| 1. |
- Hyde, K. D., et al.
(author)
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Global consortium for the classification of fungi and fungus-like taxa
- 2023
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In: MYCOSPHERE. - : Mushroom Research Foundation. - 2077-7000 .- 2077-7019. ; 14:1, s. 1960-2012
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Journal article (peer-reviewed)abstract
- 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 fungus-like 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.
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| 2. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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How, not if, is the question mycologists should be asking about DNA-based typification
- 2023
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In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :96, s. 143-157
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Journal article (peer-reviewed)abstract
- Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings chal-lenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.
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| 3. |
- Abarenkov, Kessy, et al.
(author)
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Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)
- 2016
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In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
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Journal article (peer-reviewed)abstract
- Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).
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| 4. |
- Bergstrand, Sten, et al.
(author)
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A gravitational telescope deformation model for geodetic VLBI
- 2019
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In: Journal of Geodesy. - : Springer Science and Business Media LLC. - 0949-7714 .- 1432-1394. ; 93:5, s. 669-680
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Journal article (peer-reviewed)abstract
- We have measured the geometric deformations of the Onsala 20 m VLBI telescope utilizing a combination of laser scanner, laser tracker, and electronic distance meters. The data put geometric constraints on the electromagnetic raypath variations inside the telescope. The results show that the propagated distance of the electromagnetic signal inside the telescope differs from the telescope’s focal length variation, and that the deformations alias as a vertical or tropospheric component. We find that for geodetic purposes, structural deformations of the telescope are more important than optic properties, and that for geodetic modelling the variations in raypath centroid rather than focal length should be used. All variations that have been identified as significant in previous studies can be quantified. We derived coefficients to model the gravitational deformation effect on the path length and provide uncertainty intervals for this model. The path length variation due to gravitational deformation of the Onsala 20 m telescope is in the range of 7–11 mm, comparing elevation 0$$^{\circ }$$∘and 90$$^{\circ }$$∘, and can be modelled with an uncertainty of 0.3 mm.
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| 5. |
- Bergstrand, Sten, 1971, et al.
(author)
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Geometric Variations of a Geodetic Radio Telescope
- 2017
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In: Proceedings of the 23rd European VLBI Group for Geodesy and Astrometry Working Meeting. - 9789188041104 ; , s. 61-64
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Conference paper (other academic/artistic)
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| 6. |
- Guillory, J, et al.
(author)
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An SI-traceable multilateration coordinate measurement system with half the uncertainty of a laser tracker
- 2023
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In: Measurement science and technology. - : Institute of Physics. - 0957-0233 .- 1361-6501. ; 34:6
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Journal article (peer-reviewed)abstract
- We have validated the performance of a prototype coordinate measurement system based on multilateration by comparing it to a laser tracker, i.e. a well-proven instrument widely used in the industry. After establishing the uncertainty budget of the different systems, we performed position measurements with both instruments on common targets. Using the estimated uncertainties associated with the measurements, we found that the multilateration system provided lower position uncertainties than the laser tracker: on average 18 µm versus 33 µm for distances up to 12 m. The uncertainties represented by confidence ellipsoids are compatible between the two systems: for confidence regions of 95% probability, they overlap as expected, i.e. in 94% of the cases. We also measured the length of a 0.8 m long reference scale bar with the multilateration system at an error of only 2 µm. This cross-comparison is a new and key step in the characterization of this SI-traceable multilateration system. © 2023 The Author(s).
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| 7. |
- Larsson, K. H., et al.
(author)
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Reassessment of the generic limits for Hydnellum and Sarcodon (Thelephorales, Basidiomycota)
- 2019
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In: Mycokeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :54, s. 31-47
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Journal article (peer-reviewed)abstract
- DNA sequences from the nuclear LSU and ITS regions were used for phylogenetic analyses of Thelephorales with a focus on the stipitate hydnoid genera Hydnellum and Sarcodon. Analyses showed that Hydnellum and Sarcodon are distinct genera but that the current division, based on basidioma texture, makes Sarcodon paraphyletic with respect to Hydnellum. In order to make genera monophyletic several species are moved from Sarcodon to Hydnellum and the following new combinations are made: Hydnellum amygdaliolens, H. fennicum, H. fuligineoviolaceum, H. fuscoindicum, H. glaucopus, H. joeides, H. lepidum, H. lundellii, H. martioflavum, H. scabrosum, H. underwoodii, and H. versipelle. Basidiospore size seems to separate the genera in most cases. Hydnellum species have basidiospore lengths in the range 4.45-6.95 mu m while the corresponding range for Sarcodon is 7.4-9 mu m. S. quercinofibulatus deviates from this pattern with an average spore length around 6 mu m. Neotropical Sarcodon species represent a separate evolutionary lineage.
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| 8. |
- Larsson, Karl-Henrik, 1948, et al.
(author)
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Seven new species in Piloderma (Atheliales, Basidiomycota) from the Northern Hemisphere recovered through morphological and molecular methods
- 2024
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In: Fungal Systematics and Evolution. - 2589-3831. ; 14, s. 57-76
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Journal article (peer-reviewed)abstract
- The ectomycorrhizal genus Piloderma (Atheliales, Basidiomycota) is studied using morphological and molecular methods. Seven new species are identified and described, viz. P. cinicola, P. craurum, P. egens, P. exiguum, P. humile, P. ochraceum, and P. rallum, bringing the total number of accepted species to 13. All new species are supported by ITS sequences from basidiomata and from environmental soil and root-tip sequences available in public databases. A key to all species in Piloderma is provided.
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| 9. |
- Nilsson, R. Henrik, 1976, et al.
(author)
-
Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK)
- 2018
-
In: Mycokeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :28, s. 65-82
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Journal article (peer-reviewed)abstract
- Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi - whether transient visitors or more persistent residents - may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions - such as country and host/substrate of collection - are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10-11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS bar-code sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes - including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences - were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment.
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| 10. |
- Nilsson, R. Henrik, 1976, et al.
(author)
-
Top 50 most wanted fungi
- 2016
-
In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 12, s. 29-40
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Journal article (peer-reviewed)abstract
- Environmental sequencing regularly recovers fungi that cannot be classified to any meaningful taxonomic level beyond “Fungi”. There are several examples where evidence of such lineages has been sitting in public sequence databases for up to ten years before receiving scientific attention and formal recognition. In order to highlight these unidentified lineages for taxonomic scrutiny, a search function is presented that produces updated lists of approximately genus-level clusters of fungal ITS sequences that remain unidentified at the phylum, class, and order levels, respectively. The search function (https://unite.ut.ee/top50.php) is implemented in the UNITE database for molecular identification of fungi, such that the underlying sequences and fungal lineages are open to third-party annotation. We invite researchers to examine these enigmatic fungal lineages in the hope that their taxonomic resolution will not have to wait another ten years or more.
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