Evolution of helotialean fungi (Leotiomycetes, Pezizomycotina): a nuclear rDNA phylogeny

The highly divergent characters of morphology, ecology, and biology in the Helotiales make it one of the most problematic groups in traditional classification and molecular phylogeny. Sequences of three rDNA regions, SSU, LSU, and 5.8S rDNA, were generated for 50 helotialean fungi, representing 11 out of 13 families in the current classification. Data sets with different compositions were assembled, and parsimony and Bayesian analyses were performed. The phylogenetic distribution of lifestyle and ecological factors was assessed. Plant endophytism is distributed across multiple clades in the Leotiomycetes. Our results suggest that (1) the inclusion of LSU rDNA and a wider taxon sampling greatly improves resolution of the Helotiales phylogeny, however, the usefulness of rDNA in resolving the deep relationships within the Leotiomycetes is limited; (2) a new class Geoglossomycetes, including Geoglossum, Trichoglossum, and Sarcoleotia, is the basal lineage of the Leotiomyceta; (3) the Leotiomycetes, including the Helotiales, Erysiphales, Cyttariales, Rhytismatales, and Myxotrichaceae, is monophyletic; and (4) nine clades can be recognized within the Helotiales.     

Molecular phylogeny and radiation time of Erysiphales inferred from the nuclear ribosomal DNA sequences

Phylogenetic relationships of Erysiphales within Ascomycota were inferred from the newly determined sequences of the 18S rDNA and partial sequences of the 28S rDNA including the D1 and D2 regions of 10 Erysiphales taxa. Phylogenetic analyses revealed that the Erysiphales form a distinct clade among ascomycetous fungi suggesting that the Erysiphales diverged from a single ancestral taxon. The Myxotrichaceae of the Onygenales was distantly related to the other onygenalean families and was the sister group to the Erysiphales calde, with which it combined to form a clade. The Erysiphales/Myxotrichaceae clade was also closely related to some discomycetous fungi (Leotiales, Cyttariales and Thelebolaceae) including taxa that form cleistothecial ascomata. The present molecular analyses as well as previously reported morphological observations suggest the possible existence of a novel evolutionary pathway from cleistothecial discomycetous fungi to Erysiphales and Myxotrichaceae. However, since most of these fungi, except for the Erysiphales, are saprophytic on dung and/or plant materials, the questions of how and why an obligate biotroph like the Erysiphales radiated from the saprophytic fungi remain to be addressed. We also estimated the radiation time of the Erysiphales using the 18S rDNA sequences and the two molecular clockes that have been previously reported. The calculation showed that the Erysiphales split from the Myxotrichaceae 190–127 myr ago. Since the radiation time of the Erysiphales does not exceed 230 myr ago, even when allowance is made for the uncertainty of the molecular clocks, it is possible to consider that the Erysiphales evolved after the radiation of angiosperms. The results of our calculation also showed that the first radiation within the Erysiphales (138–92 myr ago) coincided with the date of a major diversification of angiosperms (130–90 myr ago). These results may support our early assumption that the radiation of the Erysiphales coincided with the evolution of angiosperm plants. Contribution No. 152 from the Laboratory of Plant Pathology, Mie University     

Molecular phylogeny reveals a core clade of Rhytismatales

Rhytismatales (Leotiomycetes, Pezizomycotina, Ascomycota) are an order of mostly plant-associated ascomycetes with a global distribution. Well known taxa include the Rhytisma tar spots on Acer spp. and several needle-cast pathogens in genera Lophodermium and Meloderma. Critical studies are lacking at all taxonomic ranks from order to species, and in particular the genus taxonomy in the order has been criticized for being unnatural. We used nuclear LSU and mitochondrial SSU sequences in Bayesian phylogenetic analyses to define a core clade of Rhytismatales sensu stricto. Some of the genera traditionally placed within the Rhytismatales, Ascodichaena, Marthamyces, Mellitiosporium, Potebniamyces, Propolis and Pseudophacidium, are shown to be phylogenetically distinct, all related to various other taxa at present placed in the polyphyletic Helotiales. Within the core clade only Cudonia, Spathularia and Terriera are supported as monophyletic. The large genera Coccomyces, Hypoderma and Lophodermium all are polyphyletic as are a few smaller genera. The traditionally used characters of ascoma and spore shape are shown to be unreliable for the delimitation of monophyletic genera but in some cases can be useful when combined with other characters. In this study we provide 72 new nrLSU and 64 new mtSSU sequences. Together with publicly available sequences data for 103 specimens representing 91 species of Rhytismatales are now available. Despite this taxon sampling intensity is still too low to propose an alternative generic taxonomy.     

