The Taxon Hypothesis Paradigm - On the Unambiguous Detection and Communication of Taxa
Research output: Contribution to journal › Journal article › Research › peer-review
Standard
The Taxon Hypothesis Paradigm - On the Unambiguous Detection and Communication of Taxa. / Koljalg, Urmas; Nilsson, Henrik R.; Schigel, Dmitry; Tedersoo, Leho; Larsson, Karl-Henrik; May, Tom W.; Taylor, Andy F. S.; Jeppesen, Thomas Stjernegaard; Frøslev, Tobias Guldberg; Lindahl, Björn D.; Pöldmaa, Kadri; Saar, Irja; Suija, Ave; Savchenko, Anton; Yatsiuk, Iryna; Adojaan, Kristjan; Ivanov, Filipp; Piirmann, Timo; Pöhönen, Raivo; Zirk, Allan; Abarenkov, Kessy.
In: Microorganisms, Vol. 8, No. 12, 1910, 2020.Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
APA
Vancouver
Author
Bibtex
}
RIS
TY - JOUR
T1 - The Taxon Hypothesis Paradigm - On the Unambiguous Detection and Communication of Taxa
AU - Koljalg, Urmas
AU - Nilsson, Henrik R.
AU - Schigel, Dmitry
AU - Tedersoo, Leho
AU - Larsson, Karl-Henrik
AU - May, Tom W.
AU - Taylor, Andy F. S.
AU - Jeppesen, Thomas Stjernegaard
AU - Frøslev, Tobias Guldberg
AU - Lindahl, Björn D.
AU - Pöldmaa, Kadri
AU - Saar, