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  • 1
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    Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-03-27
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-18
    Description: Different distance-based threshold selection approaches were used to assess and compare use of the internal transcribed spacer (ITS) region to distinguish among 901 Cortinarius species represented by 〉3000 collections. Sources of error associated with genetic markers and selection approaches were explored and evaluated using MOTUs from genus and lineage based-alignments. Our study indicates that 1%–2% more species can be distinguished by using the full-length ITS barcode as compared to either the ITS1 or ITS2 regions alone. Optimal threshold values for different picking approaches and genetic marker lengths inferred from a subset of species containing major lineages ranged from 97.0% to 99.5% sequence similarity using clustering optimization and UNITE SH, and from 1% to 2% sequence dissimilarity with CROP. Errors for the optimal cutoff ranged from 0% to 70%, and these can be reduced to a maximum of 22% when excluding species lacking a barcode gap. A threshold value of 99% is suitable for distinguishing species in the majority of lineages in the genus using the entire ITS region but only 90% of the species could be identified using just the ITS1 or ITS2 region. Prior identification of species, lacking barcode gaps and their subsequent separate analyses, maximized the accuracy of threshold approaches.
    Print ISSN: 0168-6496
    Electronic ISSN: 1574-6941
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi (2014)
    Oxford University Press
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    Publication Date: 2014-06-30
    Electronic ISSN: 1758-0463
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Cortinarius section Bicolores and section Saturnini (Basidiomycota, Agaricales), a morphogenetic overview of European and North American species (2017)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (1878-9080) vol.39 (2017) p.175
    Details
    Publication Date: 2017-09-12
    Description: Cortinarius is the largest genus of ectomycorrhizal fungi worldwide. Recent molecular studies have shown high levels of morphological homoplasy within the genus. Importantly, DNA phylogenies can reveal characteristics that have been either over- or underemphasized in taxonomic studies. Here we sequenced and phylogenetically analysed a large set of pan-European and North American collections taxonomically studied and placed in Cortinarius sect. Bicolores and sect. Saturnini, according to traditional morpho-anatomical criteria. Our goal was to circumscribe the evolutionary boundaries of the two sections, to stabilize both the limits and nomenclature of relevant species, and to identify described taxa which, according to our current understanding, belong to other lineages. Our analysis resolves two clades: /Bicolores, including 12 species, one of which is new to science, and /Saturnini, including 6 species. Fifteen binomials, traditionally treated in these two sections based on morphology, do not belong to the above two phylogenetic clades. Instead, six of these latter are clearly placed in other clades that represent sect. Bovini, sect. Sciophylli, sect. Duracini and sect. Brunneotincti. The presence or absence of blue pigments and the detection of specific odours emerge as clearly misleading taxonomic features, but more surprisingly, spore size and ecology can be misleading as well. A total of 63 type specimens were sequenced, 4 neotypes and 2 epitypes are proposed here, and 1 new combination is made.
    Keywords: Bicolores ; Cortinarius phylogeny ; integrative taxonomy ; Saturnini ; Telamonia
    Repository Name: National Museum of Natural History, Netherlands
    Type: Article / Letter to the editor
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  • 5
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    The largest type study of Agaricales species to date: bringing identification and nomenclature of Phlegmacium (Cortinarius) into the DNA era (2014)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (0031-05850) vol.33 (2014) nr.1 p.98
    Details
    Publication Date: 2015-04-20
    Description: Cortinarius is a species-rich and morphologically challenging genus with a cosmopolitan distribution. Many names have not been used consistently and in some instances the same species has been described two or more times under separate names. This study focuses on subg. Phlegmacium as traditionally defined and includes species from boreal and temperate areas of the northern hemisphere. Our goals for this project were to: i) study type material to determine which species already have been described; ii) stabilize the use of Friesian and other older names by choosing a neo- or epitype; iii) describe new species that were discovered during the process of studying specimens; and iv) establish an accurate ITS barcoding database for Phlegmacium species. A total of 236 types representing 154 species were studied. Of these 114 species are described only once whereas 40 species had one ore more synonyms. Of the names studied only 61 were currently represented in GenBank. Neotypes are proposed for 21 species, and epitypes are designated for three species. In addition, 20 new species are described and six new combinations made. As a consequence ITS barcodes for 175 Cortinarius species are released.
