| 1. |
- Divakar, Pradeep K., et al.
(författare)
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Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi
- 2015
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 208:4, s. 1217-1226
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Tidskriftsartikel (refereegranskat)abstract
- We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.
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| 2. |
- Hognabba, Filip, et al.
(författare)
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Phylogenetic position of the crustose Stereocaulon species
- 2014
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Ingår i: The Lichenologist. - 0024-2829 .- 1096-1135. ; 46:1, s. 103-114
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic relationships of Stereocaulon with emphasis on the crustose taxa were studied based on nuclear ribosomal ITS1-5.8S-ITS2 and partial beta-tubulin sequences. The placement of four of the six crustose species currently included in the genus has previously been confirmed based on molecular data. It has, however, remained unresolved whether the crustose growth form is a plesiomorphic or apomorphic feature within Stereocaulon, due to contradictory placements of the crustose species in earlier studies. The aim of this study was to clarify the position of the crustose species by including additional data, especially of S. nivale and S. plicatile, which have not been included in previous analyses. The inclusion of S. plicatile in the genus is of particular interest as it is the only species in the genus with submurifrom to muriform ascospores. Altogether 37 specimens representing 31 species of the ingroup, including all the crustose Stereocaulon species, were incorporated in the analyses. Conventional, as well as direct optimization parsimony, maximum likelihood and Bayesian analyses were performed. The results show that the crustose species do not form a monophyletic entity and that the crustose growth form is a plesiomorphic feature within Stereocaulon. The crustose S. nivale and S. plicatile are nested within the genus and their inclusion in Stereocaulon is thereby confirmed. The nested position of S. plicatile indicates that the submuriform to muriform spore type has been gained independently within the genus. Here, S. plicatile is also reported for the first time from Scandinavia.
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| 3. |
- Launis, Annina, et al.
(författare)
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Sharpening species boundaries in the Micarea prasina group, with a new circumscription of the type species M. prasina
- 2019
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Ingår i: Mycologia. - : TAYL. - 0027-5514 .- 1557-2536. ; 111:4, s. 574-592
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Tidskriftsartikel (refereegranskat)abstract
- Micarea is a lichenized genus in the family Pilocarpaceae (Ascomycota). We studied the phylogeny and reassessed the current taxonomy of the M. prasina group. We focused especially on the taxonomic questions concerning the type species M. prasina and, furthermore, challenges concerning type specimens that are too old for successful DNA barcoding and molecular studies. The phylogeny was reconstructed using nuc rDNA internal transcribed spacer region (ITS1-5.8S-ITS2 = ITS), mitochrondrial rDNA small subunit (mtSSU), and replication licensing factor MCM7 gene from 31 species. Fifty-six new sequences were generated. The data were analyzed using maximum parsimony and maximum likelihood methods. The results revealed four undescribed, well-supported lineages. Three lineages represent new species described here as M. fallax, M. flavoleprosa, and M. pusilla. In addition, our results support the recognition of M. melanobola as a distinct species. Micarea fallax is characterized by a vivid to olive green thallus composed of aggregated granules and whitish or brownish apothecia sometimes with grayish tinge (Sedifolia-gray pigment).Micarea flavoleprosa has a thick, wide-spreading yellowish green, whitish green to olive green sorediate thallus and lacks the Sedifolia-gray pigmentation. The species is mostly anamorphic, developing apothecia rarely. Micarea melanobola is characterized by a pale to dark vivid green granular thallus and darkly pigmented apothecia (Sedifolia-gray). Micarea pusilla is characterized by a whitish green to olive green thinly granular or membranous thallus, numerous and very small whitish apothecia lacking the Sedifolia-gray pigment, and by the production of methoxymicareic acid. Micarea fallax, M. flavoleprosa, and M. melanobola produce micareic acid. The reliability of crystalline granules as a character for species delimitation was investigated and was highly informative for linking the old type specimen of M. prasina to fresh material.
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| 4. |
- Lohtander, Katileena, et al.
(författare)
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New entities in Physcia aipolia-P-caesia group (Physciaceae, Ascomycetes) : an analysis based on mtSSU, ITS, group I intron and betatubulin sequences
- 2009
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Ingår i: Annales Botanici Fennici. - 0003-3847 .- 1797-2442. ; 46:1, s. 43-53
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Tidskriftsartikel (refereegranskat)abstract
- We have revisited the phylogenetic evaluation of the Physcia aipolia-P. caesia lichen group (sect. Caesiae; Physciaceae, Lecanorales) in order to investigate whether new sequence data and extensive sampling can help us to understand the phylogenetic relationships in that group. We combined partial mtSSU DNA data with two previously used nuclear gene regions (betatubulin, ITS) and a group I intron. We also compared the resulting phylogenies with chemical and morphological characters. Altogether 52 specimens of the P. aipolia-P. caesia group were analysed. Direct optimization of the molecular data revealed several well-supported groups. Our results essentially agreed with those of the earlier studies, and we were able to confirm the independent taxonomic status of some controversial morphotaxa. We also discovered at least two distinct clades that potentially represent species new to science. A new nomenclatural combination, Physcia alnophila (Vain.) Loht., Moberg, Myllys & Tehler, is proposed.
