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- 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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| 2. |
- Loizides, Michael, et al.
(författare)
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Has taxonomic vandalism gone too far? A case study, the rise of the pay-to-publish model and the pitfalls of Morchella systematics
- 2022
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Ingår i: Mycological progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 21:1, s. 7-38
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Tidskriftsartikel (refereegranskat)abstract
- The genus Morchella has gone through turbulent taxonomic treatments. Although significant progress in Morchella systematics has been achieved in the past decade, several problems remain unresolved and taxonomy in the genus is still in flux. In late 2019, a paper published in the open-access journal Scientific Reports raised serious concerns about the taxonomic stability of the genus, but also about the future of academic publishing. The paper, entitled “High diversity of Morchella and a novel lineage of the esculenta clade from the north Qinling Mountains revealed by GCPSR-based study” by Phanpadith and colleagues, suffered from gross methodological errors, included false results and artifactual phylogenies, had misapplied citations throughout, and proposed a new species name invalidly. Although the paper was eventually retracted by Scientific Reports in 2021, the fact that such an overtly flawed and scientifically unsound paper was published in a high-ranked Q1 journal raises alarming questions about quality controls and safekeeping procedures in scholarly publishing. Using this paper as a case study, we provide a critical review on the pitfalls of Morchella systematics followed by a series of recommendations for the delimitation of species, description of taxa, and ultimately for a sustainable taxonomy in Morchella. Problems and loopholes in the academic publishing system are also identified and discussed, and additional quality controls in the pre- and post-publication stages are proposed.
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| 3. |
- Olariaga, Ibai, et al.
(författare)
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A monograph of Otidea (Pyronemataceae, Pezizomycetes)
- 2015
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Ingår i: Persoonia. - Netherlands : ingentaconnect. - 0031-5850 .- 1878-9080. ; 35, s. 166-229
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Tidskriftsartikel (refereegranskat)abstract
- The easily recognised genus Otidea is subjected to numerous problems in species identification. A numberof old names have undergone various interpretations, materials from different continents have not been compared andmisidentifications occur commonly. In this context, Otidea is monographed, based on our multiple gene phylogeniesassessing species boundaries and comparative morphological characters (see Hansen & Olariaga 2015). All namescombined in or synonymised with Otidea are dealt with. Thirty-three species are treated, with full descriptions andcolour illustrations provided for 25 of these. Five new species are described, viz. O. borealis, O. brunneoparva,O. oregonensis,O. pseudoleporina and O. subformicarum. Otidea cantharella var. minor and O. onotica var. brevisporaare elevated to species rank. Otideopsis kaushalii is combined in the genus Otidea. A key to the species of Otideais given. An LSU dataset containing 167 sequences (with 44 newly generated in this study) is analysed to placecollections and determine whether the named Otidea sequences in GenBank were identified correctly. Fourty-ninenew ITS sequences were generated in this study. The ITS region is too variable to align across Otidea, but had lowintraspecific variation and it aided in species identifications. Thirty type collections were studied, and ITS and LSUsequences are provided for 12 of these. A neotype is designated for O. cantharella and epitypes for O. concinna,O. leporina and O. onotica, along with several lectotypifications. The apothecial colour and shape, and spore charactersare important for species identification. We conclude that to distinguish closely related or morphologicallysimilar species, a combination of additional features are needed, i.e. the shape of the paraphyses, ectal excipulumstructure, types of ectal excipulum resinous exudates and their reactions in Melzer’s reagent and KOH, tomentumand basal mycelium colours and exudates. The KOH reaction of excipular resinous exudates and basal myceliumare introduced as novel taxonomic characters.
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