Towards a molecular phylogeny for the lichen family Pannariaceae (Lecanorales, Ascomycota)

2002 ◽  
Vol 80 (6) ◽  
pp. 625-634 ◽  
Author(s):  
Stefan Ekman ◽  
Per Magnus Jørgensen
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sampling Procedure ◽  
Nuclear Ribosomal Dna ◽  
Dna Phylogeny ◽  
Green Algal ◽  
The Family ◽  
Optimal Trees

The phylogeny of the family Pannariaceae (Lecanorales, lichenized Ascomycota) was investigated using ITS1–5.8S–ITS2 nuclear ribosomal DNA sequences representing 21 species. Phylogenetic estimations were performed using parsimony and a Bayesian Markov chain Monte Carlo (MCMC) tree sampling procedure. Several phylogenetic null hypotheses were tested, also using MCMC. The results indicate that Pannariaceae, as currently treated, is polyphyletic and that Degelia sect. Amphiloma, Fuscopannaria subg. Micropannaria, and Moelleropsis s.str. do not belong in the family. The inclusion of Parmeliella in the Pannariaceae could not be rejected, although it falls outside the family in the optimal trees. Psoroma, Santessoniella, Protopannaria, Fuscopannaria subg. Fuscopannaria, Moelleropsis s.str., and Pannaria unequivocally belong to the family. The Pannaria sphinctrina group belongs in Pannaria despite its green-algal photobiont. Protopannaria pezizoides is not, as sometimes treated, a Pannaria, although a relationship with Psoroma could not be ruled out. In the optimal trees, Moelleropsis s.str. is nested inside Fuscopannaria subg. Fuscopannaria and Santessoniella inside Psoroma, but null hypotheses of their independence from these genera could not be rejected. Pannaria cannot be divided into two monophyletic subgenera, Pannaria and Chryopannaria. The photobiont has changed twice or three times and the ascus apex and hymenial amyloidity twice within the Pannariaceae.Key words: lichens, Pannariaceae, ITS, ribosomal DNA, phylogeny, MCMC.

scholarly journals DNA phylogeny of Ryukyus Leucothoidae (Crustacea: Amphipoda)

2012 ◽  
Vol 81 (3) ◽  
pp. 159-S2 ◽  
Author(s):  
Kristine N. White ◽  
James D. Reimer
Keyword(s):  
Ribosomal Dna ◽  
Sibling Species ◽  
Dna Sequences ◽  
Ryukyu Archipelago ◽  
Generic Level ◽  
Coral Rubble ◽  
Dna Phylogeny ◽  
The Family ◽  
Sequences Analysis ◽  
Morphological Species

Commensal leucothoid amphipods collected from sponges, ascidians, and coral rubble from the Ryukyu Archipelago, Japan, were investigated using nuclear 18S ribosomal DNA sequences. Analysis of sequences from 21 species in three genera supported the current morphological species designations and the separation of the family into two clades. Additionally, a possible new generic-level clade was identified and the separation of the genera Anamixis and Paranamixis was not supported. Our results demonstrate that host specificity appears to evolve rapidly in sibling species in this family.

Reviewing lymnaeid vectors of fascioliasis by ribosomal DNA sequence analyses

2005 ◽  
Vol 79 (3) ◽  
pp. 257-267 ◽  
Author(s):  
M.D. Bargues ◽  
S. Mas-Coma
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Fasciola Hepatica ◽  
Rdna Sequence ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Nuclear Rdna ◽  
Natural Classification ◽  
The Family

AbstractSnails of the family Lymnaeidae are of great parasitological importance due to the numerous helminth species they transmit, mainly trematodiases (such as fascioliasis) of considerable medical and veterinary impact. The present knowledge of the genetics and host–parasite relationships of this gastropod group is far from adequate. Fascioliasis is caused by two species, Fasciola hepatica and F. gigantica, which, as in the case of other trematodes, show a marked snail host specificity. Many lymnaeid species involved in fascioliasis transmission still show a confused systematic-taxonomic status. The need for tools to distinguish and characterize species and populations of lymnaeids is evident and the present review concerns new molecular tools developed in recent years using nuclear ribosomal DNA sequences. The small subunit or 18S gene and the internal transcribed spacers ITS-2 and ITS-1 are analysed and evaluated as markers for taxon differentiation and relationships within the Lymnaeidae from genus and species levels to subspecies and population levels. rDNA sequence differences and genetic distances, and their value for reconstructing phylogenetic trees using different methods are considered. Nuclear rDNA sequences are appropriate tools on which to base a review of the systematics and taxonomy of the family Lymnaeidae, without excluding other valuable snail characteristics already available. A reconstruction of the lymnaeid system towards a more natural classification will undoubtedly be helpful in understanding parasite transmission and epidemiological features as well the dispersion of an emerging-reemerging disease such as fascioliasis. Nomenclature for nuclear rDNA genotyping in lymnaeids includes the main rDNA sequence regions able to furnish important information on interspecific differentiation and grouping as well as intraspecific variability of lymnaeid species. The composite haplotype code includes the rDNA markers arranged in order according to their well-known usefulness, in its turn related to their respective, more or less rapid evolutionary ratios, to distinguish between different taxonomic levels, from supraspecific taxa to the species level and up to the population level.

scholarly journals Relationships of Nematodirus Species and Nematodirus battus Isolates (Nematoda: Trichostrongyloidea) Based on Nuclear Ribosomal DNA Sequences

2000 ◽  
Vol 86 (3) ◽  
pp. 588 ◽  
Author(s):  
Steven A. Nadler ◽  
Eric P. Hoberg ◽  
Deborah S. S. Hudspeth ◽  
Lora G. Rickard
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Nuclear Ribosomal Dna

