Commentary |
Corresponding author: Martin Ryberg ( martin.ryberg@ebc.uu.se ) Academic editor: Thorsten Lumbsch
© 2018 Martin Ryberg, R. Henrik Nilsson.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Ryberg M, Nilsson R (2018) New light on names and naming of dark taxa. MycoKeys 30: 31-39. https://doi.org/10.3897/mycokeys.30.24376
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A growing proportion of fungal species and lineages are known only from sequence data and cannot be linked to any physical specimen or resolved taxonomic name. Such fungi are often referred to as “dark taxa” or “dark matter fungi”. As they lack a taxonomic identity in the form of a name, they are regularly ignored in many important contexts, for example in legalisation and species counts. It is therefore very urgent to find a system to also deal with these fungi. Here, issues relating to the taxonomy and nomenclature of dark taxa are discussed and a number of questions that the mycological community needs to consider before deciding on what system/s to implement are highlighted.
Taxonomy, nomenclature, mycology, biodiversity
The first step in wisdom is to know the things themselves; this notion consists in having a true idea of the objects; objects are distinguished and known by classifying them methodically and giving them appropriate names. Therefore, classification and name-giving will be the foundation of our science.
Public DNA sequence databases abound with fungal entries that defy all attempts at taxonomic identification. These poorly understood lineages are known from more or less all imaginable substrates and environments, including soil, wood and water but also spacecraft, tumuli and residential areas (e.g.
The mycological community has been aware of the problem of dark taxa for a long time (
In the context of dark taxa, the distinction between taxonomy (delimiting and characterising taxa) and nomenclature (naming and, to some extent, diagnosing taxa) must be stressed. While these are connected and commonly discussed together, blurring their distinction, they are fundamentally different (
According to the ICN, only a validly published name can be considered for the correct name of a taxon (the name that should be used for the taxon). Two of the requirements for a name to be validly published are that it is published with a diagnosis or description and that a type is designated. The diagnosis can be based on molecular characters (
Since the description of taxa is only controlled by the regular scientific principles for publishing, taxa may be described and diagnosed based solely on molecular characters. Such taxa can also be given a name (
Names are used for communicating objects and concepts. Unless an object or concept is very straightforward indeed, the lack of a name is a major obstacle in its communication and may – implicitly or not – be taken to mean that its communication is not necessary to begin with. This is a general societal issue, but it certainly pertains to mycology as well. Many newly described taxa have, in fact, been represented in DNA sequence databases for 10 years or more before they piqued somebody’s interest or were possible to typify according to the ICN (see examples in
Communication of taxa includes aspects such as incorporation into biodiversity datasets, sequence repositories and legislation but also regular scientific and societal communication. What type of name to use will depend on the identity of the communicating parties. For computers, accession numbers such as DOIs will suffice for communication. DOIs are, however, less suitable for human communication (e.g. http://dx.doi.org/10.15156/BIO/SH004915.07FU versus Vishniacozyma victoriae). For scientists, latinised binomials may work well, while society at large may prefer vernacular names.
For efficient communication, it is important to consider that one taxon should have only one name and that any name should refer to only one taxon. One of the major purposes of the ICN is to ensure and uphold these relations, while vernacular names are not governed by and, indeed, often violate such rules. The use of parallel naming systems does little to facilitate unambiguous naming in biological systematics. For instance, one and the same name can be the correct or valid name for different taxa under the ICN and the International Code for Zoological nomenclature at the same time, e.g. Erica in Ericaceae (Viridiplantae) and Arachnida (Metazoa). For ambiregnal taxa, different names may be the correct/valid name under different nomenclature codes. For instance, a dinoflagellate genus was named Phalacroma under the ICN, a name that subsequently was found to be already occupied under the zoological code. Thus, the name Prodinophysis was introduced for the same genus (
Descriptions of taxa may be based on different sets of characters, for example sexual or asexual reproductive structures, physiological parameters or DNA bases. It may therefore be difficult to tell whether a taxon, described based on one type of character, is the same as a taxon described from another character type or set of characters. This is the basis behind both the former dual system of naming for “Eumycota” vis-à-vis “Deuteromycota” and the situation which is now faced with dark taxa. In the case of dark taxa, it is not immediately clear how to correlate a species delimited from environmental sequence data to, say, a range of physiological parameters quantified in the lab or a handful of morphological traits gleaned from microscopy studies of soil samples. Obtaining such additional data and mapping them to individual species will not be straightforward from heterogeneous, mixed-species substrates such as soil and water, but emerging single-cell techniques (e.g.
As taxon delimitation and naming are two different things, another complication in what a name refers to is that different taxonomists may advocate different circumscriptions of taxa while the name itself is determined by the ICN. In these cases, the same name may be the correct name for different taxa, with little overlap in the underlying organisms. Furthermore, a name can be correct for some taxon or a synonym of another name depending on the specific taxonomy. If it is required that taxa be monophyletic, then changes in the taxonomy should be expected due to changes in the understanding of evolutionary relationships. Even if this stabilises with time as better estimates of evolutionary relationships are obtained, there may still be conflicts as to what clades are considered as taxa and at what taxonomic level. For example,
The species level is often viewed as a separate evolutionary lineage of special standing (
Without a reference to which taxonomy is employed, what is referred to by a name is more or less ambiguous. The UNITE species hypothesis system provides an unambiguous way to refer to sets of sequences at approximately the species level and additions and removals of sequences to those species hypotheses can be traced back in time (e.g. https://unite.ut.ee/bl_forw_sh.php?sh_name=SH181628.07FU). However, this approach is limited to sequences included in the underlying dataset, the given set of hypotheses and to taxa represented by ITS sequence data in the first place. Changes between taxonomies are a part of the progress in understanding nature and only scientific advances, together with a dialogue amongst scientists to arrive at a consensus, can resolve this problem. However, without some sort of names for communication such progress seems difficult.
The number of dark taxa increases with more or less every new metabarcoding study, but the pace at which these taxa are formalised is many orders of magnitude slower (
These questions are urgent, because dark taxa permeate mycology and the fungal tree of life, and ad hoc names are being used to communicate them without any system to ensure stability of those names (
MR would like to acknowledge his colleagues at the Systematic Biology Programme, Uppsala University for fruitful discussions on taxonomy and nomenclature over the years. RHN and the UNITE database acknowledge financial support from the Alfred P. Sloan Foundation. David Hibbett, Urmas Kõljalg, Karl-Henrik Larsson, Mikael Thollesson, and Mats Thulin provided useful comments on previous drafts of this paper, but they do not necessarily agree with the opinions expressed herein.