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.     

The molecular phylogeny of aquatic hyphomycetes with affinity to the Leotiomycetes

Aquatic hyphomycetes play a key role in decomposition of submerged organic matter and stream ecosystem functioning. We examined the phylogenetic relationships among various genera of aquatic hyphomycetes belonging to the Leotiomycetes (Ascomycota) using sequences of internal transcribed spacer (ITS) and large subunit (LSU) regions of rDNA generated from 42 pure cultures including 19 ex-types. These new sequence data were analyzed together with additional sequences from 36 aquatic hyphomycetes and 60 related fungi obtained from GenBank. Aquatic hyphomycetes, characterized by their tetraradiate or sigmoid conidia, were scattered in nine supported clades within the Helotiales (Leotiomycetes). Tricladium, Lemonniera, Articulospora, Anguillospora, Varicosporium, Filosporella, and Flagellospora are not monophyletic, with species from the same genus distributed among several major clades. The Gyoerffyella clade and the Hymenoscyphus clade accommodated species from eight and six different genera, respectively. Thirteen aquatic hyphomycete taxa were grouped in the Leotia-Bulgaria clade while twelve species clustered within the Hymenoscyphus clade along with several amphibious ascomycetes. Species of Filosporella and some species from four other aquatic genera were placed in the Ascocoryne-Hydrocina clade. It is evident that many aquatic hyphomycetes have relatives of terrestrial origin. Adaptation to colonize the aquatic environment has evolved independently in multiple phylogenetic lineages within the Leotiomycetes.     

Naemacyclus culmigenus,a newly reported potential pathogen to Miscanthus sinensis,new to Japan

Since the summer of 2010, a discomycete with erumpent apothecia associated with a leaf blight of Miscanthus leaves, were often collected. The morphological characteristics of the fungus suggested it was a member of the Helotiales rather than the Rhytismatales and this was supported by a phylogenetic analysis. Based on a morphological comparison with the type specimen of Naemacyclus culmigenus, currently known from Poaceae (Andropogon and Panicum), it was identified as N. culmigenus, new to Japan. The molecular phylogenetic analysis showed that the generic delimitation of Naemacyclus and related species requires clarification, as does their higher classification within the Leotiomycetes.     

Interrelationships of Staphyliniform groups inferred from 18S and 28S rDNA sequences, with special emphasis on Hydrophiloidea (Coleoptera, Staphyliniformia)

The series Staphyliniformia is one of the mega‐diverse groups of Coleoptera, but the relationships among the main families are still poorly understood. In this paper we address the interrelationships of staphyliniform groups, with special emphasis on Hydrophiloidea and Hydraenidae, based on partial sequences of the ribosomal genes 18S rDNA and 28S rDNA. Sequence data were analysed with parsimony and Bayesian posterior probabilities, in an attempt to overcome the likely effect of some branches longer than the 95% cumulative probability of the estimated normal distribution of the path lengths of the species. The inter‐family relationships in the trees obtained with both methods were in general poorly supported, although most of the results based on the sequence data are in good agreement with morphological studies. In none of our analyses a close relationship between Hydraenidae and Hydrophiloidea was supported, contrary to the traditional view but in agreement with recent morphological investigations. Hydraenidae form a clade with Ptiliidae and Scydmaenidae in the tree obtained with Bayesian probabilities, but are placed as basal group of Staphyliniformia (with Silphidae as subordinate group) in the parsimony tree. Based on the analysed data with a limited set of outgroups Scarabaeoidea are nested within Staphyliniformia. However, this needs further support. Hydrophiloidea s.str., Sphaeridiinae, Histeroidea (Histeridae + Sphaeritidae), and all staphylinoid families included are confirmed as monophyletic, with the exception of Hydraenidae in the parsimony tree. Spercheidae are not a basal group within Hydrophiloidea, as has been previously suggested, but included in a polytomy with other Hydrophilidae in the Bayesian analyses, or its sistergroup (with the inclusion of Epimetopidae) in the parsimony tree. Helophorus is placed at the base of Hydrophiloidea in the parsimony tree. The monophyly of Hydrophiloidea s.l. (including the histeroid families) and Staphylinoidea could not be confirmed by the analysed data. Some results, such as a placement of Silphidae as subordinate group of Hydraenidae (parsimony tree), or a sistergroup relationship between Ptiliidae and Scydmaenidae, appear unlikely from a morphological point of view.     

