| 1. |
- Hyde, K. D., et al.
(författare)
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Global consortium for the classification of fungi and fungus-like taxa
- 2023
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Ingår i: MYCOSPHERE. - : Mushroom Research Foundation. - 2077-7000 .- 2077-7019. ; 14:1, s. 1960-2012
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Tidskriftsartikel (refereegranskat)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.
(författare)
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How, not if, is the question mycologists should be asking about DNA-based typification
- 2023
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :96, s. 143-157
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Tidskriftsartikel (refereegranskat)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.
(författare)
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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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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
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Tidskriftsartikel (refereegranskat)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.
(författare)
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A gravitational telescope deformation model for geodetic VLBI
- 2019
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Ingår i: Journal of Geodesy. - : Springer Science and Business Media LLC. - 0949-7714 .- 1432-1394. ; 93:5, s. 669-680
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Tidskriftsartikel (refereegranskat)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.
(författare)
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Geometric Variations of a Geodetic Radio Telescope
- 2017
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Ingår i: Proceedings of the 23rd European VLBI Group for Geodesy and Astrometry Working Meeting. - 9789188041104 ; , s. 61-64
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 6. |
- Guillory, J, et al.
(författare)
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An SI-traceable multilateration coordinate measurement system with half the uncertainty of a laser tracker
- 2023
-
Ingår i: Measurement science and technology. - : Institute of Physics. - 0957-0233 .- 1361-6501. ; 34:6
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Tidskriftsartikel (refereegranskat)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.
(författare)
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Reassessment of the generic limits for Hydnellum and Sarcodon (Thelephorales, Basidiomycota)
- 2019
-
Ingår i: Mycokeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :54, s. 31-47
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Tidskriftsartikel (refereegranskat)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.
(författare)
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Seven new species in Piloderma (Atheliales, Basidiomycota) from the Northern Hemisphere recovered through morphological and molecular methods
- 2024
-
Ingår i: Fungal Systematics and Evolution. - 2589-3831. ; 14, s. 57-76
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Tidskriftsartikel (refereegranskat)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.
(författare)
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Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK)
- 2018
-
Ingår i: Mycokeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :28, s. 65-82
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Tidskriftsartikel (refereegranskat)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.
(författare)
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Top 50 most wanted fungi
- 2016
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 12, s. 29-40
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Tidskriftsartikel (refereegranskat)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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| 11. |
- Nitare, Johan, et al.
(författare)
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Four new species of Hydnellum (Thelephorales, Basidiomycota) with a note on Sarcodon illudens
- 2021
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Ingår i: Fungal Systematics and Evolution. - : Westerdijk Fungal Biodiversity Institute. - 2589-3823 .- 2589-3831. ; 7, s. 233-254
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Tidskriftsartikel (refereegranskat)abstract
- Four new Hydnellum species are described. Hydnellum roseoviolaceum sp. nov. grows in dry pine heaths on acidic, sandy soil. It is close to H. fuligineoviolaceum, another pine-associated species, but differs by smaller spores, an initially rose-coloured instead of violet flesh in fresh basidiomata and a mild taste. Hydnellum scabrosellum sp. nov. grows in coniferous forests on calcareous soil. It shares a general morphology with H. scabrosum, which also is its closest relative. It differs by having smaller and slenderer basidiomata and by the yellowish ochraceous colour of flesh and spines in dried specimens compared to the whitish or reddish brown colour seen in H. scabrosum. Hydnellum fagiscabrosum sp. nov. is another species with morphological and phylogenetic affinities to H. scabrosum. However, it is associated with trees from Fagales whereas H. scabrosum is associated with Pinaceae. Hydnellum nemorosum sp. nov. is yet another species that associates with broadleaved trees. It seems to be a rare species, morphologically reminiscent of H. fuligineoviolaceum, H. ioeides and H. scabrosum, but it is phylogenetically close to H. fennicum. Sequences from the type specimens of H. glaucopus, H. lepidum, H. scabrosum, Sarcodon illudens and S. regalis are included in the analyses. Specimens given the provisional name “Sarcodon pseudoglaucopus” in Sweden are now shown to be referable to S. illudens. The analyses further showed that S. illudens is close to H. lepidum. The new combination Hydnellum illudens is proposed. Sarcodon regalis and H. lepidum are shown to be conspecific and, although their basionyms were simultaneously published, the name S. regalis was only validated in a later publication. Hydnellum lepidum therefore takes priority and S. regalis becomes a synonym.
