Phylogenetic relationships among Taphrina, Saitoella, and other higher fungi

To determine the phylogenetic placement of the major groups of higher fungi, we sequenced the DNA sequences from the small-subunit ribosomal RNA (18S rRNA) coding regions from Taphrina wiesneri (synonym: T. cerasi) and Saitoella complicata and compared them to 18S rRNA sequences from the oomycetes, chytridiomycetes, zygomycetes, ascomycetes, and basidiomycetes. Here we demonstrate that the ascomycetes have at least two major evolutionary lineages. Taphrina wiesneri and Saitoella complicata form a monophyletic branch that diverged prior to the separation of other ascomycetes. The same treatment could be accorded to Schizosaccharomyces pombe.      

Loss of meiosis in Aspergillus

If strictly mitotic asexual fungi lack recombination, the conventional view predicts that they are recent derivatives from older meiotic lineages. We tested this by inferring phylogenetic relationships among closely related meiotic and strictly mitotic taxa with Aspergillus conidial (mitotic) states. Phylogenies were constructed by using DNA sequences from the mitochondrial small ribosomal subunit, the nuclear ribosomal internal transcribed spacers, and the nuclear 5.8S ribosomal gene. Over 920 bp of sequence was analyzed for each taxon. Phylogenetic analysis of both the mitochondrial and nuclear data sets showed at least four clades that possess both meiotic and strictly mitotic taxa. These results support the hypothesis that strictly mitotic lineages arise frequently from more ancient meiotic lineages with Aspergillus conidial states. Many of the strictly mitotic species examined retained characters that may be vestiges of a meiotic state, including the production of sclerotia, sclerotium-like structures, and hulle cells.      

Small subunit ribosomal DNA characterization of an unidentified aurantiactinomyxon form and its oligochaete host Tubifex ignotus

In this study, the small subunit (18S) ribosomal DNA gene from an aurantiactinomyxon form of unknown taxonomic position (A1) and from its aquatic oligochaete host (Tubifex ignotus) were characterized. Molecular sequence information on A1 was obtained to allow comparisons of this gene with known sequences from known myxosporean forms, and therefore to investigate possible relationships between this organism and its alternate myxosporean stage. Sequence data for the oligochaete host, together with morphological features, will allow reliable identification of this species in the future. Sequence data derived from the 18S DNA gene and data from other related or non-related organisms were analyzed and used to construct a phylogenetic tree. Phylogenetic studies provided an insight into the taxonomic position of A1. Sequence similarities within the 18S rDNA A1 gene and compared organisms indicated that A1 was most closely related to members of the sub-order Variisporina (Myxidium lieberkuehni [Ml] and Sphaerospora oncorhynchi [So]). Clustering of the 3 organisms in the same branch was well supported by high bootstrap values (81%). A1 showed higher similarities with sequences of Ml (approximately 80%) than with So (approximately 79%). Myxosporean sequence analysis indicated that phylogenetic arrangements do not support traditional classification based on morphological criteria of the spores, but rather support arrangement by tissue location. Marine actinosporeans Triactinomyxon sp. and Tetraspora discoidea were found to be associated with Platysporinid myxosporeans, supporting previous findings. In this study, 18S rDNA sequence data are generated for first time for the aquatic oligochaete T. ignotus. Phylogenetic 18S rDNA gene analyses performed with T. ignotus support and confirm existing morphological and molecular phylogenetic studies. Paraphyly of the Tubificidae family was noticed.     

Phylogenetic relationships of ascomycetes and basidiomycetes based on comparative genomics analysis

The relationship between ascomycetes and basidiomycetes, the two main phyla of non-flagellated fungi, has rarely been investigated. In this study, we performed a comparative genomics analysis of genome sequences of 55 ascomycetes and 26 basidiomycetes species and detected 81 universal markers, 875 homologous genes and a conserved contig in the glucose-regulated protein gene. In dendrograms based on simple sequence repeat markers and homologous genes, ascomycetes and basidiomycetes formed distinct clusters, with each set of taxa having a high coefficient of relatedness. Ascomycetes and basidiomycetes also constituted distinct groups in a phylogenetic tree based on a conserved contig in the glucose-regulated protein gene. These results provide evidence that basidiomycetes may be derived from ascomycetes but are definitely genetically differentiated at the genomic level. The phylogenetic relationships of ascomycetes and basidiomycetes uncovered in this study provide new insights for future research related to fungal classification and evolution.     

