| 1. |
- Myllys, L, et al.
(författare)
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New genes for phylogenetic studies of lichenized fungi: glyceraldehyde-3-phosphate dehydrogenase and beta-tubulin genes
- 2002
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Ingår i: Lichenologist. - : Cambridge University Press (CUP). - 0024-2829. ; 34:3, s. 237-246
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Tidskriftsartikel (refereegranskat)abstract
- Primers for amplification and sequencing of partial glyceraldehyde-3-phosphate dehydrogenase (gpd) gene were designed for lichenized fungi. The 5' gpd primer is most probably fungal specific, since a BLAST search in GenBank found identical sequences only from ascomycetous taxa, whereas the 3' gpd primer was more universal. Utility of the gpd primers and previously designed beta-tubulin primers was tested in nine lichen taxa. Both the gpd and beta-tubulin primer pairs amplified in most of the taxa examined: the gpd primers generated a c. 1100 nucleotide fragment, whereas the PCR product obtained from the beta-tubulin primers was c. 900 nucleotides long. The gpd amplification products of Cladonia arbuscula and C. rangiferina were sequenced and both were found to contain three introns, the length of which varied between 49 to 83 nucleotides. To examine the applicability of gpd sequences in resolving relationships within Ascomycota, trees were calculated from 22 fungal gpd sequences obtained from GenBank together with the two Cladonia sequences using parsimony jackknifing. The gpd tree was compared with the SSU rDNA tree of the respective species (or genera). A similar analysis of the beta-tubulin gene was not performed, because only a few beta-tublin sequences from the same taxa were available in GenBank. The gpd tree was well resolved but in conflict with the SSU rDNA tree. In contrast to the SSU rDNA tree, the gpd tree did not support the monophyly of the Ascomycota. Analysis of the combined data set produced a tree very similar to that of the SSU rDNA data. However, the relationship of Lecanorales to the other orders remained unresolved. Even though gpd and beta-tubulin are highly conserved proteins, the third codon positions and introns are variable and both genes have the potential for inferring phylogenetic relationships at the lower taxonomic levels in the lichenized fungi. The two genes may be useful even below species level, depending on the species investigated.
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| 2. |
- Myllys, L, et al.
(författare)
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Phylogeny of bipolar Cladonia arbuscula and Cladonia mitis (Lecanorales, Euascomycetes)
- 2003
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Ingår i: Molecular Phylogenetics and Evolution. - 1095-9513. ; 27:1, s. 58-69
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic relationships and levels of geographic differentiation of two closely related bipolar taxa, Cladonia arbuscula and Cladonia mitis, were cladistically examined with ITS regions, SSU rDNA introns, partial P-tubulin, and partial glyceraldehyde 3-phosphate dehydrogenase (GAPDH) genes. In the combined analysis of the four genes, C arbuscula was paraphyletic, while C mitis, nested within C arbuscula, formed a strongly supported monophyletic group. C arbuscula samples were divided into three separate clades: "arbuscula I," appearing as basal to the other ingroup taxa, "arbuscula II," and "arbuscula III" (the latter represented by only one specimen), which were not correlated with any morphological trait. Only C mitis specimens formed a morphologically and chemically distinct group. None of the main clades was correlated with geographic origin. The separate analyses were poorly resolved, and in most cases samples from "arbuscula I,'' ''arbuscula, II," and "arbuscula III" clades were intermixed. An incongruence test revealed conflict among the four gene regions in almost all cases. Only ITS regions and introns were not significantly incongruent, suggesting lack of recombination within the ribosomal DNA locus. Incomplete lineage sorting and recombination were considered to be the main reasons accounting for the incongruencies. The high proportion of shared polymorphisms between the "arbuscula F and "arbuscula II" clades, especially found from the beta-tubulin gene and from the ITS regions, and the lack of corroborating morphological characters both indicate a short history of reproductive isolation among the groups. The lack of genetic differentiation among the northern and southern samples within the main clades indicates a relatively recent gene flow, which may have resulted from migrations during the Pleistocene glaciations or from more recent long-distance dispersal. (C) 2002 Elsevier Science (USA). All rights reserved.
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| 3. |
- Stenroos, S, et al.