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| 12. |
- Spirin, V., et al.
(författare)
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New records of intrahymenial heterobasidiomycetes (Basidiomycota) in north Europe
- 2016
-
Ingår i: Nordic Journal of Botany. - : Wiley. - 0107-055X. ; 34:4, s. 475-477
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Tidskriftsartikel (refereegranskat)abstract
- The first records of Occultifur corticiorum, Spiculogloea occulta, S. subminuta (Pucciniomycotina), Phragmoxenidium mycophilum and Serendipita sigmaspora (Agaricomycotina) from Norway and Sweden are presented, and morphological characters and ecology of these species are discussed. In addition, Spiculogloea limonispora and S. minuta are reported as new to Russia, and Serendipita evanescens as new to USA.
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| 13. |
- Svantesson, Sten, et al.
(författare)
-
Polyozellus vs. Pseudotomentella: generic delimitation with a multi-gene dataset
- 2021
-
Ingår i: Fungal Systematics and Evolution. - : Westerdijk Fungal Biodiversity Institute. - 2589-3823. ; 8, s. 143-154
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Tidskriftsartikel (refereegranskat)abstract
- Polyozellus and Pseudotomentella are two genera of closely related, ectomycorrhizal fungi in the order Thelephorales; the former stipitate and the latter corticioid. Both are widespread in the Northern Hemisphere and many species from both genera seem to be restricted to old growth forest. This study aimed to: a) identify genetic regions useful in inferring the phylogenetic relationship between Polyozellus and Pseudotomentella, b) infer this relationship with the regions identified and c) make any taxonomic changes warranted by the result. RPB2, mtSSU and nearly full-length portions of nrLSU and nrSSU were found to be comparatively easy to sequence and provide a strong phylogenetic signal. A STACEY species tree of these three regions revealed that Polyozellus makes Pseudotomentella paraphyletic. As a result, nearly all species currently placed in Pseudotomentella were recombined to Polyozellus. Pseudotomentella larsenii was found to be closer to Tomentellopsis than Polyozellus, but its placement needs further study and it was hence not recombined.
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| 14. |
- Svantesson, Sten, et al.
(författare)
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Pseudotomentella badjelanndana, Pseudotomentella sorjusensis and Tomentella viridibasidia—three new corticioid Thelephorales species from the Scandes Mountains
- 2021
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Ingår i: Phytotaxa. - : Magnolia Press. - 1179-3155 .- 1179-3163. ; 497:2, s. 61-78
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Tidskriftsartikel (refereegranskat)abstract
- One Tomentella and two Pseudotomentella species are described from alpine areas of Sweden and Norway. Tomentella viridibasidia sp. nov. is genetically closely related to T. bryophila, but is morphologically most similar to T. olivascens and T. stuposa. Pseudotomentella badjelanndana sp. nov. and P. sorjusensis sp. nov. belong to the P. tristis group. At least P. sorjusensis must currently be regarded as morphologically cryptic with P. rotundispora. Basidiomata of the new species have only been encountered in the Scandes Mountains, but root-tip and soil sequences indicate that all three are geographically widespread. An updated key to the Pseutomentella tristis group is provided.
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| 15. |
- Svantesson, Sten, et al.
