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| 2. |
- Grewe, F., et al.
(författare)
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Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota)
- 2020
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Ingår i: IMA Fungus. - : Springer Science and Business Media LLC. - 2210-6340 .- 2210-6359. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Parmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow.
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| 3. |
- Hawksworth, David, et al.
(författare)
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Racoleus, a new genus of sterile filamentous lichen-forming fungi from the tropics, with observations on the nomenclature and typification of Cystocoleus and Racodium
- 2011
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Ingår i: IMA Fungus. - 2210-6340 .- 2210-6359. ; 2:1, s. 71-79
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Tidskriftsartikel (refereegranskat)abstract
- Racoleus trichophorus gen. sp. nov. is described for a ;tropical sterile filamentous lichenized fungus which overgrows various crustose lichens on bark. It shares some features with Cystocoleus and Racodium, but is unique in having non-lichenized arcuate lateral spines. The genus, which is known from China, the Ivory Coast, and Peru, is of uncertain systematic position; on the basis of morphological similarities, however, it may be referred to "? Capnodiales (incertae sedis)" ad interim. In addition, the nomenclature and typification of the monotypic genera Cystocoleus and Racodium are reviewed, and lectotypes selected for the type of each. The available information on the ecology and distribution of these two genera is also summarized, and scanning electron micrographs (SEM) of all three species are presented for the first time.
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| 4. |
- Healy, Rosanne, et al.
(författare)
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Competing sexual-asexual generic names of Pezizomycetes and recommendations for use.
- 2016
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Ingår i: IMA Fungus. - Ingenta : Springer Science and Business Media LLC. - 2210-6340 .- 2210-6359. ; 7:2, s. 285-288
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Tidskriftsartikel (refereegranskat)abstract
- Following the change that eliminated dual naming of sexual and asexual morphs of fungi, generic names of Pezizomycetes have been evaluated to determine which of the competing names should be recommended for use. Evaluation is based on congruence of type species to determine if the names are congeneric and which name is most commonly cited as well as priority. In the Pezizomycetes six pairs of generic names were determined to compete. In all cases the older name, representing the sexual morph, is recommended for use, specifically Caloscypha rather than Geniculodendron, Desmazierella rather than Verticicladium, Miladina rather than Actinosporella, Morchella rather than Costantinella, Sarcoscypha rather than Molliardiomyces, and Trichophaea rather than Dichobotrys.
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| 5. |
- Kalsoom Khan, Faheema, et al.
(författare)
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Naming the untouchable - environmental sequences and niche partitioning as taxonomical evidence in fungi
- 2020
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Ingår i: IMA Fungus. - : BMC. - 2210-6340 .- 2210-6359. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Due to their submerged and cryptic lifestyle, the vast majority of fungal species are difficult to observe and describe morphologically, and many remain known to science only from sequences detected in environmental samples. The lack of practices to delimit and name most fungal species is a staggering limitation to communication and interpretation of ecology and evolution in kingdom Fungi. Here, we use environmental sequence data as taxonomical evidence and combine phylogenetic and ecological data to generate and test species hypotheses in the class Archaeorhizomycetes (Taphrinomycotina, Ascomycota). Based on environmental amplicon sequencing from a well-studied Swedish pine forest podzol soil, we generate 68 distinct species hypotheses of Archaeorhizomycetes, of which two correspond to the only described species in the class. Nine of the species hypotheses represent 78% of the sequenced Archaeorhizomycetes community, and are supported by long read data that form the backbone for delimiting species hypothesis based on phylogenetic branch lengths. Soil fungal communities are shaped by environmental filtering and competitive exclusion so that closely related species are less likely to co-occur in a niche if adaptive traits are evolutionarily conserved. In soil profiles, distinct vertical horizons represent a testable niche dimension, and we found significantly differential distribution across samples for a well-supported pair of sister species hypotheses. Based on the combination of phylogenetic and ecological evidence, we identify two novel species for which we provide molecular diagnostics and propose names. While environmental sequences cannot be automatically translated to species, they can be used to generate phylogenetically distinct species hypotheses that can be further tested using sequences as ecological evidence. We conclude that in the case of abundantly and frequently observed species, environmental sequences can support species recognition in the absences of physical specimens, while rare taxa remain uncaptured at our sampling and sequencing intensity.
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| 6. |
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| 7. |
- Lantz, Henrik, et al.
(författare)
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Xerochrysium gen. nov. and Bettsia, genera encompassing xerophilic species of Chrysosporium
- 2013
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Ingår i: IMA fungus. - : Springer Science and Business Media LLC. - 2210-6340 .- 2210-6359. ; 4, s. 229-241
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Tidskriftsartikel (refereegranskat)abstract
- On the basis of a study of ITS sequences, Vidal et al. (Rev. Iber. Micol. 17: 22, 2000) recommended that the genus Chrysosporium be restricted to species belonging to Onygenales. Using nrLSU genes, we studied the majority of clades examined by Vidal et al. and showed that currently accepted species in Chrysosporium phylogenetically belong in six clades in three orders. Surprisingly, the xerophilic species of Chrysosporium, long thought to be a single grouping away from the majority of Chrysosporium species, occupy two clades, one in Leotiales, the other in Eurotiales. Species accepted in Leotiales are related to the sexual genus Bettsia. One is the type species B. alvei, and related asexual strains classified as C. farinicola, the second is C. fastidium transferred to Bettsia as B. fastidia. Species in the Eurotiales are transferred to Xerochrysium gen. nov., where the accepted species are X. xerophilum and X. dermatitidis, the correct name for C. inops on transfer to Xerochrysium. All accepted species are extreme xerophiles, found in dried and concentrated foods.
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| 8. |
- Parra, Luis A., et al.
(författare)
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Proposals for consideration at IMC11 to modify provisions related solely to fungi in the International Code of Nomenclature for algae, fungi, and plants
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. I-III
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Seven proposals to modify the provisions of the International Code of Nomenclature for algae, fungi, and plants (ICN) at the 11th International Mycological Congress (IMC11) in July 2018 had been received by the proscribed date of 1 March 2018. These proposals are formally presented together here. The topics addressed relate to the clarification of the meaning of "original material" in relation to the typification of sanctioned names, the indication of the nomenclatural status of sanctioned names in author citations, the use of DNA sequences as nomenclatural types, and the possibility of including repository identifiers as an alternative to author citations. A synopsis of the proposals will be provided during April, and the mycological community will be invited to provide a guiding vote up to 10 June 2018. Final decisions on these proposals are to be made following debate at the Fungal Nomenclature Session of IMC11.
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| 9. |
- Redondo, Miguel Angel, et al.
(författare)
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Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation
- 2021
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Ingår i: IMA fungus. - : Springer Science and Business Media LLC. - 2210-6340 .- 2210-6359. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.
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| 10. |
- Robert, Vincent, et al.
(författare)
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MycoBank gearing up for new horizons
- 2013
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Ingår i: IMA Fungus. - : Ingentaconnect. - 2210-6340 .- 2210-6359. ; 4:2, s. 371-379
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Tidskriftsartikel (refereegranskat)
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