Independent terrestrial origins of the Halosphaeriales (marine Ascomycota)

A phylogenetic study of marine ascomycetes was initiated to test and refine evolutionary hypotheses of marine-terrestrial transitions among ascomycetes. Taxon sampling focused on the Halosphaeriales, the largest order of marine ascomycetes. Approximately 1050 base pairs (bp) of the gene that codes for the nuclear small subunit (SSU) and 600 bp of the gene that codes for the nuclear large subunit (LSU) ribosomal RNAs (rDNA) were sequenced for 15 halosphaerialean taxa and integrated into a data set of homologous sequences from terrestrial ascomycetes. An initial set of phylogenetic analyses of the SSU rDNA from 38 taxa representing 15 major orders of the phylum Ascomycota confirmed a close phylogenetic relationship of the halosphaerialean species with several other orders of perithecial ascomycetes. A second set of analyses, which involved more intensive taxon sampling of perithecial ascomycetes, was performed using the SSU and LSU rDNA data in combined analyses. These second analyses included 15 halosphaerialean taxa, 26 terrestrial perithecial fungi from eight orders, and five outgroup taxa from the Pezizales. In these analyses the Halosphaeriales were polyphyletic and comprised two distinct lineages. One clade of Halosphaeriales comprised 12 taxa from 11 genera and was most closely related to terrestrial fungi of the Microascales. The second clade of halosphaerialean fungi comprised taxa from the genera Lulworthia and Lindra and was an isolated lineage among the perithecial fungi. Both the main clade of Halosphaeriales and the Lulworthia/Lindra clade are supported by the data as being independently derived from terrestrial ancestors.     

Time flies, a new molecular time-scale for brachyceran fly evolution without a clock

The insect order Diptera, the true flies, contains one of the four largest Mesozoic insect radiations within its suborder Brachycera. Estimates of phylogenetic relationships and divergence dates among the major brachyceran lineages have been problematic or vague because of a lack of consistent evidence and the rarity of well-preserved fossils. Here, we combine new evidence from nucleotide sequence data, morphological reinterpretations, and fossils to improve estimates of brachyceran evolutionary relationships and ages. The 28S ribosomal DNA (rDNA) gene was sequenced for a broad diversity of taxa, and the data were combined with recently published morphological scorings for a parsimony-based phylogenetic analysis. The phylogenetic topology inferred from the combined 28S rDNA and morphology data set supports brachyceran monophyly and the monophyly of the four major brachyceran infraorders and suggests relationships largely consistent with previous classifications. Weak support was found for a basal brachyceran clade comprising the infraorders Stratiomyomorpha (soldier flies and relatives), Xylophagomorpha (xylophagid flies), and Tabanomorpha (horse flies, snipe flies, and relatives). This topology and similar alternative arrangements were used to obtain Bayesian estimates of divergence times, both with and without the assumption of a constant evolutionary rate. The estimated times were relatively robust to the choice of prior distributions. Divergence times based on the 28S rDNA and several fossil constraints indicate that the Brachycera originated in the late Triassic or earliest Mesozoic and that all major lower brachyceran fly lineages had near contemporaneous origins in the mid-Jurassic prior to the origin of flowering plants (angiosperms). This study provides increased resolution of brachyceran phylogeny, and our revised estimates of fly ages should improve the temporal context of evolutionary inferences and genomic comparisons between fly model organisms.     

Ribosomal DNA and resolution of branching order among the ascomycota: how many nucleotides are enough?

