Abstract
Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction.
Highlights
Systematics face the daunting task of classifying our living world into monophyletic groups in a hierarchical Linnean system
We describe the taxon hypothesis (TH) paradigm and in parallel give examples of how it is implemented in the UNITE system
Mycology operates under a nomenclatural code conceived during a time where the study of fungi was largely restricted to physical manifestations of species, and where researchers communicated more or less exclusively through scientific papers
Summary
Systematics face the daunting task of classifying our living world into monophyletic groups in a hierarchical Linnean system. The study of fungi—mycology—is further compounded by the nature of fungal life, which we know to be largely subterranean, substrate-dwelling, or otherwise inconspicuous, typically with only sporadic physical manifestations of the underlying species. Already from the onset the molecular data hinted at the complexity of the evolutionary history of fungi. Convergent evolution as well as multiple gains and losses of characters and character states were found to permeate the fungal tree of life, and hitherto unrecognized species and higher taxa seemed to abound. As ever-increasing swathes of the fungal kingdom were subjected to molecular scrutiny, it became painstakingly clear that very substantial modifications to the classification and naming of fungi and fungal groups were looming on the horizon [3]
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