    Keywords: Basidiomycota ; diversity ; DNA barcoding ; ITS ; taxonomy ; typification
    Repository Name: National Museum of Natural History, Netherlands
    Type: Article / Letter to the editor
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  • 6
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    The largest type study of Agaricales species to date: bringing identification and nomenclature of Phlegmacium (Cortinarius) into the DNA era (2014)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 33 no. 1, pp. 98-140
    Details
    Publication Date: 2024-01-12
    Description: Cortinarius is a species-rich and morphologically challenging genus with a cosmopolitan distribution. Many names have not been used consistently and in some instances the same species has been described two or more times under separate names. This study focuses on subg. Phlegmacium as traditionally de\xef\xac\x81ned and includes species from boreal and temperate areas of the northern hemisphere. Our goals for this project were to: i) study type material to determine which species already have been described; ii) stabilize the use of Friesian and other older names by choosing a neo- or epitype; iii) describe new species that were discovered during the process of studying specimens; and iv) establish an accurate ITS barcoding database for Phlegmacium species. A total of 236 types representing 154 species were studied. Of these 114 species are described only once whereas 40 species had one ore more synonyms. Of the names studied only 61 were currently represented in GenBank. Neotypes are proposed for 21 species, and epitypes are designated for three species. In addition, 20 new species are described and six new combinations made. As a consequence ITS barcodes for 175 Cortinarius species are released.
    Keywords: Basidiomycota ; diversity ; DNA barcoding ; ITS ; taxonomy ; typi\xef\xac\x81cation
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 7
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    Cortinarius section Bicolores and section Saturnini (Basidiomycota, Agaricales), a morphogenetic overview of European and North American species (2017)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 39, pp. 175-200
    Details
    Publication Date: 2024-01-12
    Description: Cortinarius is the largest genus of ectomycorrhizal fungi worldwide. Recent molecular studies have shown high levels of morphological homoplasy within the genus. Importantly, DNA phylogenies can reveal characteristics that have been either over- or underemphasized in taxonomic studies. Here we sequenced and phylogenetically analysed a large set of pan-European and North American collections taxonomically studied and placed in Cortinarius sect. Bicolores and sect. Saturnini, according to traditional morpho-anatomical criteria. Our goal was to circumscribe the evolutionary boundaries of the two sections, to stabilize both the limits and nomenclature of relevant species, and to identify described taxa which, according to our current understanding, belong to other lineages. Our analysis resolves two clades: /Bicolores, including 12 species, one of which is new to science, and /Saturnini, including 6 species. Fifteen binomials, traditionally treated in these two sections based on morphology, do not belong to the above two phylogenetic clades. Instead, six of these latter are clearly placed in other clades that represent sect. Bovini, sect. Sciophylli, sect. Duracini and sect. Brunneotincti. The presence or absence of blue pigments and the detection of specific odours emerge as clearly misleading taxonomic features, but more surprisingly, spore size and ecology can be misleading as well. A total of 63 type specimens were sequenced, 4 neotypes and 2 epitypes are proposed here, and 1 new combination is made.
    Keywords: Bicolores ; Cortinarius phylogeny ; integrative taxonomy ; Saturnini ; Telamonia
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 8
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    Hygrophorus sect. Olivaceoumbrini: new boundaries, extended biogeography and unexpected diversity unravelled by transatlantic studies (2021)
    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 46, pp. 272-312
    Details
    Publication Date: 2024-04-15
    Description: As currently delineated, Hygrophorus sect. Olivaceoumbrini is a polyphyletic assembly within subg. Colorati, encompassing glutinous and pigmented taxa. According to available literature, between a dozen and twenty species may belong in the section, mostly represented in continental and boreal forests of Europe and North America. However, the limited phylogenetic and biogeographic coverage of the genus does not presently allow for a reliable assessment of its taxonomic boundaries, nor does it provide a complete picture of species diversity within sect. Olivaceoumbrini. In an ongoing effort to confer an evolutionary backbone to Hygrophorus systematics, we assembled and analysed a dataset comprising 268 intercontinental sequences, including holotypes of 7 taxa previously not positioned phylogenetically, and enriched with collections from largely unexplored Mediterranean and Anatolian ecosystems. Overall, 30 clades are identified within 5 distinct lineages, including 11 species putatively new to science. Seven of these are formally described here as H. agathosmoides, H. albofloccosus, H. canadensis, H. limosus, H. marcocontui, H. pinophilus and H. pustulatoides spp. nov. This enriched coverage of section Olivaceoumbrini s.lat. calls for a re-evaluation of its natural boundaries into a core monophyletic clade, including H. olivaceoalbus and five closely related lookalikes, as well as the assignment of the section rank to the four remaining lineages: sect. Fuscocinerei sect. nov., sect. Limacini sect. nov., sect. Nudolidi sect. nov. and sect. Tephroleuci, respectively. We also stabilize the usage of six historical names, H. glutinifer, H. hyacinthinus, H. mesotephrus, H. olivaceoalbus, H. pustulatus and H. tephroleucus, through designation of two neotypes, three lectotypes and four epitypes.
