&lt;I&gt;Geoglossomycetes&lt;/I&gt; cl. nov., &lt;I&gt;Geoglossales&lt;/I&gt; ord. nov. and taxa above class rank in the &lt;I&gt;Ascomycota&lt;/I&gt; Tree of Life

Schoch, Conrad L.; Wang, Z. Z.; Townsend, Jeffrey P.; Spatafora, Joseph W.

doi:10.3767/003158509x461486

Cited by 61 publications

(55 citation statements)

References 58 publications

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“…Our results for the MCM7 gene are in agreement with Schoch et al's study as Geoglossomycetes is shown as a monophyletic group with strong MLBS and BPP support (Fig 2, Table 4), but, however, without strong support for its placement in relation to other classes of Leotiomyceta as noted previously (Schoch et al 2009b). We did not recover support for the expanded subclass Pleosporomycetidae as found in a previous multi-gene study focused only on Dothideomycetes (Schoch et al 2009c) and the influence of additional gene data and improved taxon sampling cannot be ruled out.…”

Section: Class-level Relationshipssupporting

confidence: 82%

“…We show that all classes in the present study are monophyletic, which corroborates earlier hypotheses by Eriksson and Winka (1997). Recently, Schoch et al (2009b) proposed a new class, Geoglossomycetes, based on a multi-gene phylogeny.…”

Section: Class-level Relationshipsmentioning

confidence: 99%

“…We assembled datasets of each gene for the same 89 taxa. Six classes from within the rankless taxon Leotiomyceta (Schoch et al 2009b): Dothideomycetes, Eurotiomycetes, Geoglossomycetes, Lecanoromycetes, Leotiomycetes, and Sordariomycetes, were sampled. Based on results of previous phylogenetic analyses (James et al 2006, Lutzoni et al 2004, one representative each from Saccharomycotina and Taphrinomycotina was used as outgroup taxa for all analyses.…”

Section: Taxon Samplingmentioning

confidence: 99%

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Testing the phylogenetic utility of MCM7 in the Ascomycota

Raja¹,

Schoch²,

Hustad³

et al. 2011

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The Ascomycota are a group of filamentous fungi that occur as saprobes, pathogens, and symbionts. They are of immense industrial, medical, ecological, and economical importance. The search for new markers appropriate for molecular phylogenetic analysis of Ascomycota remains a challenging problem. In this study, we explore the phylogenetic utility of a single copy protein-coding gene, MCM7; newly recognized as useful for inferring phylogenetic relationships among the major classes of the Ascomycota. Our specific goals were to: 1) test the phylogenetic utility of MCM7 for estimating phylogenies at various taxonomic ranks (class and below) with an emphasis on non-lichenized ascomycetes; and, 2) compare the congruence, robustness and resolving power of MCM7-based phylogenies with that of nuclear large subunit rDNA (LSU)-based phylogenies for the same taxon set. A dataset of sequence data for MCM7 as well as LSU was assembled for 80 species belonging to 63 genera of lichenized and non-lichenized ascomycetes in the classes Dothideomycetes, Eurotiomycetes, Geoglossomycetes, Lecanoromycetes, Leotiomycetes, and Sordariomycetes. We obtained 93 new sequences of which 65 are MCM7 and 28 are LSU. MaximumLikelihood and Bayesian analyses were performed using single as well as combined gene datasets and partitions. We also assessed substitution saturation for the MCM7 gene. Results indicate that MCM7 can be used successfully for determining phylogenetic relationships of ascomycetes and provided good resolution and support at half the cost compared to LSU. Phylogenetic informativeness profiles showed that MCM7 was more phylogenetically informative than LSU. The MCM7 gene is also a valuable phylogenetic marker for both lower as well as higher level phylogenetic analyses within the Ascomycota, especially when used in MycoKeysLaunched to accelerate biodiversity research Huzefa A. Raja et al. / MycoKeys 1: 63-94 (2011) 64 combination with the LSU gene. We found that although the third codon position of MCM7 is saturated, it was better to analyze the dataset with all codon positions included. Phylogenetic performance of MCM7 with and without the third codon position is discussed.