Phylogenetics of Helotiales and Rhytismatales Based on Partial Small Subunit Nuclear Ribosomal DNA Sequences

Mycologia ◽  
2001 ◽  
Vol 93 (5) ◽  
pp. 915 ◽  
Author(s):  
David S. Gernandt ◽  
Jamie L. Platt ◽  
Jeffrey K. Stone ◽  
Joseph W. Spatafora ◽  
Arne Holst-Jensen ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Small Subunit ◽  
Nuclear Ribosomal Dna

Phylogeny of the Genus Omphalotus Based on Nuclear Ribosomal DNA-Sequences

Mycologia ◽  
2004 ◽  
Vol 96 (6) ◽  
pp. 1253 ◽  
Author(s):  
Martin Kirchmair ◽  
Sandra Morandell ◽  
Daniela Stolz ◽  
Reinhold Poder ◽  
Christian Sturmbauer
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Nuclear Ribosomal Dna

Towards a new classification of tribe Stachydeae (Lamiaceae): naming clades using molecular evidence

2019 ◽  
Vol 190 (4) ◽  
pp. 345-358 ◽  
Author(s):  
Yasaman Salmaki ◽  
Günther Heubl ◽  
Maximilian Weigend
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Nuclear Ribosomal Dna ◽  
Molecular Evidence ◽  
New Classification ◽  
Formal Classification ◽  
Phylogenetic Nomenclature

AbstractStachydeae, comprising c. 470 species, are one of the most diverse and taxonomically puzzling groups in Lamioideae. In the present study, the phylogenetic relationships in the Eurystachys clade (a phylogenetic name for all genera attributed to Stachydeae except Melittis) were reconstructed utilizing nuclear ribosomal DNA sequences (nrETS, 5S-NTS) from 148 accessions in 12 genera. Our phylogenetic results recovered Stachys as paraphyletic with numerous traditionally recognized genera nested in it. A broadly defined Eurystachys clade, however, was monophyletic. Unlike previous studies, the present study was able to resolve the group into 12 well-supported clades, named here as (1) Eriostomum, (2) Stachys, (3) Prasium, (4) Setifolia, (5) Distantes, (6) Burgsdorfia, (7) Hesiodia, (8) Empedoclia, (9) Sideritis, (10) Marrubiastrum, (11) Swainsoniana and (12) Olisia. These 12 clades were formally named in a phylogenetic nomenclature for the Eurystachys clade. Several infrageneric units were retrieved as monophyletic, namely Sideritis sections Burgsdorfia, Empedoclia and Hesiodia, Sideritis subgenus Marrubiastrum and Stachys sections Eriostomum (including Stachys section Mucronata) and Setifolia. The findings of this study also provide the basis for a future formal classification, with two options: (1) splitting of the Eurystachys clade into 12 monophyletic genera, all of them based on pre-existing genus names and redefined to encompass additional taxa, but without clear morphological apomorphies; or (2) lumping of all segregates into a broadly defined Stachys, including widely recognized and well-defined segregates such as Prasium and Sideritis.

Evolutionary relationships ofHyphodiscus hymeniophilus(anamorphCatenulifera rhodogena) inferred from β-tubulin and nuclear ribosomal DNA sequences

2006 ◽  
Vol 84 (2) ◽  
pp. 243-253 ◽  
Author(s):  
Wendy A. Untereiner ◽  
Françoise A. Naveau ◽  
Jason Bachewich ◽  
Andrea Angus
Keyword(s):  
Phylogenetic Relationship ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Its Sequences ◽  
Nuclear Ribosomal Dna ◽  
Phialocephala Fortinii ◽  
Piptoporus Betulinus ◽  
Close Phylogenetic Relationship ◽  
Relationship Of ◽  
Β Tubulin

During an investigation of lignicolous ascomycetes from Luxembourg, we isolated a Phialophora -like species that produced striking red colonies. To confirm the identity of this fungus as Catenulifera rhodogena , we compared it with isolates of Catenulifera rhodogena and Hyphodiscus hymeniophilus on a variety of media. Portions of the β-tubulin gene and the nuclear ribosomal DNA cistron (internal transcribed spacers (ITS) and large subunit (LSU)) were sequenced to examine the relationship of isolates of Catenulifera rhodogena and Hyphodiscus hymeniophilus from different substrates and to test the hypothesis that Cadophora and Catenulifera are congeneric. The phylogenetic position of Catenulifera within the Ascomycota was investigated based on the analysis of the small-subunit (SSU) rDNA sequences. The isolates examined were indistinguishable micromorphologically and closely related phylogenetically. Three strains of Catenulifera rhodogena from bark or wood and one strain from Piptoporus betulinus formed a strongly supported clade in analyses of β-tubulin and ITS sequences. This clade did not encompass the ex-type isolates of Cistella rubescens and Scopulariopsis rhodogena or a second isolate of Catenulifera rhodogena from Piptoporus betulinus. Analysis of partial LSU sequences confirmed the close phylogenetic relationship of Catenulifera rhodogena and Hyphodiscus hymeniophilus but provided no evidence that the isolates could be grouped by substrate or that Catenulifera is synonymous with Cadophora. The position of Catenulifera within the Helotiales was not resolved based on the comparison of LSU and SSU sequences, but the isolate for which we obtained complete SSU sequence grouped with the root endophyte Phialocephala fortinii. Comparison of ITS sequences confirmed the close phylogenetic relationship of Hyphodiscus to members of the Dermateaceae and Hyaloscyphaceae.

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