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- Hansen, Karen, et al.
(författare)
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Species limits and relationships within Otidea inferred from multiple gene phylogenies
- 2015
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Ingår i: Persoonia. - Netherlands. - 0031-5850 .- 1878-9080. ; 35, s. 148-165
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Tidskriftsartikel (refereegranskat)abstract
- The genus Otidea is one of the more conspicuous members of the Pyronemataceae, with high speciesdiversity in hemiboreal and boreal forests. The genus is morphologically coherent and in previous higher-level multigeneanalyses it formed a highly supported monophyletic group. Species delimitation within Otidea is controversialand much confusion has prevailed in the naming of taxa. To provide a phylogenetic hypothesis of Otidea, elucidatespecies diversity and limits we compiled a four-gene dataset including the nuclear LSU rDNA and three nuclearprotein-coding genes (RPB1, RPB2 and EF-1α) for 89 specimens (total 4 877 nucleotides). These were selected froma larger sample of material studied using morphology and 146 ITS (ITS1-5.8S-ITS2) and 168 LSU rDNA sequencesto represent the full genetic diversity. Using genealogical concordance phylogenetic species recognition (GCPSR),Bayesian and maximum likelihood analyses of the individual datasets resolved 25 species of Otidea. An additionaleight singletons are considered to be distinct species, because they were genetically divergent from their sisters.Sequences of multiple genes were included from 13 holotypes, one neotype and three epitypes. Otidea angusta,O. myosotis and O. papillata f. pallidefurfuracea are nested within O. nannfeldtii, O. leporina and O. tuomikoskii,respectively and are considered synonyms. Otidea cantharella var. minor is shown to be a distinct species. Fivenew species were discovered: O. oregonensis and O. pseudoleporina for North America; and O. borealis, O. brunneoparvaand O. subformicarum for Europe. The analyses of the individual four gene datasets yielded phylogeniesthat were highly concordant topologically, except for the RPB1 that showed supported conflict for some nodes inBayesian analysis. Excluding the RPB1 from the combined analyses produced an identical topology to the four-genephylogeny, but with higher support for several basal nodes and lower support for several shallow nodes. We argueto use the three-gene dataset to retrieve the maximum support for the higher-level relationships in Otidea, but stillutilise the signal from the RPB1 for the delimitation and relationships of closely related species. From the four generegions utilised, EF-1α and RPB1 have the strongest species recognition power, and with higher amplification successEF-1α may serve as the best secondary barcoding locus for Otidea (with ITS being a primary). The phylogenyfrom the three- and four-gene datasets is fully resolved and strongly supported in all branches but one. Two majorclades, as part of six inclusive clades A–F, are identified – and ten subclades within these: A) O. platyspora andO. alutacea subclades, and B) O. papillata, O. leporina, O. tuomikoskii, O. cantharella, O. formicarum, O. unicisa,O. bufonia-onotica and O. concinna subclades. Morphological features in Otidea appear to be fast evolving andprone to shifts, and are poor indicators of higher-level relationships. Nevertheless, a conspicuous spore ornament isa synapomorphy for the O. unicisa subclade (/Otideopsis); all other species in Otidea have smooth or verruculose (inSEM) spores. Exclusively pale to bright yellow apothecia and straight to curved, broadly clavate to distinctly capitateparaphyses are synapomorphies for a restricted O. concinna subclade (/Flavoscypha). The curved to hooked apicesof the paraphyses is suggested to be a symplesiomorphic trait for the genus. The reaction of resinous exudateson the outermost excipular cells that coalesce into amber drops in Melzer’s reagent is likely an ancestral state forclade B. We estimate that Otidea consists of 47 species worldwide, based on all available information (includingmorphology, ITS or LSU sequences, and literature descriptions). Three fifths of the species occur in Europe, with20 species recognised as endemic. At least 14 species occur in North America and 17 in Asia, with eight and tenspecies considered endemic to each continent, respectively. Our knowledge about Otidea in Asia is still fragmentaryand the diversity likely much higher.
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- Jaklitsch, Walter M., et al.
