscypha austriaca, Sarcosoma globosum, Sarcosphaera coronaria, Scutellinia scutellata and S. torrentis, Sphaerosporella brunnea, Tarzetta catinus, Thelebolus crustaceus, Trichophaea hybrida, Trichophaeopsis bicuspis, and Wilcoxina mikolae. Two taxon and character matrices were subjected to maximum parsimony, maximum likelihood, and neighbor-joining analyses. The first matrix included 28 taxa and a full character set of 1600 bp, and the second matrix 37 taxa and a restricted set of 1053 characters. The analyses using the restricted character set generally yielded the same topology as the full character set but the resolution was reduced. Three main evolutionary lineages were detected within the order: (1) Pezizaceae and Ascobolaceae, (2) Helvellaceae, Morchellaceae, Tuberaceae, and Caloscypha (Otideaceae), and (3) Sarcoscyphaceae, Sarcosomataceae, Ascodes-midaceae, Glaziellaceae, Otideaceae and Pyronemataceae. The inferred subordinal grouping is compared to extant classification schemes of the Pezizales. Sarcosomataceae and Sarcoscyphaceae are recognized as separate monophyletic groups. The analyses did not support recognition of Pyronemataceae, Ascodesmida-ceae, and Glaziellaceae as separate from the Otideaceae. Thelebolus (Thelebolaceae) clusters with extra-pezizalean genera and does not belong to the order.     

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 phylogenetic analysis of ant subfamily relationship inferred from rDNA sequences

The relationships among ant subfamilies were studied by phylogenetic analysis of rDNA sequences of 15 species from seven subfamilies. PCR primers were designed on the basis of the rDNA sequence of the Australian bulldog ant, Myrmecia croslandi, previously determined. Phylogenetic trees were constructed using sequences of a fragment of 18S rDNA (1.8 kb), a fragment of 28S rDNA (0.7 kb excluding variable regions) and a combination of the 18S and 28S rDNAs, by neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML). rDNA sequences corresponding to the same fragments from three non-ant hymenopteran species (a sawfly, a bee and a wasp) were employed as outgroups. These trees indicated that the ant subfamilies were clustered singly, and, among the seven subfamilies examined, Ponerinae and six other subfamilies are in a sister-groups relationship. The relationship among the six subfamilies, however, was not clarified. The phylogenetic trees constructed in the present study are not in contradiction to the tree from cladistic analysis of morphological data by Baroni Urbani et al. (1992) and the tree from morphological and molecular data (Ward and Brady, 2003), but are inconsistent with the traditional phylogeny. The present results thus raise a question as to the status of some traditionally employed "key" morphological characters. The present results also call for a reexamination of Amblyopone traditionally treated as a member of Ponerinae as belonging to a new subfamily.     

Acroscyphus sphaerophoroides (lichenized Ascomycota, Caliciaceae) in Hengduanshan Mountains

The chemical variability of Acroscyphus sphaerophoroides, a lichenized Ascomycota commonly found in the Hengduanshan Mountains, has been investigated by high performance liquid chromatography (HPLC) and thin layer chromatography (TLC). Gyrophoric acid (GA) is shown to be the constant major component, together with skyrin, graciliformin and rugulosin. Two chemical races are recognized, which show some correlations with substrates. The obtained data indicated that the chemistry of A. sphaerophoroides distributed in Hengduanshan Mountains is different from that growing in the other areas of the world according to previous reports. Meanwhile, a detailed morphological study has also been carried out, and the taxonomy, distribution, as well as ecology of this species are discussed.     

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.     

Molecular phylogeny of ocelloid-bearing dinoflagellates (Warnowiaceae) as inferred from SSU and LSU rDNA sequences

Background  

Dinoflagellates represent a major lineage of unicellular eukaryotes with unparalleled diversity and complexity in morphological features. The monophyly of dinoflagellates has been convincingly demonstrated, but the interrelationships among dinoflagellate lineages still remain largely unresolved. Warnowiid dinoflagellates are among the most remarkable eukaryotes known because of their possession of highly elaborate ultrastructural systems: pistons, nematocysts, and ocelloids. Complex organelles like these are evolutionary innovations found only in a few athecate dinoflagellates. Moreover, the taxonomy of warnowiids is extremely confusing and inferences about the evolutionary history of this lineage are mired by the absence of molecular phylogenetic data from any member of the group. In this study, we provide the first molecular phylogenetic data for warnowiids and couple them with a review of warnowiid morphological features in order to formulate a hypothetical framework for understanding character evolution within the group. These data also enabled us to evaluate the evolutionary relationship(s) between warnowiids and the other group of dinoflagellates with complex organelles: polykrikoids.     