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; Hygrophorus latitabundus ; Hygrophorus olivaceoalbus ; Hygrophorus persoonii ; phylogeny ; taxonomy ; waxcap
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 9
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    Cortinarius subgenus Leprocybe, unexpected diversity and significant differences in species compositions between western and eastern North America (2021)
    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 46, pp. 216-239
    Details
    Publication Date: 2024-04-19
    Description: The focus of this paper is the North American species of Cortinarius in subg. Leprocybe. Eighteen species, including twelve new ones, and two tentative (aff.) species, are delimited based on morphological and molecular data (DNA ITS-LSU sequences). Existing type specimens of species in subg. Leprocybe were also studied, and neo- or epitypes designated for C. cotoneus, C. melanotus, C. phrygianus and C. venetus to stabilize the nomenclature. In addition, to improve the infrasubgeneric classification of Leprocybe three new sections are proposed: sect. Fuscotomentosi, sect. Melanoti and sect. Squamiveneti. This study adds substantial information to the knowledge of subg. Leprocybe in North America against a background of European species. To date only two species, C. phrygianus and C. squamivenetus have been reported from both continents.
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; Agaricales ; barcodes ; Cortinariaceae ; ectomycorrhiza ; Europe ; ITS ; North America
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 10
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    Global consortium for the classification of fungi and fungus-like taxa (2023)
    Mushroom Research Foundation
    In:  Mycosphere vol. 14 no. 1, pp. 1960-2012
    Details
    Publication Date: 2024-04-22
    Description: The Global Consortium for the Classification of Fungi and fungus-like taxa is an international initiative of more than 550 mycologists to develop an electronic structure for the classification of these organisms. The members of the Consortium originate from 55 countries/regions worldwide, from a wide range of disciplines, and include senior, mid-career and early-career mycologists and plant pathologists. The Consortium will publish a biannual update of the Outline of Fungi and funguslike taxa, to act as an international scheme for other scientists. Notes on all newly published taxa at or above the level of species will be prepared and published online on the Outline of Fungi website (https://www.outlineoffungi.org/), and these will be finally published in the biannual edition of the Outline of Fungi and fungus-like taxa. Comments on recent important taxonomic opinions on controversial topics will be included in the biannual outline. For example, ‘to promote a more stable taxonomy in Fusarium given the divergences over its generic delimitation’, or ‘are there too many genera in the Boletales?’ and even more importantly, ‘what should be done with the tremendously diverse ‘dark fungal taxa?’ There are undeniable differences in mycologists’ perceptions and opinions regarding species classification as well as the establishment of new species. Given the pluralistic nature of fungal taxonomy and its implications for species concepts and the nature of species, this consortium aims to provide a platform to better refine and stabilise fungal classification, taking into consideration views from different parties. In the future, a confidential voting system will be set up to gauge the opinions of all mycologists in the Consortium on important topics. The results of such surveys will be presented to the International Commission on the Taxonomy of Fungi (ICTF) and the Nomenclature Committee for Fungi (NCF) with opinions and percentages of votes for and against. Criticisms based on scientific evidence with regards to nomenclature, classifications, and taxonomic concepts will be welcomed, and any recommendations on specific taxonomic issues will also be encouraged; however, we will encourage professionally and ethically responsible criticisms of others’ work. This biannual ongoing project will provide an outlet for advances in various topics of fungal classification, nomenclature, and taxonomic concepts and lead to a community-agreed classification scheme for the fungi and fungus-like taxa. Interested parties should contact the lead author if they would like to be involved in future outlines.
    Keywords: Plant Science ; Ecology ; Evolution ; Behavior and Systematics
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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