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Section: Class-level Relationshipssupporting

confidence: 82%

Section: Class-level Relationshipsmentioning

confidence: 99%

Section: Taxon Samplingmentioning

confidence: 99%

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Testing the phylogenetic utility of MCM7 in the Ascomycota

Raja¹,

Schoch²,

Hustad³

et al. 2011

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“…Many character evolution studies have been carried out within the past 15 years (e.g. Liu and Hall 2004;Li et al 2005;Schoch et al 2009;Schmitt 2011;Kumar et al 2012). However still there are many incomplete points to resolve.…”

Section: Character Evolution Studiesmentioning

confidence: 99%

Can we use environmental DNA as holotypes?

et al. 2018

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The advantages and disadvantages of giving a valid name to a sequence of DNA detected from environmental specimens is presently a hot debate amongst the mycological community. The idea of using intracellular DNA (''mgDNA'') from environmental samples as holotypes seems at face value, to be a good idea, considering the expansion of knowledge among these 'dark taxa' or 'dark matter fungi' that it could provide (i.e. sequence based taxa without physical specimens and formal nomenclature). However, the limitations of using mgDNA as holotypes needs careful thought, i.e. can we use a short mgDNA fragment, which may contain a small amount of genetic information, to allow discrimination between species? What is the point and are the potential problems of giving valid scientific names to mgDNA? Numerous mycologists and taxonomists, who have many years of experience working on the taxonomy and phylogeny of different groups of fungi, are concerned about the consequences of providing valid names to mgDNA. There has been much debate, through several publications on the considerable problems of using mgDNA as holotypes. The proponents have tried to debate the virtues of using mgDNA as holotypes. Those against have shown that identification to species using mgDNA does not work in many fungal groups, while those for have shown cases where species can be identified with mgDNA. Different disciplines have different reasons and opinions for using mgDNA as holotypes, however even groups of the same disciplines have dissimilar ideas. In this paper we explore the use of mgDNA as holotypes. We provide evidences and opinions as to the use of mgDNA as holotypes from our own experiences. In no way do we attempt to degrade the study of DNA from environmental samples and the expansion of knowledge in to the dark taxa, but relate the issues to fungal taxonomy. In fact we show the value of using sequence data from these approaches, in dealing with the discovery of already named taxa, taxa numbers and ecological roles. We discuss the advantages and the pitfalls of using mgDNA from environmental samples as holotypes. The impacts of expanding the nomenclatural concept to allow using mgDNA from environmental samples as holotypes are also discussed. We provide evidence from case studies on Botryosphaeria, Colletotrichum, Penicillium and Xylaria. The case studies show that we cannot use mgDNA due to their short fragments and the fact that most ITS sequence data presently result from environmental sequencing. We conclude from the evidence that it is highly undesirable to use mgDNA as holotypes in naming fungal species. If this approach adopted, it would result in numerous problems where species identification cannot be confirmed due to limited sequence data available for the holotypes. We also propose an alternative DNA-based system for naming DNA based species which would provide considerably less problems and should be adopted.

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“…The discussion on p. 419 fails to catch up with the creation of class Geoglossomycetes and order Geoglossales by Schoch et al (2009), except that their view is vaguely hinted at in the preface. The last paragraph on p. 419 points out that Thuemenidium atropurpureum belongs to Leotiomycetes (Ohenoja et al, 2010, Schoch et al, 2009), but it is here retained in Geoglossaceae. Microglossum, another genus best placed in Leotiomycetes, is also retained.…”

Section: Species Descriptionsmentioning

confidence: 84%

Book Review

Parslow¹

2015

Field Mycology

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<I>Geoglossomycetes</I> cl. nov., <I>Geoglossales</I> ord. nov. and taxa above class rank in the <I>Ascomycota</I> Tree of Life

Cited by 61 publications

References 58 publications

Testing the phylogenetic utility of MCM7 in the Ascomycota

Testing the phylogenetic utility of MCM7 in the Ascomycota

Can we use environmental DNA as holotypes?

Book Review

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