Molecular phylogenies for the fungi in the Ascomycota rely heavily on 18S rRNA gene sequences but this gene alone does not answer all questions about relationships. Particularly problematical are the relationships among the first ascomycetes to diverge, the Archiascomycetes, and the branching order among the basal filamentous ascomycetes, the Euascomycetes. Would more data resolve branching order? We used the jackknife and bootstrapping resampling approach that constitutes the "pattern of resolved nodes" method to address the relationship between number of variable sites in a DNA sequence alignment and support for taxonomic clusters. We graphed the effect of increasing sizes of subsamples of the 18S rRNA gene sequences on bootstrap support for nodes in the Ascomycota tree. Nodes responded differently to increasing data. Some nodes, those uniting the filamentous ascomycetes for example, would still have been well supported with only two thirds of the 18S rRNA gene. Other nodes, like the one uniting the Archiascomycetes as a monophyletic group, would require about double the number of variable sites available in the 18S gene for 95% neighbor-joining bootstrap support. Of the several groups emerging at the base of the filamentous ascomycetes, the Pezizales receive the most support as the first to diverge. Our analysis suggests that we would also need almost three times as much sequence data as that provided by the 18S gene to confirm the basal position for the Pezizales and more than seven times as much data to resolve the next group to diverge. If more data from other genes show the same pattern, the lack of resolution for the filamentous ascomycetes may indicate rapid radiation within this clade.     

New insights into diversity and selectivity of trentepohlialean lichen photobionts from the extratropics

Aerial green algae of Trentepohliaceae can form conspicuous free-living colonies, be parasites of plants or photobionts of lichen-forming ascomycetes. So far, their diversity in temperate regions is still poorly known as it has been mostly studied by phenotypic approaches only. We present new insights in the phylogenetic relationships of lichenized representatives from temperate and Mediterranean parts of Europe by analysis of 18S rRNA and rbcL gene fragments, and nuclear ITS sequence data. For this purpose we isolated the trentepohlialean photobionts from lichens representing different genera. Algal cultures from lichenized and free-living Trentepohliaceae were used to design new primers for amplification of the marker loci. We constructed a phylogenetic hypothesis to reveal the phylogenetic placements of lichenized lineages with 18S rRNA and rbcL sequences. ITS variation among the clades was substantial and did not allow including them in the general phylogenetic assessment, yet ITS appears to be a promising marker for DNA-barcoding approaches. Specific algae were found in particular lichen but the overall diversity of photobionts was limited. The multilocus tree does not support the current morphological classification of genera in Trentepohliaceae, suggesting that morphology is more variable than previously thought in this group of algae.     

Phylogeny of the neotropical moth tribe Josiini (Notodontidae: Dioptinae): comparing and combining evidence from DNA sequences and morphology

DNA sequences were gathered from mitochondrial COII and nuclear ribosomal 18S and 28S genes for 21 moth species in the tribe Josiini (Notodontidae: Dioptinae) and two outgroup genera. These data complement a previously published morphological character set for the same taxa. We examine whether relationships in the Josiini are best reflected by a single phylogenetic analysis of all the data, or by a consensus of separate trees generated from DNA and morphology. Even in cases where analyses of partitioned data produce incongruent cladograms, the underlying disagreement between partitions is relatively small. While both molecular and morphological data provide useful character information by themselves, we conclude that the best supported phylogenetic hypothesis is the one derived from combined analysis.     

Phylogenetic relationships of Cryphonectria and Endothia species, based on DNA sequence data and morphology

The fungal genera Endothia and Cryphonectria include some of the most important pathogens of forest trees. Despite available new technology, no comprehensive comparative study based on DNA sequence data and morphology has been done on the available isolates representing these two genera. The main objectives of this study were to assess the phylogenetic relationships among species of Cryphonectria and Endothia, for which cultures are available, and to establish a taxonomic framework based on DNA sequence and morphological data, which will aid future studies and identification of species in these and related genera. Comparisons were based on sequence variation found in the ITS region of the ribosomal RNA operon and two regions of the β-tu-bulin gene. In addition, the morphology of these species was examined. The phylogenetic data indicated that Endothia and Cryphonectria reside in two distinct phylogenetic clades. Cryphonectria parasitica, C. macrospora, C. nitschkei, C. eucalypti and C. radicalis represented the Cryphonectria clade. Endothia gyrosa and E. singularis were included in the Endothia clade. An isolate representing E. viridistroma grouped outside the Endothia clade and separately from other groups. Other clades outside the one encompassing Cryphonectria were those represented by the C. cubensis isolates and fungi isolated from Elaeocarpus dentatus originating from New Zealand. These clades could be distinguished from Endothia and Cryphonectria, based on anamorph morphology, stromatal structure and ascospore septation. Cryphonectria and Endothia, therefore, appear to be paraphyletic and taxonomic relationships for these fungi need to be revised.     