Outline of phylogeny and character evolution in Rhizocarpon (Rhizocarpaceae, lichenized Ascomycota) based on nuclear ITS and mitochondrial SSU ribosomal DNA sequences

The phylogeny of the lichen genus Rhizocarpon (Rhizocarpaceae, lichenized Ascomycota) was investigated using nucleotide sequences from the ITS region of the nuclear ribosomal DNA and the SSU region of the mitochondrial ribosomal DNA from 13 species of Rhizocarpon , Catolechia wahlenbergii and Poeltinula cerebrina . Phylogenetic estimations were performed using maximum parsimony and Bayesian MCMC tree sampling. Twelve phylogenetic null hypotheses were tested using MCMC tree sampling. The evolution of five morphological characters was assessed by mapping them onto MCMC tree samples. The results indicate that Rhizocarpon in its current sense is polyphyletic and can only be made monophyletic if R. hochstetteri is excluded or Poeltinula , and possibly also Catolechia , are included. The root placement in the Rhizocarpaceae is ambiguous, either Catolechia or Poeltinula + R. hochstetteri being the sistergroup to the rest of the family. Previously suggested infrageneric arrangements based on presence or absence of the yellow substance rhizocarpic acid in the thallus or the septation of the ascospores are unnatural. Some species with grey or brown thallus may have evolved from a yellow ancestor. Spore septation and colour, amyloidity of the thalline medulla, and the presence of stictic acid complex and rhizocarpic acid are shown to have changed multiple times during the course of evolution.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 535–546.     

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.     

Phylogenetic relationships in the harmful dinoflagellate Cochlodinium polykrikoides (Gymnodiniales, Dinophyceae) inferred from LSU rDNA sequences

Phylogenetic relationships among chain-forming Cochlodinium species, including the harmful red tide forming dinoflagellate Cochlodinium polykrikoides, were investigated using specimens collected from coastal waters of Canada, Hong Kong, Japan, Korea, Malaysia, México, Philippines, Puerto Rico, and USA. The phylogenetic tree inferred from partial (D1–D6 regions) large subunit ribosomal RNA gene (LSU rDNA) sequences clearly differentiated between C. polykrikoides and a recently described species, Cochlodinium fulvescens. Two samples collected from the Pacific coasts of North America (British Columbia, Canada and California, USA) having typical morphological characters of C. fulvescens such as the sulcus located in the intermediate region of the cingulum, were closely related to C. fulvescens from western Japan in the phylogenetic tree. Cochlodinium polykrikoides formed a monophyletic group positioned as a sister group of the C. fulvescens clade with three well-supported sub-clades. These three clades were composed of (1) East Asian, including specimens collected from Hong Kong, western Japan, and southern Korea, (2) Philippines, from Manila Bay, Philippines and Omura Bay, Japan, and (3) American/Malaysian, from the Atlantic coasts of USA, the Pacific coast of México, Puerto Rico, and Borneo Island, Malaysia. Each of these clades is considered to be a so-called “ribotype” representing the population inhabiting each region, which is distinguished based on ribosomal RNA gene sequences in the species despite similarities in their morphological characters.     

Phylogenetic relationships of major clades of Catostomidae (Teleostei: Cypriniformes) as inferred from mitochondrial SSU and LSU rDNA sequences

Suckers (Family Catostomidae) are holarctic in distribution and include 76 recent species in 14 genera, with 13 genera and 75 species occurring in North and Central America and Siberia. Although this group constitutes a significant component of many aquatic ecosystems, most historic systematic effort has been either alpha- or limited beta-level studies focusing on the two largest tribes within the family, the Catostomini and the Moxostomatini. A recent phylogenetic study based on morphological, biochemical, and early life history characters has advanced current understanding of relationships among catostomid fishes. To further examine phylogenetic relationships among basal lineages of catostomids, we sequenced the entire mitochondrial (mt) SSU and LSU rRNA genes from genera representing all subfamilies and tribes within Catostomidae. Phylogenetic analysis of gene sequences yielded monophyletic Catostomidae, Ictiobinae, and Catostominae and para- or polyphyletic Cycleptinae, with Myxocyprinus as the basal-most taxon and Cycleptus as either the next most-basal taxon or the taxon basal to the Catostominae. Relationships within the Catostominae were generally consistent with those proposed in the above-noted recent phylogenetic study although Thoburnia and Hypentelium were either a clade sister to or a grade group relative to Moxostoma and Scartomyzon. In all trees, Scartomyzon was paraphyletic and embedded within Moxostoma. Phylogenetic affinities of Erimyzon and Minytrema varied depending on data set and character weighting scheme employed. To better reflect phylogenetic relationships resolved in this extensive analysis, we propose the following changes to the classification of catostomids: formation of the new subfamily Myxocyprininae, containing Myxocyprinus from China; restriction of the Cycleptinae to the two species of Cycleptus from North America; restriction of the tribe Moxostomatini to Moxostoma and Scartomyzon; Erimyzon and Minytrema are incertae sedis within Catostominae; and resurrection of the tribe Thoburniini, containing Thoburnia and expanded to include Hypentelium.     