(författare)
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Phylogeny of the genus Cladonia s.lat. (Cladoniaceae, Ascomycetes) inferred from molecular, morphological, and chemical data
- 2002
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Ingår i: Cladistics. - 1096-0031. ; 18:3, s. 237-278
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Forskningsöversikt (refereegranskat)abstract
- Phylogenetic relationships within the genus Cladonia, including Cladina (Cladoniaceae, Lecanoromycetes), were reconstructed based upon simultaneous analyses of DNA sequences and morphological and chemical data. We used sequences from the internal transcribed spacer 1 (ITS1), the 5.8 rDNA gene, and the internal transcribed spacer 2 (ITS2) of the nuclear rDNA gene cluster, and partial sequences from the protein-coding beta-tubulin gene. The analyses included 235 specimens of 168 taxa representing all currently recognized sections of Cladonia and Cladina and the outgroup genera Cladia, Pycnothelia, and Rainalea. Analyses were performed using optimization alignment with three different parameter values. The results of all analyses support the inclusion of Cladina in Cladonia. The current sectional division of Cladonia was not supported, and a new provisional classification for the genus is proposed.
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| 4. |
- Thell, Arne, et al.
(författare)
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Monophyletic groups within the Parmeliaceae identified by ITS rDNA, beta-tubulin and GAPDH sequences
- 2004
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Ingår i: Mycological Progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 3:4, s. 297-314
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic relationships within the Parmeliaceae are analysed cladistically on the basis of DNA characters from partial beta-tubulin, partial glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and ITS sequences. 100 taxa representing 73 of the 88 genera currently recognised are included in the analyses. Eight monophyletic groups including two or more genera were identified in the tree calculated from the combined data matrix. Three of the groups cover almost half of the species of the family. The largest and strongest supported group includes seven genera with their distribution centres in the Southern Hemisphere: Almbornia, Chondropsis, Karoowia, Namakwa, Neofuscelia, Xanthomaculina and Xanthoparmelia. The second group is a clade of four essentially tropical genera: Concamerella, Flavoparmelia, Parmotrema and Rimelia. The third large group with strong support is the core of cetrarioid lichens, distributed primarily in cold areas of the Northern Hemisphere. The genus Parmelia sensu Hale is not closely related with most of its segregates. One new combination, Cetrariella commixta, is proposed. Coelopogon abraxas is reported from South America for the first time.
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| 5. |
- Thell, Arne, et al.
(författare)
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Phylogeny and ecology of Cetraria obtusata, Coelopogon epiphorellus, and related taxa (Parmeliaceae, lichenized ascomycetes).
- 2002
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Ingår i: Mitteilungen aus dem Institut fuer Allgemeine Botanik Hamburg. - 0344-5615. ; 30-32, s. 283-296
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The phylogeny of two lichens, Cetraria obtusata from the Alps and Coelopogon epiphorellus occurring in the southern hemisphere is studied. A DNA-matrix based on ITS 1 and ITS 2 sequences of the rDNA is compared with a data set composed of morphology and secondary chemistry characters in phylogeny analyses using PAUP 4.0. The two data sets were entirely congruent. Neither Cetraria obtusata nor Coelopogon epiphorellus, both earlier segregated from the Cetraria aculeata group (Coelocaulon), are closely related with Cetraria s. str. Ecology notes of the two species are added and their phylogenetic affinities are discussed.
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| 6. |
- Thell, Arne, et al.
(författare)
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Phylogeny of cetrarioid lichens (Parmeliaceae) inferred from ITS and beta-tubulin sequences, morphology, anatomy and secondary chemistry.
- 2002
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Ingår i: Mycological Progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 1:4, s. 335-354
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic relationships within the family Parmeliaceae (lichenized ascomycetes) with emphasis on the heterogeneous group of cetrarioid lichens are reconstructed. The results are based on cladistic analyses of DNA-sequences, morphological and chemical data. Almost all currently recognized cetrarioid genera were included in the analyses together with parmelioid and alectorioid members of the presumably monophyletic family Parmeliaceae. We tried to sample taxonomic diversity of the family as widely as possible. The ITS1-5.8S-ITS2 region of the rDNA and a partial beta-tubulin gene from 126 samples representing 82 species were analysed. Cetrarioid lichens were identified as a monophyletic group, supported by both ITS and beta-tubulin characters. This group was reanalysed using 47 morphological, anatomical and secondary chemistry characters combined with the DNA data matrix. ITS and beta-tubulin sequences provide congruent information, and a clear correlation between DNA-data and conidial shape is observed. The current taxonomy of the cetrarioid lichens is discussed and compared with the phylogenetic trees obtained here. A comprehensive study of the phylogeography of some bipolar or subcosmopolitic species with representatives from both hemispheres was performed. Cetraria aculeata is the only taxon where correlation between DNA-data and geographic origin is observed.
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