(författare)
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Solving the taxonomic identity of Pseudotomentella tristis s.l. (Thelephorales, Basidiomycota) - a multi-gene phylogeny and taxonomic review, integrating ecological and geographical data
- 2019
-
Ingår i: Mycokeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 50, s. 1-77
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Tidskriftsartikel (refereegranskat)abstract
- P. tristis is an ectomycorrhizal, corticioid fungus whose name is frequently assigned to collections of basidiomata as well as root tip and soil samples from a wide range of habitats and hosts across the northern hemisphere. Despite this, its identity is unclear; eight heterotypic taxa have in major reviews of the species been considered synonymous with or morphologically similar to P. tristis, but no sequence data from type specimens have been available. With the aim to clarify the taxonomy, systematics, morphology, ecology and geographical distribution of P. tristis and its morphologically similar species, we studied their type specimens as well as 147 basidiomata collections of mostly North European material. We used gene trees generated in BEAST 2 and PhyML and species trees estimated in STACEY and ASTRAL to delimit species based on the ITS, LSU, Tef1 alpha and mtSSU regions. We enriched our sampling with environmental ITS sequences from the UNITE database. We found the P. tristis group to contain 13 molecularly and morphologically distinct species. Three of these, P. tristis, P. umbrina and P. atrofusca, are already known to science, while ten species are here described as new: P. sciastra sp. nov., P. tristoides sp. nov., P. umbrinascens sp. nov., P. pinophila sp. nov., P. alnophila sp. nov., P. alobata sp. nov., P. pluriloba sp. nov., P. abundiloba sp. nov., P. rotundispora sp. nov. and P. media sp. nov. We discovered P. rhizopunctata and P. atrofusca to form a sister clade to all other species in P. tristis s.l. These two species, unlike all other species in the P. tristis complex, are dimitic. In this study, we designate epitypes for P. tristis, P. umbrina and Hypochnopsis fuscata and lectotypes for Auricularia phylacteris and Thelephora biennis. We show that the holotype of Hypochnus sitnensis and the lectotype of Hypochnopsis fuscata are conspecific with P. tristis, but in the absence of molecular information we regard Pseudotomentella longisterigmata and Hypochnus rhacodium as doubtful taxa due to their aberrant morphology. We confirm A. phylacteris, Tomentella biennis and Septobasidium arachnoideum as excluded taxa, since their morphology clearly show that they belong to other genera. A key to the species of the P. tristis group is provided. We found P. umbrina to be a common species with a wide, Holarctic distribution, forming ectomycorrhiza with a large number of host species in habitats ranging from tropical forests to the Arctic tundra. The other species in the P. tristis group were found to be less common and have narrower ecological niches.
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| 16. |
- Svantesson, Sten
(författare)
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Taxonomy and Systematics of Thelephorales – Glimpses Into its Hidden Hyperdiversity
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The order Thelephorales is a widespread group of many thousands of species of ecologically important, ectomycorrhizal fungi, of which only a fraction have been described to date. Most species are corticioid (skin-like) and form complexes of morphologically similar, closely related species. At the same time the names that do exist are often old, have unclear synonymy and their common presence within such complexes often hinders the description of new species. For the comparatively few stipitate (with cap and stipe) Thelephorales species taxonomic knowledge is more complete but the phylogenetic relationships between taxa is largely unknown; most existing genera have been circumscribed based on macromorphology. Many stipitate species occurring in the Nordic countries are dependent on old growth forest and are hence included in the national Red Lists, while the conservational situation for nearly all corticioid species is unknown, due to their unclear taxonomy. Pseudotomentella tristis s.l. is a seemingly common, widespread and ecologically very plastic, corticioid morphospecies with an old name and nine heterotypic synonyms. Through a combination of type studies, precise spore measurements, ecological data and a multi-gene phylogeny, three species are identified under already existing names and another ten are described as new. One species, P. umbrina, is found to indeed be a common and widespread species with a wide ecological amplitude, while the remaining 12 are less common, possibly less widespread, have narrower ecological niches and in a few cases seem to be host-restricted. In similarity to stipitate species, a large proportion of the newly described species seem to only occur in old growth forest. Three corticioid species from the Scandes mountains, two Pseudotomentella species and one Tomentella, are described as new, based on ITS-LSU phylogenies. The Pseudotomentella species belong to the P. tristis group, where they are more or less cryptic with another newly described species. A new, stipitate species in the hitherto corticioid genus Amaurodon is described, the stipitate genera Hydnellum and Sarcodon are delimited against each other and the stipitate genus Polyozellus is delimited against the corticioid genus Pseudotomentella – the former two with phylogenies based on ITS and LSU sequences and the latter based on a multi-gene dataset. Hydnellum is found to make Sarcodon paraphyletic, as does Polyozellus Pseudotomentella. To amend this, twelve species are recombined from Hydnellum to Sarcodon, while all species, including the type, are moved from Pseudotomentella to Polyozellus. In conclusion, this thesis demonstrates that corticioid species complexes in Thelephorales with many taxa and old names can be successfully disentangled and presents a method for doing so; it identifies molecular markers and sets a standard of measuring spores and collating ecological data that will facilitate further taxonomic work within the order. In addition, it shows that basidiomata shape is a poor predictor of generic affinity, even when derived from such striking differences as the separation of stipitate and corticioid forms. Consequently, the extinction threat previously documented for stipitate species is likely not restricted to such, and this is also tentatively shown for corticioid Polyozellus species.