Diversity of non-reducing polyketide synthase genes in the Pertusariales (lichenized Ascomycota): a phylogenetic perspective

Lichenized fungi synthesize a great variety of secondary metabolites. These are typically crystalline compounds, which are deposited extracellularly on the fungal hyphae. While we know a lot about the chemical properties and structures of these substances, we have very little information on the molecular background of their biosynthesis. In the current study we analyze the diversity of non-reducing polyketide synthase (PKS) genes in members of the lichenized Pertusariales. This order primarily contains fully oxidized secondary metabolites from different substance classes, and is chemically and phylogenetically well studied. Using a degenerate primer approach with subsequent cloning we detected up to five non-reducing PKS sequences in a single PCR product. Eighty-five new KS sequence fragments were obtained for this study. Analysis of the 157 currently available fungal KS sequence fragments in a Bayesian phylogenetic framework revealed 18 highly supported clades that included only lichenized taxa, only non-lichenized taxa, or both. Some Pertusarialean groupings of PKS sequences corresponded partly to phylogenetic groupings based on ribosomal DNA. This is reasonable, because a correlation between well-supported phylogenetic lineages and the occurrence of secondary metabolites in the Pertusariales has been observed before. However, no clear linkage was found between the PKS genes analyzed and the ability to produce a particular secondary substance. Several PKS clades did not reveal obvious patterns of secondary compound distribution or phylogenetic association. Compared with earlier phylogenetic analyses of KS sequences the increased sampling in the current study allowed us to detect many new groupings within the fungal non-reducing PKSs.     

基于rDNA ITS序列探讨中国栽培灵芝菌株的亲缘关系

利用ITS序列分析技术对中国栽培灵芝菌株进行了亲缘关系分析。结果发现中国栽培灵芝菌株分布于5个聚类组,其中树舌亚属、紫芝组的菌株各自聚成一组,灵芝组的菌株分成3组,85·7%灵芝组菌株均聚于同一组,表明树舌亚属、紫芝组和灵芝组间的遗传差异较大,灵芝组内虽然存在着一定的遗传差异,但总体上亲缘关系比较近,遗传多样性并不丰富。聚类结果也表明仅仅根据形态学特征并不能将灵芝属菌株进行有效的分类,利用分子生物学的技术手段对灵芝菌种进行分类是一种更有效的方法。     

Phylogeny of Neoparamoeba strains isolated from marine fish and invertebrates as inferred from SSU rDNA sequences

ABSTRACT: We characterised 9 strains selected from primary isolates referable to Paramoeba/Neoparamoeba spp. Based on ultrastructural study, 5 strains isolated from fish (amoebic gill disease [AGD]-affected Atlantic salmon and dead southern bluefin tuna), 1 strain from netting of a floating sea cage and 3 strains isolated from invertebrates (sea urchins and crab) were assigned to the genus Neoparamoeba Page, 1987. Phylogenetic analyses based on SSU rDNA sequences revealed affiliations of newly introduced and previously analysed Neoparamoeba strains. Three strains from the invertebrates and 2 out of 3 strains from gills of southern bluefin tunas were members of the N. branchiphila clade, while the remaining, fish-isolated strains, as well as the fish cage strain, clustered within the clade of N. pemaquidensis. These findings and previous reports point to the possibility that N. pemaquidensis and N. branchiphila can affect both fish and invertebrates. A new potential fish host, southern bluefin tuna, was included in the list of farmed fish endangered by N. branchiphila. The sequence of P. eilhardi (Culture Collection of Algae and Protozoa [CCAP] strain 1560/2) appeared in all analyses among sequences of strain representatives of Neoparamoeba species, in a position well supported by bootstrap value, Bremer index and Bayesian posterior probability. Our research shows that isolation of additional strains from invertebrates and further analyses of relations between molecular data and morphological characters of the genera Paramoeba and Neoparamoeba are required. This complexity needs to be considered when attempting to define molecular markers for identification of Paramoeba/Neoparamoeba species in tissues of fish and invertebrates.     

地衣型真菌新种小囊网盘衣(微孢衣科,子囊菌门)（英文）

本文根据表型与基因型分析结果描述了网盘衣属一新种小囊网盘衣。文中提供了新种的特征提要及其描述。     

Diversity of the lichenized fungi in King George Island, Antarctica, revealed by phylogenetic analysis of partial large subunit rDNA sequences

Lichens are predominant and important components of flora in the terrestrial ecosystem of Antarctica. However, relatively few researches on the phylogenetic position of Antarctic lichen-forming fungi have been accomplished. In this study, partial sequences of nuclear large subunit rDNAs from 50 Antarctic specimens were obtained and the phylogeny was reconstructed. Antarctic lichen species were distributed among 4 orders, including the monophyletic order Agyrales, paraphyletic orders Pertusariales and Teloschistales, and polyphyletic order Lecanorales. Species diversity was highest in the order Lecanorales, followed by Teloschistales and Pertusariales. Based on the phylogeny and sequence similarity analyses, it is proposed that the taxonomy of Stereocaulon alpinum, Physcia caesia, Usnea aurantiacoatra, and Cladonia species should be revised by careful examination of their phenotypic and molecular characteristics. Six species known to be endemic to Antarctica, Catillaria corymbosa, Himantormia lugubris, Leptogium puberulum, Pertusaria pertusa, Rhizoplaca aspidophora, and Umbilicaria antarctica, formed unique lineages, implying independent origins in the Antarctic area.