A five-gene phylogeny of Pezizomycotina

Pezizomycotina is the largest subphylum of Ascomycota and includes the vast majority of filamentous, ascoma-producing species. Here we report the results from weighted parsimony, maximum likelihood and Bayesian phylogenetic analyses of five nuclear loci (SSU rDNA, LSU rDNA, RPB1, RPB2 and EF-lalpha) from 191 taxa. Nine of the 10 Pezizomycotina classes currently recognized were represented in the sampling. These data strongly supported the monophyly of Pezizomycotina, Arthoniomycetes, Eurotiomycetes, Orbiliomycetes and Sordariomycetes. Pezizomycetes and Dothideomycetes also were resolved as monophyletic but not strongly supported by the data. Lecanoromycetes was resolved as paraphyletic in parsimony analyses but monophyletic in maximum likelihood and Bayesian analyses. Leotiomycetes was polyphyletic due to exclusion of Geoglossaceae. The two most basal classes of Pezizomycotina were Orbiliomycetes and Pezizomycetes, both of which comprise species that produce apothecial ascomata. The seven remaining classes formed a monophyletic group that corresponds to Leotiomyceta. Within Leotiomyceta, the supraclass clades of Leotiomycetes s.s. plus Sordariomycetes and Arthoniomycetes plus Dothideomycetes were resolved with moderate support.     

Phylogenetic relationships of Chalara and allied species inferred from ribosomal DNA sequences

The phylogenetic relationships of Chalara and allied taxa are studied based on ribosomal DAN sequences. Partial 28S rDNA and 18S rDNA regions from 26 strains were sequenced in this study. These and related sequences from GenBank were analyzed using parsimony and Bayesian analyses. Most of the Chalara species clustered in a strongly supported monophyletic lineage representing Helotiales. However, a few Chalara species appeared closely related to Xylariales. The phylogenetic significance of morphological characters observed in Chalara species are evaluated based on our sequence analyses. Conidial septation, conidial width and conidiophore pigmentation are thought to be indicative in understanding their evolutionary relationships. Sterile setae, which traditionally have been used to delimitate Chaetochalara from Chalara, are phylogenetically insignificant.     

Searching for natural lineages within the Cerylonid Series (Coleoptera: Cucujoidea)

Phylogenetic relationships within the diverse beetle superfamily Cucujoidea are poorly known. The Cerylonid Series (C.S.) is the largest of all proposed superfamilial cucujoid groups, comprising eight families and representing most of the known cucujoid species diversity. The monophyly of the C.S., however, has never been formally tested and the higher-level relationships among and within the constituent families remain equivocal. Here we present a phylogenetic study based on 18S and 28S rDNA for 16 outgroup taxa and 61 C.S. ingroup taxa, representing seven of the eight C.S. families and 20 of 39 subfamilies. We test the monophyly of the C.S., investigate the relationships among the C.S. families, and test the monophyly of the constituent families and subfamilies. Phylogenetic reconstruction of the combined data was achieved via standard static alignment parsimony analyses, Direct Optimization using parsimony, and partitioned Bayesian analysis. All three analyses support the paraphyly of Cucujoidea with respect to Tenebrionoidea and confirm the monophyly of the C.S. The C.S. families Bothrideridae, Cerylonidae, Discolomatidae, Coccinellidae and Corylophidae are supported as monophyletic in all analyses. Only the Bayesian analysis recovers a monophyletic Latridiidae. Endomychidae is recovered as polyphyletic in all analyses. Of the 14 subfamilies with multiple terminals in this study, 11 were supported as monophyletic. The corylophid subfamily Corylophinae and the coccinellid subfamilies Chilocorinae and Scymninae are recovered as paraphyletic. A sister grouping of Anamorphinae+Corylophidae is supported in all analyses. Other taxonomic implications are discussed in light of our results.     