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| 17. |
- Svantesson, Sten, et al.
(författare)
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"The Mouldy Marshmallow" Amaurodon caeruleocaseus (Thelephorales, Basidiomycota) - the first stipitate species in the genus Amaurodon
- 2022
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Ingår i: Sydowia. - 0082-0598. ; 74, s. 181-192
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Tidskriftsartikel (refereegranskat)abstract
- Amaurodon (Thelephorales, Basidiomycota) constitutes a small but globally distributed genus in the order Thelephorales that is thought to be saprotrophic. Previously described species are soft and corticioid, with a smooth or hydnoid, blue to green hymenitun which turns green after drying and have spores that turn purple in KOH. Based on sequences from the nuclear rDNA regions ITS1-5.8S-ITS2 (ITS) and 28S Amaurodon caeruleocaseus is described from Western Australia a species that has all the morphological features common to the genus, with the interesting exception of forming a stipitate basidiome with a marshmallow-like consistency. Its closest relative is shown to be A. mustialaensis. The two species are unique within Thelephorales in having spores that appear smooth rather than ornamented illider a light microscope. A key to the genus Amaumdon is a Iso provided.
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| 18. |
- Wurzbacher, Christian, 1980, et al.
(författare)
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Fungal communities in groundwater springs along the volcanic zone of Iceland
- 2020
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Ingår i: Inland Waters. - : Informa UK Limited. - 2044-2041 .- 2044-205X. ; 10:3, s. 418-27
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Tidskriftsartikel (refereegranskat)abstract
- Aquatic fungi are a largely unexplored group of organisms with a still unknown diversity of ecological niches. Groundwater biomes comprise vast but poorly explored habitats. In this study, we sampled the Icelandic groundwater, a unique system that has been separated and isolated into distinct basins for millions of years due to volcanic activity. The aim was to explore the fungal diversity of the basins and its connection with the surface waters. We screened the DNA-based fungal diversity of 11 Icelandic groundwater springs and their emerging surface waters by ITS metabarcoding, revealing that the species turnover was indeed distinct for each groundwater basin. Furthermore, the groundwater taxa, which include many psychrophilic yeast-like and ascomycete fungi, seem to serve as a constant inoculum for the surface water. Nevertheless, the groundwater springs had a lower sequence proportion of early diverging, primary aquatic fungal lineages (10%) and completely unknown lineages (13%) than the surface waters (41% and 22%, respectively), likely explained by the lower diversity of suitable hosts for these presumed parasitic lineages. Our results highlight the importance of overlooked organism groups in the resolution of overarching research questions in ecology, nutrient circulation, and global change biology at large.
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| 19. |
- Wurzbacher, Christian, 1980, et al.
(författare)
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Introducing ribosomal tandem repeat barcoding for fungi
- 2019
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-0998 .- 1755-098X. ; 19:1, s. 118-127
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Tidskriftsartikel (refereegranskat)abstract
- Sequence comparison and analysis of the various ribosomal genetic markers are the dominant molecular methods for identification and description of fungi. However, new environmental fungal lineages known only from DNA data reveal significant gaps in our sampling of the fungal kingdom in terms of both taxonomy and marker coverage in the reference sequence databases. To facilitate the integration of reference data from all of the ribosomal markers, we present three sets of general primers that allow for amplification of the complete ribosomal operon from the ribosomal tandem repeats. The primers cover all ribosomal markers: ETS, SSU, ITS1, 5.8S, ITS2, LSU and IGS. We coupled these primers successfully with third-generation sequencing (PacBio and Nanopore sequencing) to showcase our approach on authentic fungal herbarium specimens (Basidiomycota), aquatic chytrids (Chytridiomycota) and a poorly understood lineage of early diverging fungi (Nephridiophagidae). In particular, we were able to generate high-quality reference data with Nanopore sequencing in a high-throughput manner, showing that the generation of reference data can be achieved on a regular desktop computer without the involvement of any large-scale sequencing facility. The quality of the Nanopore generated sequences was 99.85%, which is comparable with the 99.78% accuracy described for Sanger sequencing. With this work, we hope to stimulate the generation of a new comprehensive standard of ribosomal reference data with the ultimate aim to close the huge gaps in our reference datasets.
