| 1. |
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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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| 11. |
- Stryamets, Nataliya
(författare)
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"But how true that is, I do not know": the influence of written sources on the medicinal use of fungi across the western borderlands of the former Soviet Union
- 2024
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Ingår i: IMA fungus. - 2210-6340 .- 2210-6359. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Fungi have been used for medicinal purposes for many centuries. This study, based on 35 historical written sources and 581 in-depth semi-structured interviews from eight countries in the western borderlands of the former Soviet Union, investigates the medicinal use of fungi by local communities. We compared the taxa and uses obtained from fieldwork and historical sources with works that advocated fungi use within Soviet herbals, representing the centralised medical system. During fieldwork, we identified eight locally used fungi and one lichen. The highest numbers of medicinal uses were documented in Russia, Estonia and Ukraine. Studies published before the Soviet era listed 21 fungal taxa and one lichen species used in the study region. However, only six of these taxa were mentioned as used by people in our field studies (Amanitamuscaria, Boletusedulis, Lycoperdon, Morchella, Phallusimpudicus and Cetrariaislandica). Notably, these same six taxa were consistently endorsed in Soviet herbals. Of the remaining three taxa recorded in the fieldwork, none were mentioned in historical written sources. However, they were promoted either in Soviet herbals (Inonotusobliquus, Kombucha) or later popular publications (Cantharelluscibarius). This highlights the significant influence of written sources on the use of fungi for medicinal purposes within the studied local communities.
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| 12. |
- Tibuhwa, Donatha D., et al.
(författare)
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Afrocantharellus gen. stat. nov. is part of a rich diversity of African Cantharellaceae
- 2012
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Ingår i: IMA Fungus. - : Springer Science and Business Media LLC. - 2210-6340 .- 2210-6359. ; 3:1, s. 25-38
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Tidskriftsartikel (refereegranskat)abstract
- A new genus in the Cantharellaceae, Afrocantharellus, is recognized based on results from phylogenetic analyses of rDNA LSU and concatenated LSU/5.8-ITS2/ATP6 data. It was previously recognized as a subgenus, but comprehensive fieldwork and the acquisition of numerous sequences for previously neglected African Cantharellus species formed the basis for a reappraisal of generic and species delimitations. Afrocantharellus is characterized morphologically by the basidiomes having thick, distantly spaced diverging folds of variegated colour. In contrast to most of Cantharellus, Afrocantharellus mostly lacks clamp connections. Phylogenies of Cantharellus and Afrocantharellus based on LSU and a concatenated data set are provided, along with descriptions of and a key to the four species and one form of Afrocantharellus recognized. Six new combinations are made.
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| 13. |
- Vinnere Pettersson, Olga, et al.
(författare)
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The Amsterdam Declaration on Fungal Nomenclature
- 2011
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Ingår i: IMA fungus. - : Springer Science and Business Media LLC. - 2210-6340 .- 2210-6359. ; 2, s. 105-112
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Tidskriftsartikel (refereegranskat)abstract
- The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19-20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature of fungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented.
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| 14. |
- 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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