Phylogenetic analysis of the Metastrongyloidea (Nematoda: Strongylida) inferred from ribosomal RNA gene sequences

Phylogenetic relationships among nematodes of the strongylid superfamily Metastrongyloidea were analyzed using partial sequences from the large-subunit ribosomal RNA (LSU rRNA) and small-subunit ribosomal RNA (SSU rRNA) genes. Regions of nuclear ribosomal DNA (rDNA) were amplified by polymerase chain reaction, directly sequenced, aligned, and phylogenies inferred using maximum parsimony. Phylogenetic hypotheses inferred from the SSU rRNA gene supported the monophyly of representative taxa from each of the 7 currently accepted metastrongyloid families. Metastrongyloid taxa formed the sister group to representative trichostrongyloid sequences based on SSU data. Sequences from either the SSU or LSU RNA regions alone provided poor resolution for relationships within the Metastrongyloidea. However, a combined analysis using sequences from all rDNA regions yielded 3 equally parsimonious trees that represented the abursate Filaroididae as polyphyletic, Parafilaroides decorus as the sister species to the monophyletic Pseudaliidae, and a sister group relationship between Oslerus osleri and Metastrongylus salmi. Relationships among 3 members of the Crenosomatidae, and 1 representative of the Skrjabingylidae (Skrjabingylus chitwoodorum) were not resolved by these combined data. However, members of both these groups were consistently resolved as the sister group to the other metastrongyloid families. These relationships are inconsistent with traditional classifications of the Metastrongyloidea and existing hypotheses for their evolution.     

基于28S rDNA D1-D2基因片段与16S rDNA部分序列联合分析的叶肢介系统发育研究

叶肢介(Conchostraca)的系统发育问题一直是甲壳动物研究中颇具争议的一个课题.本研究测定了我国2种叶肢介(Eocyzicus mongolianus,Eoc yzicus orientalis)的28S rDNA D1-D2区基因序列和16S rDNA E-G区序列,并与GenBank中的20种叶肢介序列一起...     

Ascoma development and phylogeny of an apothecioid dothideomycete, Catinella olivacea

Catinella olivacea is a discomycetous fungus often found fruiting within cavities in rotting logs. Because this habitat would lack the air currents upon which discomycete species normally rely for the dispersal of their forcibly ejected ascospores, we suspected an alternative disseminative strategy might be employed by this species. An examination of the development of the discomycetous ascomata in pure culture, on wood blocks, and on agar showed that the epithecium was gelatinous at maturity and entrapped released ascospores in a slimy mass. We interpreted this as an adaptation for ascospore disperal by arthropods. Developmental data also showed that C. olivacea was unusual among other discomycetes in the Helotiales (Leotiomycetes). For example, the ascoma developed from a stromatic mass of meristematically dividing cells and involved the formation of a uniloculate cavity within a structure better considered an ascostroma than an incipient apothecium. Furthermore, the ascus had a prominent ocular chamber and released its ascospores through a broad, bivalvate slit. These features, along with phylogenetic analyses of large subunit and small subunit rDNA, indicated that this unusual apothecial fungus is, surprisingly, more closely affiliated with the Dothideomycetes than the Leotiomycetes.     