(författare)
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Teichospora and the Teichosporaceae
- 2016
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Ingår i: Mycological progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 15:3
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Tidskriftsartikel (refereegranskat)abstract
- A multigene analysis of a combined ITS, LSU, SSU, rpb2 and tef1 sequence data matrix was applied to infer the phylogenetic position of the genus Teichospora in the Pleosporales, based on isolates from freshly collected material of the generic type T. trabicola and several additional species. Phylogenetic analyses revealed that Misturatosphaeria and Floricola are synonyms of Teichospora. All species of these genera and several species recently described in the genus Curreya belong to Teichospora and are thus combined in this genus. Also, Melanomma radicans and Ramusculicola thailandica are combined in Teichospora. The new name Teichospora parva is established for Misturatosphaeria minima. Three new species, T. melanommoides, T. pusilla and T. rubriostiolata, are described, and an expanded description of T. mariae is given. The family Teichosporaceae is currently confined to Teichospora, which can be phylogenetically clearly separated from Lophiostoma, the type genus of the Lophiostomataceae. The family name Floricolaceae is a synonym of Teichosporaceae. All species described here form apically free paraphyses among immature asci. This finding contradicts the current general dogma that apically free paraphyses are absent in the Pleosporales and questions the wide use of the term pseudoparaphysis.
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- Olariaga, Ibai, et al.
(författare)
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A monograph of Otidea (Pyronemataceae, Pezizomycetes)
- 2015
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Ingår i: Persoonia. - Netherlands : ingentaconnect. - 0031-5850 .- 1878-9080. ; 35, s. 166-229
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Tidskriftsartikel (refereegranskat)abstract
- The easily recognised genus Otidea is subjected to numerous problems in species identification. A numberof old names have undergone various interpretations, materials from different continents have not been compared andmisidentifications occur commonly. In this context, Otidea is monographed, based on our multiple gene phylogeniesassessing species boundaries and comparative morphological characters (see Hansen & Olariaga 2015). All namescombined in or synonymised with Otidea are dealt with. Thirty-three species are treated, with full descriptions andcolour illustrations provided for 25 of these. Five new species are described, viz. O. borealis, O. brunneoparva,O. oregonensis,O. pseudoleporina and O. subformicarum. Otidea cantharella var. minor and O. onotica var. brevisporaare elevated to species rank. Otideopsis kaushalii is combined in the genus Otidea. A key to the species of Otideais given. An LSU dataset containing 167 sequences (with 44 newly generated in this study) is analysed to placecollections and determine whether the named Otidea sequences in GenBank were identified correctly. Fourty-ninenew ITS sequences were generated in this study. The ITS region is too variable to align across Otidea, but had lowintraspecific variation and it aided in species identifications. Thirty type collections were studied, and ITS and LSUsequences are provided for 12 of these. A neotype is designated for O. cantharella and epitypes for O. concinna,O. leporina and O. onotica, along with several lectotypifications. The apothecial colour and shape, and spore charactersare important for species identification. We conclude that to distinguish closely related or morphologicallysimilar species, a combination of additional features are needed, i.e. the shape of the paraphyses, ectal excipulumstructure, types of ectal excipulum resinous exudates and their reactions in Melzer’s reagent and KOH, tomentumand basal mycelium colours and exudates. The KOH reaction of excipular resinous exudates and basal myceliumare introduced as novel taxonomic characters.
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| 8. |
- Olariaga, Ibai, et al.
(författare)
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Lectotypification of Typhula graminum and description of T-berthieri sp nov.
- 2008
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Ingår i: Cryptogamie Mycologie. - 0181-1584 .- 1776-100X. ; 29:2, s. 145-155
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Tidskriftsartikel (refereegranskat)abstract
- Two syntypes of T graminum were examined, one of which is designated as lectotype and is described in detail. The synonymy between T graminum and T. incarnata, as currently supported, seems doubtful. The white basidiomata and the presence of conidiomata with sympodulospores on the sclerotia were not reported by Berthier and Remsberg, who studied the original material of T graminum, nor for T. incarnata. A review of the history of T graminum is made and the synonymy is fully discussed. T. berthieri sp. nov. is proposed for T. graminum sensu Berthier. Berthier (1976) used the name T. graminum for a species growing on Molinia and with striate epidermoid layer, and therefore excluding the type of T. graminum. The holotype and an isotype are selected amongst the collections cited by Berthier. All the materials agree with Berthier's description, except for the presence of scarce clamps and for a cuticle of up to 8 mu m thick in old sclerotia, two characteristics not mentioned by Berthier.
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| 13. |
- Schoch, Conrad L., et al.
(författare)
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
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Ingår i: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
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Tidskriftsartikel (refereegranskat)abstract
- DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
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| 14. |
- Wijayawardande, N.N., et al.
(författare)
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Notes for genera – Ascomycota
- 2017
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Ingår i: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 86, s. 1-594
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Tidskriftsartikel (refereegranskat)
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| 15. |
- 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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