| 1. |
- 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. |
- 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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| 3. |
- Looney, Brian P., et al.
(författare)
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Into and out of the tropics : global diversification patterns in a hyperdiverse clade of ectomycorrhizal fungi
- 2016
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 25:2, s. 630-647
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Tidskriftsartikel (refereegranskat)abstract
- Ectomycorrhizal (ECM) fungi, symbiotic mutualists of many dominant tree and shrub species, exhibit a biogeographic pattern counter to the established latitudinal diversity gradient of most macroflora and fauna. However, an evolutionary basis for this pattern has not been explicitly tested in a diverse lineage. In this study, we reconstructed a mega-phylogeny of a cosmopolitan and hyperdiverse genus of ECM fungi, Russula, sampling from annotated collections and utilizing publically available sequences deposited in GenBank. Metadata from molecular operational taxonomic unit cluster sets were examined to infer the distribution and plant association of the genus. This allowed us to test for differences in patterns of diversification between tropical and extratropical taxa, as well as how their associations with different plant lineages may be a driver of diversification. Results show that Russula is most species-rich at temperate latitudes and ancestral state reconstruction shows that the genus initially diversified in temperate areas. Migration into and out of the tropics characterizes the early evolution of the genus, and these transitions have been frequent since this time. We propose the generalized diversification rate' hypothesis to explain the reversed latitudinal diversity gradient pattern in Russula as we detect a higher net diversification rate in extratropical lineages. Patterns of diversification with plant associates support host switching and host expansion as driving diversification, with a higher diversification rate in lineages associated with Pinaceae and frequent transitions to association with angiosperms.
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| 4. |
- Aignon, Hyppolite L., et al.
(författare)
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Mallocybe africana (Inocybaceae, Fungi), the first species of Mallocybe described from Africa
- 2021
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Ingår i: Phytotaxa. - : Magnolia Press. - 1179-3155 .- 1179-3163. ; 478:1, s. 49-60
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Tidskriftsartikel (refereegranskat)abstract
- The family Inocybaceae has been poorly studied in Africa. Here we describe the first species of the genus Mallocybe from West African and Zambian woodlands dominated by ectomycorrhizal trees of Fabaceae and Phyllanthaceae. The new species M. africana is characterized by orange-brown fruitbodies, a fibrillose pileus, a stipe tapered towards the base and large ellipsoid basidiospores. It resembles many north and south temperate species of Mallocybe but is most closely related to the southeast Asian tropical species, M. errata. M. africana is widely distributed in West Africa (Benin, Togo, Burkina Faso and Ivory Coast) extending to South-eastern Africa in Zambia. Phylogenetic analyses based on 5.8S rDNA, nLSU and RPB2 sequence data confirm that M. africana is nested within Mallocybe. A complete morphological description and illustrations, including photographs and line drawings, are presented.
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| 5. |
- Birkebak, Joshua M, et al.
(författare)
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A systematic, morphological and ecological overview of the Clavariaceae (Agaricales).
- 2013
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Ingår i: Mycologia. - : Informa UK Limited. - 0027-5514 .- 1557-2536. ; 105:4, s. 896-911
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Tidskriftsartikel (refereegranskat)abstract
- The Clavariaceae is a diverse family of mushroom-forming fungi composed of species that produce simple clubs, coralloid, lamellate-stipitate, hydnoid and resupinate sporocarps. Here we present a systematic and ecological overview of the Clavariaceae based on phylogenetic analysis of sequences of the nuclear large subunit ribosomal RNA (nLSU), including nine from type collections. Forty-seven sequences from sporocarps of diverse taxa across the Clavariaceae were merged with 243 environmental sequences from GenBank and analyzed phylogenetically to determine major clades within the family. Four major clades or lineages were recovered: (i) Mucronella, (ii) Ramariopsis-Clavulinopsis, (iii) Hyphodontiella and (iv) Clavaria-Camarophyllopsis-Clavicorona. Clavaria is paraphyletic, within which the lamellate and pileate-stipitate genus Camarophyllopsis is derived and composed of two independent lineages. The monotypic genus Clavicorona also appears nested within Clavaria. The monophyly of Clavaria and Camarophyllopsis, however, cannot be statistically rejected. We compared differing classification schemes for the genera Ramariopsis and Clavulinopsis, most of which are inconsistent with the molecular phylogeny and are statistically rejected. Scytinopogon, a genus classified in the Clavariaceae by several authors, shares phylogenetic affinities with the Trechisporales. Overall 126 molecular operational taxonomic units can be recognized in the Clavariaceae, roughly half of which are known only from environmental sequences, an estimate that exceeds the known number of species in the family. Stable isotope ratios of carbon and nitrogen were measured from specimens representing most major phylogenetic lineages to predict trophic strategies. These results suggest that most non-lignicolous species feature a biotrophic mode of nutrition. Ancestral state reconstruction analysis highlights the taxonomic significance of at least nine morphological traits at various depths in the family tree.
