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- Arup, Ulf, et al.
(author)
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The sister group relation of Parmeliaceae (Lecanorales, Ascomycota)
- 2007
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In: Mycologia. - : Informa UK Limited. - 0027-5514 .- 1557-2536. ; 99:1, s. 42-49
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Journal article (peer-reviewed)abstract
- The family Parmeliaceae (Lecanorales, Ascomycota) is possibly the largest, best known and most thoroughly studied lichen family within its order. Despite this fact the relationship between Parmeliaceae and other groups in Lecanorales is still poorly known. The aim of the present study is to contribute to finding the sister group of Parmeliaceae as an aid in future studies on the phylogeny and character evolution of the group. We do this by sampling all potential relatives to the Parmeliaceae that we have identified, i.e. Cypsoplaca, Japewia, Mycoblastus, Protoparmelia, and Tephromela, a good representation of the major groups within the Parmeliaceae s. lat. and a good representation of other taxa in the core Lecanorales. We use molecular data from two genes, the large subunit of the nuclear ribosomal RNA gene (nrLSU) and the small subunit of the mitochondrial ribosomal RNA gene (mrSSU), and a Bayesian analysis of the combined data. The results show that the closest relatives to Parmeliaceae are the two genera Protoparmelia and Gypsoplaca, which are crustose lichens. Parmeliaceae in our sense is a well supported group, including also the family segregates Alectoriaceae, Hypogymniaceae, Usneaceae and Anziaceae.
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| 3. |
- Berglund, Johnny, et al.
(author)
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Use of group-specific PCR primers for identification of chrysophytes by denaturing gradient gel electrophoresis
- 2005
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In: Aquatic Microbial Ecology. - Olendorf/Luhe : Inter-Research. - 0948-3055 .- 1616-1564. ; 39:2, s. 171-182
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Journal article (peer-reviewed)abstract
- The chrysophytes Chrysophyceae and Synurophyceae are ecologically important groups of autotrophic, mixotrophic and heterotrophic flagellates. The smallest forms are difficult to identify by classical microscopy but have important functions both as primary producers and as consumers of bacteria in the aquatic food chain. Group-specific primers for amplification of the 18S small sub-unit rRNA gene were developed for analysis of chrysophyte diversity by denaturing gradient gel electrophoresis (DGGE). Two different primer pairs were tested. The first primer pair (EukC1-F–Chryso-R) primarily targeted Paraphysomonadaceae and Ochromonadales, which generally have heterotrophic or mixotrophic nutrition. The second primer pair (EukC2-F–Chryso-R) targeted both Chrysophyceae and Synurophyceae. The primer pairs were tested for PCR amplification of the 18S rRNA gene of 25 cultured chrysophyte species and 6 other closely related nanoplanktonic species. Both primer pairs performed well, since PCR products were obtained for the corresponding chrysophyte cultures. None of the non-chrysophyte species were amplified with these primers. PCR products of chrysophyte cultures could be separated by DGGE in a denaturing gradient from 40 to 60%. In order to test this PCR-DGGE system for natural planktonic systems, we used field samples from a brackish water area (Baltic Sea) and a freshwater lake. The most intense DGGE bands were excised, sequenced and compared to sequences in GenBank. All obtained sequences grouped within the chrysophytes. Thus, the method seems to be promising for examining chrysophyte diversity in planktonic systems.
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| 5. |
- Crespo, Ana, et al.
(author)
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Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene
- 2007
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In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 44:2, s. 812-824
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Journal article (peer-reviewed)abstract
- Parmeliaceae is the largest family of lichen-forming fungi with more than 2000 species and includes taxa with different growth forms. Morphology was widely employed to distinguish groups within this large, cosmopolitan family. In this study we test these morphology-based groupings using DNA sequence data from three nuclear and one mitochondrial marker from 1.20 taxa that include 59 genera and represent the morphological and chemical diversity in this lineage. Parmeliaceae is strongly supported as monophyletic and six well-supported main clades can be distinguished within the family. The relationships among them remain unresolved. The clades largely agree with the morphology-based groupings and only the placement of four of the genera studied is rejected by molecular data, while four other genera belong to clades previously unrecognised. The classification of these previously misplaced genera, however, has already been questioned by some authors based on morphological evidence. These results support morphological characters as important for the identification of monophyletic clades within Parmeliaceae.
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| 7. |
- Ekman, Stefan, 1965-, et al.
