Tying up loose threads: revised taxonomy and phylogeny of an avian-dispersed Neotropical rhizomorph-forming fungus

Koch, Rachel A.; Lodge, D. Jean; Sourell, Susanne; Nakasone, Karen K.; McCoy, Austin G.; Aime, M. Catherine

doi:10.1007/s11557-018-1411-8

Cited by 24 publications

(14 citation statements)

References 30 publications

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“…Some fungi are only known from vegetative structures, rendering traditional approaches to classification nearly impossible (e.g. Koch et al 2017 , 2018 ). Precise identification of fungi thus requires removal from their habitat and careful investigation in the laboratory.…”

Section: Introductionmentioning

confidence: 99%

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

et al. 2020

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True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.

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Section: Introductionmentioning

confidence: 99%

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

et al. 2020

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“…Results from preliminary phylogenetic and blast analyses indicated that the Argentina and Belize material both belong within Moniliophthora, as does Crinipellis brasiliensis -the sister species to M. perniciosa (Arruda et al 2005). Datasets were then trimmed to include: 1) all species of Moniliophthora for which ITS and/or 28S sequence data exist (only ITS data were available for M. canescens, M. aurantiaca, and M. brasiliensis); 2) newly generated sequences of the material from Argentina and Belize and from the type of C. ticoi; 3) exemplar sequences from the other related Marasmiaceae genera -Crinipellis, Marasmius, and Chaetocalathus -for context (Aime and Phillips-Mora 2005; Antonín et al 2014;Koch et al 2018). Individual datasets for each locus were aligned in GENEIOUS 9.1.5 (Biomatters Ltd., Auckland, NZ) using the MUSCLE algorithm (Edgar 2004).…”

Section: Phylogenetic Analysismentioning

confidence: 99%

“…Individual datasets for each locus were aligned in GENEIOUS 9.1.5 (Biomatters Ltd., Auckland, NZ) using the MUSCLE algorithm (Edgar 2004). Individual alignments were then concatenated in Geneious, and analyzed by maximum likelihood (RAXML; Stamatakis 2006) methods using the CIP-RES Science Gateway (Miller et al 2010), following the methods of Koch et al (2018).…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Studies of Neotropical tree pathogens in Moniliophthora: a new species, M. mayarum, and new combinations for Crinipellis ticoi and C. brasiliensis

Niveiro¹,

Ramírez²,

Michlig³

et al. 2020

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The crinipelloid genera Crinipellis and Moniliophthora (Agaricales, Marasmiaceae) are characterized by basidiomes that produce long, dextrinoid, hair-like elements on the pileus surface. Historically, most species are believed to be saprotrophic or, rarely, parasitic on plant hosts. The primary morphological diagnostic characters that separate Crinipellis and Moniliophthora are pliant vs. stiff (Crinipellis) stipes and a tendency toward production of reddish pigments (ranging from violet to orange) in the basidiome in Moniliophthora. Additionally, most species of Moniliophthora appear to have a biotrophic habit, while those of Crinipellis are predominantly saprotrophic. Recently, several new neotropical collections prompted a morphological and phylogenetic analysis of this group. Herein, we propose a new species and two new combinations: Moniliophthora mayarumsp. nov., described from Belize, is characterized by its larger pileus and narrower basidiospores relative to other related species; Moniliophthora ticoicomb. nov. (= Crinipellis ticoi) is recollected and redescribed from biotrophic collections from northern Argentina; and M. brasiliensiscomb. nov. (= Crinipellis brasiliensis), a parasite of Heteropterys acutifolia. The addition of these three parasitic species into Moniliophthora support a hypothesis of a primarily biotrophic/parasitic habit within this genus.

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“…; Koch et al . ), most cavity dwelling/nesting birds rely on fungal rots to create cavities or soften wood (Lawrence ; Jackson & Jackson ), some bowerbirds use colourful mushrooms to adorn their bowers (Elliott & Marshall ) and numerous birds use fungi for food (Simpson , ; Elliott & Vernes ). An understanding of birds' natural history is incomplete without accounting for their association with fungi – particularly how they assist with fungal dispersal.…”

Section: Natural History Notementioning

confidence: 99%

Vertebrate consumption and dispersal of the Nothofagaceae associated ascomycete Cyttaria

Elliott

2019

Austral Ecology

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Fungi are an important food source for a diversity of vertebrates and invertebrates around the world and in turn, these animals play a key part in the dispersal of many fungi. These associations have been most thoroughly studied between mammals and truffles. In this natural history note, we provide the first report of mycophagy by the Australian King-Parrot (Alisterus scapularis) and the first documentation of wildlife consumption of the genus Cyttaria in Australia. We also review the literature regarding use of this southern hemisphere endemic genus Cyttaria for food by vertebrates and how these associations may impact its dispersal.

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Tying up loose threads: revised taxonomy and phylogeny of an avian-dispersed Neotropical rhizomorph-forming fungus

Cited by 24 publications

References 30 publications

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

Studies of Neotropical tree pathogens in Moniliophthora: a new species, M. mayarum, and new combinations for Crinipellis ticoi and C. brasiliensis

Vertebrate consumption and dispersal of the Nothofagaceae associated ascomycete Cyttaria

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