How, not if, is the question mycologists should be asking about DNA-based typification

Abstract

Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings challenge the present stance of some in the mycological community – that the current situation is satisfactory and that no change is needed to “the code” – and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.

Connecting the multiple dimensions of global soil fungal diversity

“…S8 and S9). The large number of species forming the basis of our analyses supports the expectation of global fungal diversity ( 31 ), while its exceeding the number of currently named species underscores the necessity for additional efforts in describing mycobiota from various habitats ( 32 ).…”

Redefining the Genus Corollospora Based on Morphological and Phylogenetic Approaches

“…Sequences from the International Nucleotide Sequence Database Collaboration (http://www.insdc.org, accessed on 18 December 2022) are clustered in species hypothesis (SH), in steps of 0.5% pdistance value, 3% being the highest threshold value accepted for species discrimination [42]; each cluster has an SH number and DOI, to facilitate scientific communication and data assembly [43]. This platform has been increasingly used and recently was the subject of a publication [44] resuming the open discussion about how to deal with DNA-based typification, mainly involving dark fungal taxa (not cultivated in the laboratory).…”

Call me by your name: Considerations of DNA sequences as types within wider discussions on fungal nomenclature

“…Companies such as Taxon Expeditions ( www.taxonexpeditions.com ) base their business around the promise that customers will be able to name a new species. Indeed, the attractiveness of formal Latin binomials to the wider scientific community is explicitly recognised by some of the more prominent proponents of DNA-only types who admit that “informal names or numbers remain obscure without a broadly accepted, formal naming framework” (Lücking and Hawksworth 2018 ) and that formal names are necessary for dark taxa to be “taken seriously” (Nilsson et al 2023 ). Yet it might equally be argued that such a formal naming framework will be weakened through the mass addition of less-descriptive names and, that the cultural value given to species through the process of assigning a formal Latin binomial is likely to be diluted should their names derive from increasingly tenuous links.…”

“…The concept has been in discussion for over a decade (Hibbett et al 2009 , 2011 ) and was first formally proposed in 2016 (Hawksworth et al 2016 ) and again in 2018 (Lücking et al 2018 ). Whilst the initial proposals were voted down in both instances, the latter by substantial margins in the preliminary “guiding vote” (>85% of voters rejected both proposals; May and Miller 2018 ), the proposals were instead passed on to a special-purpose committee (Turland et al 2017 ; May and Redhead 2018 ) and the general proposal remains prominent in the literature with the use of DNA sequences as types still considered favourably by some mycologists (Wu et al 2019 ; Lücking et al 2021 ; Nilsson et al 2023 ).…”