New light on names and naming of dark taxa

Ryberg, Martin; Nilsson, R. Henrik

doi:10.3897/mycokeys.30.24376

Cited by 43 publications

(43 citation statements)

References 31 publications

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“…There are some benefits of naming mgDNA especially if it would bring numerous dark data into the light (Ryberg and Nilsson 2018) and monitor species diversity. However without careful considerations, this can end up in disregard of appropriate nomenclatural issues with fungi and future taxonomic problems that can arise.…”

Section: Conclusion and An Alternative Dna-based Systemmentioning

confidence: 99%

“…Fungal species which cannot be linked to any physical specimen are referred to as ''dark taxa'' or ''dark matter fungi'' (Parr et al 2012;Grossart et al 2015;Page 2016;Tedersoo and Smith 2017;Ryberg and Nilsson 2018). In recent years, a large amount of mgDNA ITS sequence data from environmental samples have been deposited in GenBank.…”

Section: Introductionmentioning

confidence: 99%

“…Ryberg and Nilsson (2018) suggested that an integrated naming system is needed to facilitate unambiguous communication, to record and accumulate data on the dark taxa. However, there are some limitations of highthroughput sequencing metabarcoding, prompting many mycologists to disagree with validating names or using mgDNA as holotypes.…”

Section: Introductionmentioning

confidence: 99%

“…Index Fungorum and MycoBank (Hibbett et al 2011). The errors in communication of using these systems have occurred from one publication to another (Hibbett et al 2011;Ryberg and Nilsson 2018). The idea of naming species from mgDNA-based data was raised to improve the efficiency of communication, reducing erroneous publication and data records, which may lead to erratic results, and ultimately, false estimates of fungal biodiversity (Hawksworth et al 2016;Ryberg and Nilsson 2018).…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Conclusion and An Alternative Dna-based Systemmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Can we use environmental DNA as holotypes?

et al. 2018

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“…The submerged lifestyle and microscopic, morphological simplicity of fungi complicates their discovery and formal nomenclature because the physical specimens required for naming species in accordance with the International Code of Nomenclature for Algae, Fungi and Plants (the Code) can often not be isolated or identi ed. Many of the undescribed fungi are known from environmental studies using amplicon sequencing (Nilsson, Anslan, et al, 2019) and are among those referred to as "dark taxa" (Ryberg & Nilsson, 2018). Efforts to culture and image "dark taxa" are scarce, and as in the case of the current study, often fruitless, in part because we know so little about these organisms.…”

Section: Introductionmentioning

confidence: 88%

Peeking into the black box – integrated taxonomy of Archaeorhizomycetes

Khan

Kluting

Tångrot

et al. 2020

Preprint

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Abstract Due to their submerged and cryptic lifestyle the vast majority of fungal species are difficult to observe and describe morphologically and many remains known to science only from sequences detected in environmental samples. The lack of rules to delimit and name most fungal species is a staggering limitation to communication and interpretation of ecology and evolution in kingdom Fungi. Here we use environmental sequence data as taxonomical evidence and take an integrated taxonomic approach by combining phylogenetic and ecological data to generate and test species hypothesis in the class Archaeorhizomycetes (Taphrinomycotina, Ascomycota). Based on environmental amplicon sequencing we recognize 68 distinct phylogenetic species hypotheses (PSHs) of Archaeorhizomycetes, including the two described species in the class, in a well-studied Swedish pine forest podzol soil. Nine of the species hypotheses, including the more abundant ones, are supported by long read data and represent 78% of the sequenced Archaeorhizomycetes community. Among well supported sister PSHs, significantly differential distribution in the soil profile provide additional ecological evidence supporting the identification of two novel species for which we provide molecular diagnostics and propose names. Our analysis indicates that frequent and abundant taxa can be phylogenetically resolved in environmental samples, while rare taxa remain un-captured at our sampling and sequencing intensity. While environmental sequences cannot be automatically translated to species hypothesis, they can be used to generate phylogenetic and ecological evidence supporting species recognition of abundant species without physical specimens.

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Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections

et al. 2023

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Premise Fungaria are an underutilized resource for understanding fungal biodiversity. The effort and cost of producing DNA barcode sequence data for large numbers of fungal specimens can be prohibitive. This study applies a modified metabarcoding approach that provides a labor‐efficient and cost‐effective solution for sequencing the fungal DNA barcodes of hundreds of specimens at once. Methods We applied a two‐step PCR approach using nested, barcoded primers to sequence the fungal nrITS2 region of 766 macrofungal specimens using the Illumina platform. The specimens represent a broad taxonomic sampling of the Dikarya. Of these, 382 Lactarius specimens were analyzed to identify molecular operational taxonomic units (MOTUs) using a phylogenetic approach. The raw sequences were trimmed, filtered, assessed, and analyzed using the DADA2 amplicon de‐noising toolkit and Biopython. The sequences were compared to the NCBI and UNITE databases and Sanger nrITS sequences from the same specimens. Results The taxonomic identities derived from the nrITS2 sequence data were >90% accurate across all specimens sampled. A phylogenetic analysis of the Lactarius sequences identified 20 MOTUs. Discussion The results demonstrate the capacity of these methods to produce nrITS2 sequences from large numbers of fungarium specimens. This provides an opportunity to more effectively use fungarium collections to advance fungal diversity identification and documentation.

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New light on names and naming of dark taxa

Cited by 43 publications

References 31 publications

Can we use environmental DNA as holotypes?

Can we use environmental DNA as holotypes?

Peeking into the black box – integrated taxonomy of Archaeorhizomycetes

Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections

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