Molecular evolution of pteridophytes and their relationship to seed plants: Evidence from complete 18S rRNA gene sequences

Complete 18S ribosomal RNA sequence data from representatives of all extant pteridophyte lineages together with RNA sequences from different seed plants were used to infer a molecular phylogeny of vascular plants that included all major land plant lineages. The molecular data indicate that lycopsids are monophyletic and are the earliest diverging group within the vascular land plants, whereasPsilotum nudum is more closely related to the seed plants than to other pteridophyte lineages. The phylogenetic trees based on maximum likelihood, parsimony and distance analyses show substantial agreement with the evolutionary relationships of land plants as interpreted from the fossil record.     

Multiple losses of sex within a single genus of Microsporidia

Background  

Most asexual eukaryotic lineages have arisen recently from sexual ancestors and contain few ecologically distinct species, providing evidence for long-term advantages of sex. Ancient asexual lineages provide rare exceptions to this rule and so can yield valuable information relating to the evolutionary forces underlying the maintenance of sex. Microsporidia are parasitic, unicellular fungi. They include many asexual species which have traditionally been grouped together into large, presumably ancient taxonomic groups. However, these putative ancient asexual lineages have been identified on the basis of morphology, life cycles and small subunit ribosomal RNA (16S rRNA) gene sequences, all of which hold questionable value in accurately inferring phylogenetic relationships among microsporidia.     

Sebacinales are common mycorrhizal associates of Ericaceae

Previous reports of sequences of Sebacinales (basal Hymenomycetes) from ericoid mycorrhizas raised the question as to whether Sebacinales are common mycorrhizal associates of Ericaceae, which are usually considered to associate with ascomycetes. Here, we sampled 239 mycorrhizas from 36 ericoid mycorrhizal species across the world (Vaccinioideae and Ericoideae) and 361 mycorrhizas from four species of basal Ericaceae lineages (Arbutoideae and Monotropoideae) that do not form ericoid mycorrhizas, but ectendomycorrhizas. Sebacinales were detected using sebacinoid-specific primers for nuclear 28S ribosomal DNA, and some samples were investigated by transmission electron microscopy (TEM). Diverging Sebacinales sequences were recovered from 76 ericoid mycorrhizas, all belonging to Sebacinales clade B. Indeed, some intracellular hyphal coils had ultrastructural TEM features expected for Sebacinales, and occurred in living cells. Sebacinales belonging to clade A were found on 13 investigated roots of the basal Ericaceae, and TEM revealed typical ectendomycorrhizal structures. Basal Ericaceae lineages thus form ectendomycorrhizas with clade A Sebacinales, a clade that also harbours ectomycorrhizal fungi. This further supports the proposition that Ericaceae ectendomycorrhizas involve ectomycorrhizal fungal taxa. When ericoid mycorrhizas evolved secondarily in Ericaceae, a shift of mycobionts occurred to ascomycetes and clade B Sebacinales, hitherto not described as ericoid mycorrhizal fungi.     

Taxonomic diversity and interactions of insect-associated ascomycetes

Many ascomycetes are associated with insects to form symbioses. The fungi are necrotrophic and biotrophic parasites, endosymbionts, insect-dispersed forms, and other obligate associates that provide nourishment for insects. Diversity among these fungi can be categorized in several different ways: taxonomic diversity, variety of interaction types occurring within a fungal lineage, and number of fungal species. Previously our inability to produce well supported phylogenetic hypotheses has obscured these views of diversity. Over the past 5 years our knowledge of insect-associated fungi has been improved by the use of DNA sequence analysis. Such studies have revealed that ascomycetes in almost all major clades are associated intimately with insects. Of particular interest has been the sorting out of relationships of taxa with convergent morphologies, unique characters, and lost characters, including those associated with sexual reproduction. Within some fungal groups the types of interactions with insects are diverse, and eventually phylogenetic analysis will help to trace the evolutionary development of symbioses. Molecular studies also contribute to our understanding of the number of species which may vary according to species concepts used in their study.     