Phylogenetics and temporal diversification of the earliest true flies (Insecta: Diptera) based on multiple nuclear genes

Abstract Relationships among families of the lower Diptera (formerly suborder ‘Nematocera’) have been exceptionally difficult to resolve. Multiple hypotheses based on morphology have been proposed to identify the earliest lineages of flies and place the phylogenetic origin of the higher flies (Brachycera), but convincing support is limited. Here we resolve relationships among the major groups of lower Diptera using sequence data from four nuclear markers, including both ribosomal (28S rDNA) and protein‐coding (CAD, TPI and PGD) genes. Our results support both novel and traditional arrangements. Most unexpectedly, the small, highly‐specialized family Deuterophlebiidae appears to be sister to all remaining Diptera. Other results include the resolution of the traditional infra‐orders Culicomorpha (including a novel superfamily Simulioidea = Thaumaleidae + Simuliidae), Tipulomorpha (Tipulidae sensu lato + Trichoceridae) and Bibionomorpha sensu lato. We find support for a limited Psychodomorpha (Blephariceridae, Tanyderidae and Psychodidae) and Ptychopteromorpha (Ptychopteridae), whereas the placement of several enigmatic families (Nymphomyiidae, Axymyiidae and Perissommatidae) remains ambiguous. According to genetic data, the infra‐order Bibionomorpha is sister to the Brachycera. Much of the phylogenetic signal for major lineages was found in the 28S rDNA gene, whereas protein‐coding genes performed variably at different levels. In addition to elucidating relationships, we also estimate the age of major lower dipteran clades, based on molecular divergence time estimates using relaxed‐clock Bayesian methods and fossil calibration points.     

Structural alignment of 18S and 28S rDNA sequences provides insights into phylogeny of Phytophaga (Coleoptera: Curculionoidea and Chrysomeloidea)

We performed a comparative study of partial rDNA sequences from a variety of Coleoptera taxa to construct an annotated alignment based on secondary structure information, which in turn, provides improved rRNA structure models useful for phylogenetic reconstruction. Subsequent phylogenetic analysis was performed to test monophyly and interfamilial relationships of the megadiverse plant feeding beetle group known as ‘Phytophaga’ (Curculionoidea and Chrysomeloidea), as well as to discover their closest relatives among the Cucujiformia. Parsimony and Bayesian analyses were performed based on the structural alignment of segments of 18S rRNA (variable regions V4‐V5, V7‐V9) and 28S rRNA (expansion segment D2). A total of 104 terminal taxa of Coleoptera were included: 96 species of Cucujiformia beetles, representing the families and most ‘subfamilies’ of weevils and chrysomeloids (Phytophaga), as well as several families of Cleroidea, Tenebrionoidea and Cucujoidea, and eight outgroups from three other polyphagan series: Scarabaeiformia, Elateriformia and Bostrichiformia. The results from the different methods of analysis agree — recovering the monophyly of the ‘Phytophaga’, including Curculionoidea and Chrysomeloidea as sister groups. The curculionoid and chrysomeloid phylogeny recovered from the aligned 18S and 28S rDNA segments, which is independent of morphological data, is in agreement with recent hypotheses or concepts based on morphological evidence, particularly with respect to familial relationships. Our results provide clues about the evolutionary origin of the phytophagan beetles within the megaclade Cucujiformia, suggesting that the sister group of ‘Curculionoidea + Chrysomeloidea’ is a clade of the ‘Cucujoidea’, represented in this study by species in Boganiidae, Erotylidae, Nitidulidae, Cucujidae and Silvanidae. The Coccinellidae and Endomychidae are not grouped with the latter, and the remaining terminal taxa are nested in Tenebrionoidea and Cleroidea. We propose that the combination of structurally aligned ribosomal RNA gene regions 18S (V4‐V5, V7‐V9) and 28S (D2) are useful in testing monophyly and resolving relationships among beetle superfamilies and families.     