(author)
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The Limitations of Ancestral State Reconstruction and the Evolution of the Ascus in the Lecanorales (Lichenized Ascomycota)
- 2008
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In: Systematic Biology. - London : Taylor & Francis. - 1063-5157 .- 1076-836X. ; 57:1, s. 141-156
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Research review (peer-reviewed)abstract
- Ancestral state reconstructions of morphological or ecological traits on molecular phylogenies are becoming increasinglyfrequent. They rely on constancy of character state change rates over trees, a correlation between neutral geneticchange and phenotypic change, as well as on adequate likelihood models and (for Bayesian methods) prior distributions.This investigation explored the outcomes of a variety of methods for reconstructing discrete ancestral state in the ascus apexof the Lecanorales, a group containing the majority of lichen-forming ascomycetes. Evolution of this character complex hasbeen highly controversial in lichen systematics for more than two decades. The phylogeny was estimated using BayesianMarkov chain Monte Carlo inference on DNA sequence alignments of three genes (small subunit of the mitochondrialrDNA, large subunit of the nuclear rDNA, and largest subunit of RNA polymerase II). We designed a novel method forassessing the suitable number of discrete gamma categories, which relies on the effect on phylogeny estimates rather thanon likelihoods. Ancestral state reconstructions were performed using maximum parsimony and maximum likelihood ona posterior tree sample as well as two fully Bayesian methods. Resulting reconstructions were often strikingly differentdepending on the method used; different methods often assign high confidence to different states at a given node. Thetwo fully Bayesian methods disagree about the most probable reconstruction in about half of the nodes, even when similarlikelihood models and similar priors are used. We suggest that similar studies should use several methods, awaiting animproved understanding of the statistical properties of the methods. A Lecanora-type ascus may have been ancestral in theLecanorales. State transformations counts, obtained using stochastic mapping, indicate that the number of state changes is12 to 24, which is considerably greater than the minimum three changes needed to explain the four observed ascus apextypes. Apparently, the ascus in the Lecanorales is far more apt to change than has been recognized. Phylogeny correspondswell with morphology, although it partly contradicts currently used delimitations of the Crocyniaceae, Haematommataceae,Lecanoraceae, Megalariaceae, Mycoblastaceae, Pilocarpaceae, Psoraceae, Ramalinaceae, Scoliciosporaceae, and Squamarinaceae.
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| 8. |
- Ihlen, P.G., et al.
(author)
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An annotated key to the lichenicolous Ascomycota (including mitosporic morphs) of Sweden
- 2008
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In: Nova Hedwigia. - : Schweizerbart. - 0029-5035. ; 86, s. 275-365
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Journal article (peer-reviewed)abstract
- An annotated key to the lichenicolous (lichen-inhabiting) Ascomycota, including mitosporic morphs, known from Sweden is presented. Recent additions, both from the literature and our own collections, of these fungi to the Swedish flora are also included. A total of 298 ascomycetes representing 83 genera, and 65 mitosporic fungi from 31 genera, have been found to occur in Sweden. Each species keyed out is followed by information and selected literature references on morphology, distribution, and ecology. Taxonomic notes and discussions are given for several critical genera and species, and selected species are illustrated.
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| 10. |
- Kruys, Åsa, et al.
(author)
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Phylogenetic relationships and an assessment of traditionally used taxonomic characters in the Sporormiaceae (Pleosporales, Dothideomycetes, Ascomycota), utilising multi-gene phylogenies
- 2009
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In: Systematics and Biodiversity. - 1477-2000 .- 1478-0933. ; 7:4, s. 465-478
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Journal article (peer-reviewed)abstract
- The family Sporormiaceae (Pleosporales, Dothideomycetes, Ascomycota) occur worldwide and a majority of the species are coprophilous. The taxonomy and classification of the family are based on a small number of morphological and ecological characters. Several taxa are easily confused by their shared morphological features, and the relationships between genera are poorly known and in need of critical study. The aims of this study were to resolve the phylogenetic relationships within the Sporormiaceae, test the current generic classification, and study the utility of traditional characters for the taxonomy in the group. To resolve these questions, we analysed combined data sets of ITS-nLSU rDNA, mtSSU rDNA and beta-tubulin sequences with parsimony and Bayesian methods. The results showed that many characters, which previously have been used in the taxonomy and classification of the Sporormiaceae, such as the substrate choice, presence or absence of an ostiole, and presence or absence of germ slits, were all homoplastic and not useful for circumscribing monophyletic groups. A number of characters may be useful for circumscribing smaller clades if used in combination with other features, such as the shape of the ascus with the shape of the ascospores. Our phylogenetic analyses show that Preussia and Sporormiella are non-monophyletic, and a constrained analysis forcing these genera into monophyly resulted in significantly worse trees. Spororminula is nested in Preussia s. lat., and Eremodothis and Pycnidiophora are nested within Westerdykella. Finally, we suggest a new generic classification for the family Sporormiaceae, including Sporormia, Preussia (including Sporomiella and Spororminula) and Westerdykella (including Eremodothis and Pycnidiophora). We also propose 14 new combinations: Preussia alloiomera (S.I. Ahmed & Cain) Kruys, Preussia antarctica (Speg.) Kruys, Preussia bipartis (Cain) Kruys, Preussia borealis (I.Egeland) Kruys, Preussia dubia (S.I. Ahmed & Cain) Kruys, Preussia lignicola (W. Phillips & Plowr.) Kruys, Preussia longisporopsis (S.I. Ahmed & Cain) Kruys, Preussia minipascua (S.I. Ahmed & Cain) Kruys, Preussia octomera (Auersw.) Kruys, Preussia splendens (Cain) Kruys, Preussia tenerifae (Arx & Aa) Kruys, Preussia tetramera (S.I. Ahmed & Cain) Kruys, Westerdykella angulata (A.C. Das) Kruys and Westerdykella aurantiaca (J.N. Rai & J.P. Tewari) Kruys.
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