Unravelling evolutionary lineages among South African velvet worms (Onychophora: Peripatopsis) provides evidence for widespread cryptic speciation

The endemic South African velvet worm genus Peripatopsis currently contains eight recognized species described from variable morphological characters and the current taxonomy is unsatisfactory. In an attempt to investigate evolutionary relationships within Peripatopsis, we collected 137 individuals from 34 sample localities for six of the eight species. Sequence data derived from two partial mitochondrial (mt)DNA gene loci (COI and 12S rRNA), as well as partial sequence data from the ribosomal nuclear 18S rDNA locus in combination with gross morphological characters and scanning electron microscopy (SEM), was used to examine evolutionary relationships. Phylogenetic relationships were investigated using minimum evolution (ME) and Bayesian inferences (BI). Additionally, we also undertook a maximum likelihood (ML) analyses on the combined DNA sequence data set. The combined DNA evidence topologies derived from the ME, BI, and ML was highly congruent and was characterized by the presence of multiple lineages within recognized taxa. Peripatopsis clavigera, Peripatopsis moseleyi, and Peripatopsis sedgwicki each comprised two evolutionary lineages; Peripatopsis capensis comprised three; and Peripatopsis balfouri comprised six operational taxonomic units respectively. Genealogical exclusivity at both mtDNA and nuclear DNA among the geographically coherent groups coupled with pronounced sequence divergence suggested a two‐fold increase in the number of species within Peripatopsis. Previously used gross morphological characters (such as the number of leg pairs and colour) were either highly variable within operational taxonomic units, or were invariant, suggesting that alternative morphological characters are necessary for species discrimination. SEM results revealed potentially useful diagnostic characters that can discriminate between at least discriminate some of the newly‐identified lineages. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society 2009, 97 , 200–216.     

Treehopper trees: phylogeny of Membracidae (Hemiptera: Cicadomorpha: Membracoidea) based on molecules and morphology

Abstract. Recent independent phylogenetic analyses of membracid relationships based on molecular and morphological data have identified monophyletic lineages within the family. However, the results of these studies have not fully resolved treehopper phylogeny, and relationships among some higher membracid lineages remain in doubt. Portions of three datasets (958 aligned nucleotides from elongation factor‐1α, 2363 aligned nucleotides from 28S ribosomal DNA, and eighty‐three morphological features of adults and nymphs) introduced in recent studies were reanalysed separately and in combination with two new molecular datasets (321 aligned nucleotides from wingless and 1829 aligned nucleotides from 18S ribosomal DNA). The results of the combined data analyses, contrary to previous analyses of morphological data alone, grouped membracids into two well‐supported lineages, one comprising Stegaspidinae and Centrotinae, the other comprising Membracinae, Darninae and Smiliinae. The analyses recovered Centrotinae, Membracinae and Darninae as monophyletic groups, but Stegaspidinae was paraphyletic with respect to Centrotinae, and Smiliinae was polyphyletic with Micrutalini placed as a sister group to the clade comprising Membracinae, Darninae and Smiliinae. These results are consistent with the following hypotheses, proposed previously based on an analysis of morphological data: (1) the posterior pronotal process was derived and lost multiple times during the evolution of Membracidae; (2) Membracidae originated in the New World and reached the Old World subsequently via dispersal; (3) maternal care evolved independently multiple times and may or may not have been preceded by the acquisition of ant mutualism.     

Strengths and limitations of molecular sequence comparisons for inferring the phylogeny of the major groups of fishes

Although the phylogenetic relationships of the major groups of fishes have been extensively studied with morphological characters, not all have been convincingly resolved. Analyses of molecular sequences from these groups may provide additional insights into problematical relationships, but are only just beginning to appear. We compare our own results from analyses of 18s ribosomal RNA sequences with those of other studies using globins, parvalbumins, insulin, 28s ribosomal RNA, and portions of two mitochondria1 genes (12S ribosomal RNA and cytochrome b ). Our evaluation of these studies reveals some of the difficulties encountered in reconstructing ancient divergences within the fishes, including unequal rates of evolution (among regions of a molecule as well as among lineages), gene duplication, extinction of lineages, and a possible rapid radiation of gnathostome higher taxa. The importance of evaluating the robustness of particular phylogenetic hypotheses is stressed. Some molecules appear to be inappropriate for investigating higher level divergences within the fishes; others are more promising, but must be examined in more taxa to allow an adequate evaluation of their utility. Convincing support for particular hypotheses of relationship will ultimately require congruence of trees generated from independent molecular data sets.