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| 20. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
-
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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| 21. |
- Zizka, Alexander, et al.
(författare)
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CoordinateCleaner : Standardized cleaning of occurrence records from biological collection databases
- 2019
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Ingår i: Methods in Ecology and Evolution. - : Wiley-Blackwell. - 2041-210X. ; 10:5, s. 744-751
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Tidskriftsartikel (refereegranskat)abstract
- Species occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues with data quality, especially incorrect geo-referencing or dating, can diminish their usefulness. Manual cleaning is time-consuming, error prone, difficult to reproduce and limited to known geographical areas and taxonomic groups, making it impractical for datasets with thousands or millions of records.Here, we present CoordinateCleaner, an r-package to scan datasets of species occurrence records for geo-referencing and dating imprecisions and data entry errors in a standardized and reproducible way. CoordinateCleaner is tailored to problems common in biological and palaeontological databases and can handle datasets with millions of records. The software includes (a) functions to flag potentially problematic coordinate records based on geographical gazetteers, (b) a global database of 9,691 geo-referenced biodiversity institutions to identify records that are likely from horticulture or captivity, (c) novel algorithms to identify datasets with rasterized data, conversion errors and strong decimal rounding and (d) spatio-temporal tests for fossils.We describe the individual functions available in CoordinateCleaner and demonstrate them on more than 90million occurrences of flowering plants from the Global Biodiversity Information Facility (GBIF) and 19,000 fossil occurrences from the Palaeobiology Database (PBDB). We find that in GBIF more than 3.4 million records (3.7%) are potentially problematic and that 179 of the tested contributing datasets (18.5%) might be biased by rasterized coordinates. In PBDB, 1205 records (6.3%) are potentially problematic.All cleaning functions and the biodiversity institution database are open-source and available within the CoordinateCleaner r-package.
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| 22. |
- Zizka, Alexander, 1986, et al.
(författare)
-
CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases
- 2019
-
Ingår i: Methods in Ecology and Evolution. - : Wiley. - 2041-210X. ; 10:5, s. 744-751
-
Tidskriftsartikel (refereegranskat)abstract
- Species occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues with data quality, especially incorrect geo-referencing or dating, can diminish their usefulness. Manual cleaning is time-consuming, error prone, difficult to reproduce and limited to known geographical areas and taxonomic groups, making it impractical for datasets with thousands or millions of records. Here, we present CoordinateCleaner, an r-package to scan datasets of species occurrence records for geo-referencing and dating imprecisions and data entry errors in a standardized and reproducible way. CoordinateCleaner is tailored to problems common in biological and palaeontological databases and can handle datasets with millions of records. The software includes (a) functions to flag potentially problematic coordinate records based on geographical gazetteers, (b) a global database of 9,691 geo-referenced biodiversity institutions to identify records that are likely from horticulture or captivity, (c) novel algorithms to identify datasets with rasterized data, conversion errors and strong decimal rounding and (d) spatio-temporal tests for fossils. We describe the individual functions available in CoordinateCleaner and demonstrate them on more than 90million occurrences of flowering plants from the Global Biodiversity Information Facility (GBIF) and 19,000 fossil occurrences from the Palaeobiology Database (PBDB). We find that in GBIF more than 3.4 million records (3.7%) are potentially problematic and that 179 of the tested contributing datasets (18.5%) might be biased by rasterized coordinates. In PBDB, 1205 records (6.3%) are potentially problematic. All cleaning functions and the biodiversity institution database are open-source and available within the CoordinateCleaner r-package.
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