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On a Non-Discrete Concept of Prokaryotic Species
Article

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

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Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia
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Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia
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Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
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Global Biodiversity Information Facility, 2100 Copenhagen, Denmark
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Royal Botanic Gardens Victoria, Birdwood Ave, Melbourne, Victoria 3004, Australia
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The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
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Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK
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GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 København, Denmark
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Systematic Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
*
Author to whom correspondence should be addressed.
Microorganisms 2020, 8(12), 1910; https://doi.org/10.3390/microorganisms8121910
Received: 31 October 2020 / Accepted: 24 November 2020 / Published: 30 November 2020
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. View Full-Text
Keywords: microbial species; taxonomy; DNA taxonomy; biodiversity informatics; discovery of species; taxon hypotheses; species hypotheses; metabarcoding microbial species; taxonomy; DNA taxonomy; biodiversity informatics; discovery of species; taxon hypotheses; species hypotheses; metabarcoding
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MDPI and ACS Style

Kõljalg, U.; Nilsson, H.R.; Schigel, D.; Tedersoo, L.; Larsson, K.-H.; May, T.W.; Taylor, A.F.S.; Jeppesen, T.S.; Frøslev, T.G.; Lindahl, B.D.; Põldmaa, K.; Saar, I.; Suija, A.; Savchenko, A.; Yatsiuk, I.; Adojaan, K.; Ivanov, F.; Piirmann, T.; Pöhönen, R.; Zirk, A.; Abarenkov, K. The Taxon Hypothesis Paradigm—On the Unambiguous Detection and Communication of Taxa. Microorganisms 2020, 8, 1910. https://doi.org/10.3390/microorganisms8121910

AMA Style

Kõljalg U, Nilsson HR, Schigel D, Tedersoo L, Larsson K-H, May TW, Taylor AFS, Jeppesen TS, Frøslev TG, Lindahl BD, Põldmaa K, Saar I, Suija A, Savchenko A, Yatsiuk I, Adojaan K, Ivanov F, Piirmann T, Pöhönen R, Zirk A, Abarenkov K. The Taxon Hypothesis Paradigm—On the Unambiguous Detection and Communication of Taxa. Microorganisms. 2020; 8(12):1910. https://doi.org/10.3390/microorganisms8121910

Chicago/Turabian Style

Kõljalg, Urmas, Henrik R. Nilsson, Dmitry Schigel, Leho Tedersoo, Karl-Henrik Larsson, Tom W. May, Andy F.S. Taylor, Thomas S. Jeppesen, Tobias G. Frøslev, Björn D. Lindahl, Kadri Põldmaa, Irja Saar, Ave Suija, Anton Savchenko, Iryna Yatsiuk, Kristjan Adojaan, Filipp Ivanov, Timo Piirmann, Raivo Pöhönen, Allan Zirk, and Kessy Abarenkov. 2020. "The Taxon Hypothesis Paradigm—On the Unambiguous Detection and Communication of Taxa" Microorganisms 8, no. 12: 1910. https://doi.org/10.3390/microorganisms8121910

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