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| 5. |
- Miadlikowska, Jolanta, et al.
(författare)
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A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.
- 2014
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1095-9513 .- 1055-7903. ; 79:Online 18 April 2014, s. 132-168
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Tidskriftsartikel (refereegranskat)abstract
- The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 635 newly generated and 3307 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, 'Candelariomycetidae'). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module ("Hypha") of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach.
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| 6. |
- Moya, Patricia, et al.
(författare)
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Phylogeography of Ramalina farinacea (Lichenized Fungi, Ascomycota) in the Mediterranean Basin, Europe, and Macaronesia
- 2023
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Ingår i: Diversity. - : MDPI. - 1424-2818. ; 15:3
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Tidskriftsartikel (refereegranskat)abstract
- Ramalina farinacea is an epiphytic lichen-forming fungus with a broad geographic distribution, especially in the Northern Hemisphere. In the eighties of the last century, it was hypothesized that R. farinacea had originated in the Macaronesian–Mediterranean region, with the Canary Islands as its probable southernmost limit, and thereafter it would have increased its distribution area. In order to explore the phylogeography of this emblematic lichen, we analyzed 120 thalli of R. farinacea collected in 38 localities distributed in temperate and boreal Europe, the Western Mediterranean Basin, and several Macaronesian archipelagos in the Atlantic Ocean. Data from two nuclear markers (nrITS and uid70) of the mycobiont were obtained to calculate genetic diversity indices to infer the phylogenies and haplotype networks and to investigate population structure. In addition, dating analysis was conducted to provide a valuable hypothesis of the timing of the origin and diversification of R. farinacea and its close allies. Our results highlight that phylogenetic species circumscription in the “Ramalina farinacea group” is complex and suggests that incomplete lineage sorting is at the base of conflicting phylogenetic signals. The existence of a high number of haplotypes restricted to the Macaronesian region, together with the diversification of R. farinacea in the Pleistocene, suggests that this species and its closest relatives originated during relatively recent geological times and then expanded its range to higher latitudes. However, our data cannot rule out whether the species originated from the Macaronesian archipelagos exclusively or also from the Mediterranean Basin. In conclusion, the present work provides a valuable biogeographical hypothesis for disentangling the evolution of this epiphytic lichen in space and time.
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| 7. |
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| 8. |
- Thell, Arne, et al.
(författare)
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Phylogeny of the cetrarioid core (Parmeliaceae) based on five genetic markers
- 2009
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Ingår i: Lichenologist. - 0024-2829. ; 41:5, s. 489-511
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Tidskriftsartikel (refereegranskat)abstract
- Fourteen genera belong to a monophyletic core of cetrarioid lichens, Ahtiana, Allocetraria, Arctocetraria, Cetraria, Cetrariella, Cetreliopsis, Flavocetraria, Kaernefeltia, Masonhalea, Nephromopsis, Tuckermanella, Tuckermannopsis, Usnocetraria and Vulpicida. A total of 71 samples representing 65 species (of 90 worldwide) and all type species of the genera are included in phylogentic analyses based on a complete ITS matrix and incomplete sets of group I intron, β-tubulin, GAPDH and mtSSU sequences. Eleven of the species included in the study are analysed phylogenetically for the first time, and of the 178 sequences, 67 are newly constructed. Two phylogenetic trees, one based solely on the complete ITS-matrix and a second based on total information, are similar, but not entirely identical. About half of the species are gathered in a strongly supported clade composed of the genera Allocetraria, Cetraria s. str., Cetrariella and Vulpicida. Arctocetraria, Cetreliopsis, Kaernefeltia and Tuckermanella are monophyletic genera, whereas Cetraria, Flavocetraria and Tuckermannopsis are polyphyletic. The taxonomy in current use is compared with the phylogenetic results, and future, probable or potential adjustments to the phylogeny are discussed. The single non-DNA character with a strong correlation to phylogeny based on DNA-sequences is conidial shape. The secondary chemistry of the poorly known species Cetraria annae is analyzed for the first time; the cortex contains usnic acid and atranorin, whereas isonephrosterinic, nephrosterinic, lichesterinic, protolichesterinic and squamatic acids occur in the medulla. Notes on the anatomy of Cetraria annae and Flavocetraria minuscula are also provided.
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| 9. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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