| 1. |
- Polme, S., et al.
(författare)
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FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles
- 2020
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Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 105:1, s. 1-16
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Tidskriftsartikel (refereegranskat)abstract
- The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.
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| 2. |
- 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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| 3. |
- Kõljalg, U., et al.
(författare)
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The taxon hypothesis paradigm—On the unambiguous detection and communication of taxa
- 2020
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Ingår i: Microorganisms. - : MDPI AG. - 2076-2607. ; 8:12
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Tidskriftsartikel (refereegranskat)abstract
- Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
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| 4. |
- Kõljalg, Urmas, et al.
(författare)
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Towards a unified paradigm for sequence-based identification of fungi.
- 2013
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Ingår i: Molecular ecology. - : Wiley. - 1365-294X .- 0962-1083. ; 22:21, s. 5271-7
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Tidskriftsartikel (refereegranskat)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.
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| 5. |
- Motiejunaite, Jurga, et al.
(författare)
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Lichens, lichenicolous and allied fungi in Asveja Regional Park (Lithuania)
- 2012
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Ingår i: Botanica Lithuanica. - 1392-1665. ; 18:2, s. 85-100
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Tidskriftsartikel (refereegranskat)abstract
- The paper reports the results of lichenological investigations in Asveja Regional Park (eastern Lithuania). A large part of the study was performed during the joint 18th Symposium of Baltic Mycologists and Lichenologists (BMLS) and Nordic Lichen Society meeting (NLF), September 19–23, 2011. A list of 259 species is presented, 30 of them are new to Lithuania. Arthonia helvola, Bacidina sulphurella, Candelariella lutella, Catillaria croatica, Cladonia conista, Gyalecta derivata, Lecanora quercicola, Leptosphaeria ramalinae, Strigula jamesii, Trichonectria rubefaciens, Verrucaria banatica, V. boblensis, V. christiansenii, V. illinoisensis, V. inornata, V. nigrofusca, V. trabicola, Zwackhiomyces diederichii are recorded for the first time in the Baltic countries. New lichens for Lithuania are: Bacidia incompta, Caloplaca crenulatella, C. pyracea, Catinaria atropurpurea, Lecanora populicola, L. semipallida, Mycobilimbia epixanthoides, Ramalina dilacerata, Verrucaria inaspecta, and new lichenicolous fungi are: Cladosporium licheniphilum, Stigmidium microspilum, Xenonectriella leptalea. Eighteen species included in the Lithuanian Red Data Book were recorded which is the highest number known for any studied area in Lithuania.
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| 6. |
- Motiejunaite, Jurga, et al.
(författare)
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Ninety-one species of lichens and allied fungi new to Latvia with a list of additional records from Kurzeme
- 2016
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Ingår i: Herzogia. - : Herzogia. - 0018-0971. ; 29:1, s. 143-163
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Tidskriftsartikel (refereegranskat)abstract
- The results of lichenological excursions of the 19th Symposium of Baltic Mycologists and Lichenologists (BMLS) in Latvia, Kurzeme region, 22–26 September 2014, are reported. A list of 290 species is presented, of which 238 are lichenized, 43 lichen-inhabiting, and nine saprotrophic fungi: ninety-one species are new to Latvia, twelve of which (Caloplaca duplicata, Cresporhaphis wienkampii, Ellisembia lichenicola, Gallowayella weberi, Gregorella humida, Lichenochora weillii, Parmelia serrana, Polycauliona phlogina, Reconditella physconiarum, Stictis brunnescens, Thelocarpon superellum, and Verrucaria tectorum) are also new for the Baltic States. Athallia alnetorum is reported here for the first time in northern Europe. The presence of Ochrolechia androgyna s. str., Athallia holocarpa and A. pyracea is confirmed for Latvia, and Parmelia submontana is reported as a new host for Homostegia piggotii.
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