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| 6. |
- Kosentka, Pawel, et al.
(författare)
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Evolution of the toxins muscarine and psilocybin in a family of mushroom-forming fungi.
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:5, s. e64646-
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Tidskriftsartikel (refereegranskat)abstract
- Mushroom-forming fungi produce a wide array of toxic alkaloids. However, evolutionary analyses aimed at exploring the evolution of muscarine, a toxin that stimulates the parasympathetic nervous system, and psilocybin, a hallucinogen, have never been performed. The known taxonomic distribution of muscarine within the Inocybaceae is limited, based only on assays of species from temperate regions of the northern hemisphere. Here, we present a review of muscarine and psilocybin assays performed on species of Inocybaceae during the last fifty years. To supplement these results, we used liquid chromatography-tandem mass spectrometry (LC-MS/MS) to determine whether muscarine was present in 30 new samples of Inocybaceae, the majority of which have not been previously assayed or that originated from either the tropics or temperate regions of the southern hemisphere. Our main objective is to test the hypothesis that the presence of muscarine is a shared ancestral feature of the Inocybaceae. In addition, we also test whether species of Inocyabceae that produce psilocybin are monophyletic. Our findings suggest otherwise. Muscarine has evolved independently on several occasions, together with several losses. We also detect at least two independent transitions of muscarine-free lineages to psilocybin-producing states. Although not ancestral for the family as a whole, muscarine is a shared derived trait for an inclusive clade containing three of the seven major lineages of Inocybaceae (the Inocybe, Nothocybe, and Pseudosperma clades), the common ancestor of which may have evolved ca. 60 million years ago. Thus, muscarine represents a conserved trait followed by several recent losses. Transitions to psilocybin from muscarine-producing ancestors occurred more recently between 10-20 million years ago after muscarine loss in two separate lineages. Statistical analyses firmly reject a single origin of muscarine-producing taxa.
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| 7. |
- Ryberg, Martin, et al.
(författare)
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Asynchronous origins of ectomycorrhizal clades of Agaricales.
- 2012
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 279:1735, s. 2003-11
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Tidskriftsartikel (refereegranskat)abstract
- The ectomycorrhizal (ECM) symbiosis is the most widespread biotrophic nutritional mode in mushroom-forming fungi. ECM fungi include, though are not limited to, about 5000 described species of Agaricales from numerous, independently evolved lineages. Two central hypotheses suggest different explanations for the origin of ECM fungal diversity: (i) dual origins, initially with the Pinaceae in the Jurassic and later with angiosperms during the Late Cretaceous, and (ii) a simultaneous and convergent radiation of ECM lineages in response to cooling climate during the Palaeogene and advancing temperate ECM plant communities. Neither of these hypotheses is supported here. While we demonstrate support for asynchronous origins of ECM Agaricales, the timing of such events appears to have occurred more recently than suggested by the first hypothesis, first during the Cretaceous and later during the Palaeogene. We are also unable to reject models of rate constancy, which suggests that the diversity of ECM Agaricales is not a consequence of convergent rapid radiations following evolutionary transitions from saprotrophic to ECM habits. ECM lineages of Agaricales differ not only in age, but also in rates of diversification and rate of substitution at nuclear ribosomal RNA loci. These results question the biological uniformity of the ECM guild.
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| 8. |
- Sheedy, Elizabeth M., et al.
(författare)
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Dating the emergence of truffle-like fungi in Australia, by using an augmented meta-analysis
- 2016
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Ingår i: Australian Systematic Botany. - 1030-1887 .- 1446-5701. ; 29:5, s. 284-302
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Tidskriftsartikel (refereegranskat)abstract
- Australia supports a high diversity of sequestrate (truffle-like) macrofungi. This has long been thought to be related to the predominantly or seasonally dry climate. The present study posits that if aridity were a key factor in the evolution of sequestrate fruit-bodies, most sequestrate species would have emerged in Australia only after it began to aridify, which occurred post-separation with Antarctica (c. 32 million years ago). Focusing on the high phylogenetic diversity of sequestrate taxa in the Agaricomycetes in Australia, dates of sequestrate nodes were compiled directly from published phylogenies (four lineages) or created using sequences available on GenBank that were processed in BEAST using a secondary calibration method (nine lineages). Although the morphologically diverse Hysterangiales was found to be the first group to become sequestrate, c. 83 million years ago, overall sequestration in Australia occurred more recently. Models were created and compared and support was found for an increased rate of sequestration in Australia at some point between 34 and 13 million years ago (during the Oligocene and Miocene). Although the rate of sequestration is shown to have increased in Australia after separation from Antarctica, the timing also overlaps with the radiation of potential mycorrhizal plant associates, and the emergence of specialised mycophagous marsupials. Although aridification is evidently not the sole driver of sequestration, it is still likely to have had a major influence on the diversity of sequestrate fungi in Australia. Comparisons with other regions of high sequestrate diversity will be informative.
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