Higher level phylogenetic relationships of euascomycetes (Pezizomycotina) inferred from a combined analysis of nuclear and mitochondrial sequence data

A combined data set of nuclear SSU rDNA, LSU rDNA, and mitochondrial SSU rDNA sequences was analyzed in order to examine the relationships of the major clades of euascomycetes. Partial sequences of 14 ascomycetes were determined and aligned with the corresponding sequences of 16 other ascomycetes retrieved from Genbank. The alignment was analyzed using maximum parsimony (MP) and a Bayesian analysis with Markov chain Monte Carlo (B/MCMC). The classification based on single-gene studies is supported, but the confidence is enhanced in the concatenated analysis. The monophyly of the superclass Leotiomyceta, which includes all euascomycetes with inoperculate asci, is strongly supported. The polyphyly of ascolocularous fungi is supported. The group is divided into two groups: the Dothideomycetes basal to all other Leotiomyceta and the Chaetothyriomycetes as sister-group to Eurotiomycetes. The Lecanoromycetes appear as a monophyletic group with strong support and form a sister-group to the Chaetothyriomycetes/Eurotiomycetes clade, but this lacks support. The Leotiomycetes and Sordariomycetes form a strongly supported sister-group. Alternative topologies are tested using parametric bootstrapping; a basal position of the Eurotiomycetes and Leotiomycetes in the Leotiomyceta cannot be rejected, while such a position can be rejected for Chaetothyriomycetes, Lecanoromycetes and Sordariomycetes. The character evolution with regard to ascoma type, ascus type and ascoma-ontogeny is examined using MP and maximum likelihood (ML). While it appears most likely that the ancestor of the inoperculate ascomycetes had apothecia and an ascohymenial ascoma-ontogeny using MP methods, the ML approach shows that there is some uncertainty at the current state of knowledge. The improvement of confidence of the combined data set in comparison with single-gene studies makes us confident that analyses with additional data sets will further improve the confidence and eventually uncover the branching order of euascomycetes.     

Molecular and morphological phylogenetics of weevils (coleoptera,curculionoidea): do niche shifts accompany diversification?

The main goals of this study were to provide a robust phylogeny for the families of the superfamily Curculionoidea, to discover relationships and major natural groups within the family Curculionidae, and to clarify the evolution of larval habits and host-plant associations in weevils to analyze their role in weevil diversification. Phylogenetic relationships among the weevils (Curculionoidea) were inferred from analysis of nucleotide sequences of 18S ribosomal DNA (rDNA; approximately 2,000 bases) and 115 morphological characters of larval and adult stages. A worldwide sample of 100 species was compiled to maximize representation of weevil morphological and ecological diversity. All families and the main subfamilies of Curculionoidea were represented. The family Curculionidae sensu lato was represented by about 80 species in 30 "subfamilies" of traditional classifications. Phylogenetic reconstruction was accomplished by parsimony analysis of separate and combined molecular and morphological data matrices and Bayesian analysis of the molecular data; tree topology support was evaluated. Results of the combined analysis of 18S rDNA and morphological data indicate that monophyly of and relationships among each of the weevil families are well supported with the topology ((Nemonychidae, Anthribidae) (Belidae (Attelabidae (Caridae (Brentidae, Curculionidae))))). Within the clade Curculionidae sensu lato, the basal positions are occupied by mostly monocot-associated taxa with the primitive type of male genitalia followed by the Curculionidae sensu stricto, which is made up of groups with the derived type of male genitalia. High support values were found for the monophyly of some distinct curculionid groups such as Dryophthorinae (several tribes represented) and Platypodinae (Tesserocerini plus Platypodini), among others. However, the subfamilial relationships in Curculionidae are unresolved or weakly supported. The phylogeny estimate based on combined 18S rDNA and morphological data suggests that diversification in weevils was accompanied by niche shifts in host-plant associations and larval habits. Pronounced conservatism is evident in larval feeding habits, particularly in the host tissue consumed. Multiple shifts to use of angiosperms in Curculionoidea were identified, each time associated with increases in weevil diversity and subsequent shifts back to gymnosperms, particularly in the Curculionidae.     

