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The Taxon Hypothesis Paradigm—On the Unambiguous Detection and Communication of Taxa

Summary

This research introduces a new system for identifying and tracking species and other taxonomic groups in biology. The system allows scientists to uniquely identify and communicate about species, even before they are formally named and described. This has important real-world implications: • Makes it easier to discover and track new species, especially microscopic organisms that are hard to study • Helps scientists communicate clearly about species across different studies and databases • Enables better monitoring of biodiversity and ecosystem changes • Supports conservation efforts by allowing faster recognition of new species before they potentially go extinct • Improves our ability to study environmental DNA samples and understand what species are present in different environments

Background

Systematics faces the challenge of classifying living organisms into monophyletic groups in a hierarchical Linnean system. This work is more complete for some groups than others, with only 4% of estimated fungal species described compared to 70% of plants. Molecular tools introduced in mycology in the 1990s revealed complex evolutionary histories and highlighted the need for modifications to fungal classification systems. Currently, different online resources use varying classifications, making it difficult to track and compare taxa across systems.

Objective

To describe and implement the taxon hypothesis (TH) paradigm for constructing, identifying, and communicating taxa as datasets. The paradigm aims to make taxon identification and communication precise and reproducible by defining taxa as datasets of individuals and their traits that can be used digitally in identification pipelines and communicated through persistent identifiers.

Results

The TH paradigm successfully enabled precise communication of both formally described and undescribed taxa through persistent identifiers. The UNITE implementation has released over half a million DOIs for SH datasets since 2015. The system allows tracking of individuals across different versions and classifications while maintaining comparability. The paradigm proved particularly valuable for communicating undescribed species discovered through environmental DNA studies. Examples showed how UNITE SHs identified new fungal species years before their formal description.

Conclusion

The TH paradigm serves as a bridge between traditional nomenclatural codes and modern needs for digital communication of taxa. While not replacing formal Latin names, it facilitates unambiguous communication of taxon circumscriptions, especially for undescribed species. The system is particularly valuable for metagenomic studies where many taxa cannot be assigned to formally described species. The paradigm helps address current challenges in taxonomy while supporting the ultimate goal of formal description for all extant species.
  • Published in:Microorganisms,
  • Study Type:Review,
  • Source: 10.3390/microorganisms8121910
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