Affinities among anostracan (Crustacea: Branchiopoda) families inferred from phylogenetic analyses of multiple gene sequences

To gain insights into the relationships among anostracan families, molecular phylogenetic analyses were performed on nuclear (28S D1-D3 ribosomal DNA) and mitochondrial (16S rDNA, COI) gene regions for representatives of seven families and an outgroup. Data matrices used in the analyses included 951 base pairs (bp) of aligned sequences for 28S, 465 bp for 16S, and 658 bp (219 amino acids) for COI. Maximum-parsimony and maximum-likelihood methods were used to construct phylogenetic trees, enabling the evaluation of both previous hypotheses of taxonomic relationships among families based on morphology, and of the relative merits of independent versus simultaneous analyses of multiple data sets for phylogeny construction. Data from various combinations of the gene regions produced relatively congruent patterns of phylogenetic affinity. In most analyses, two monophyletic groups were resolved: one cluster included the families Polyartemiidae, Chirocephalidae, Branchinectidae, Streptocephalidae, and Thamnocephalidae, while the other contained the Artemiidae and Branchipodidae. Comparative analyses showed that combining gene regions in a single matrix generally resulted in increased resolution and support for each cluster relative to those obtained from single-gene analyses. Statistical tests demonstrated that morphology-based hypotheses of relationships among families had poorer support than those determined from molecular data, reflecting the homoplasy in characters used to differentiate families.     

Performance of four ribosomal DNA regions to infer higher-level phylogenetic relationships of inoperculate euascomycetes (Leotiomyceta)

The inoperculate euascomycetes are filamentous fungi that form saprobic, parasitic, and symbiotic associations with a wide variety of animals, plants, cyanobacteria, and other fungi. The higher-level relationships of this economically important group have been unsettled for over 100 years. A data set of 55 species was assembled including sequence data from nuclear and mitochondrial small and large subunit rDNAs for each taxon; 83 new sequences were obtained for this study. Parsimony and Bayesian analyses were performed using the four-region data set and all 14 possible subpartitions of the data. The mitochondrial LSU rDNA was used for the first time in a higher-level phylogenetic study of ascomycetes and its use in concatenated analyses is supported. The classes that were recognized in Leotiomyceta (=inoperculate euascomycetes) in a classification by Eriksson and Winka [Myconet 1 (1997) 1] are strongly supported as monophyletic. The following classes formed strongly supported sister-groups: Arthoniomycetes and Dothideomycetes, Chaetothyriomycetes and Eurotiomycetes, and Leotiomycetes and Sordariomycetes. Nevertheless, the backbone of the euascomycete phylogeny remains poorly resolved. Bayesian posterior probabilities were always higher than maximum parsimony bootstrap values, but converged with an increase in gene partitions analyzed in concatenated analyses. Comparison of five recent higher-level phylogenetic studies in ascomycetes demonstrates a high degree of uncertainty in the relationships between classes.     

利用分子标记18S rDNA对天牛高阶元进化关系的研究

【目的】构建天牛总科高阶元的进化关系,为解决天牛各亚科之间进化关系和归属提供依据。【方法】本研究采用18S rDNA(V4、V7区)分子标记,分析和测定了49种天牛基因序列,并结合GenBank数据库中3科2亚科21种天牛的18S rDNA基因序列,采用邻近法(Neighbor Jointing,NJ)、贝叶斯推论法(Bayesian Inference,BI)和最大似然法(Maximum Likelihood),对天牛总科3科6亚科的70种天牛基因序列构建进化树,探讨天牛高阶元类群的进化关系。【结果】研究表明:序列分析比对后得到序列为703 bp,碱基A、T、C、G的含量分别为21.1%、26.3%、23.6%和28.9%;变异位点(Variable sites)98个占全部位点的13.9%,简约信息位点(Parsimony informative sites)45个占全部位点的6.4%;转换(Transition)/颠换(Transversion)的平均值R值为2.79,转换大于颠换。进化树结果显示沟胫天牛亚科Lamiinae、天牛亚科Cerambycinae、锯天牛亚科Prioninae和瘦天牛科Disteniidae为单系性进化群,这与传统形态学分类结果相似。【结论】本研究成功构建了天牛总科高阶元的系统发育树,研究证明18S rDNA(V4、V7区)是探讨天牛高级阶元分类有效的分子标记。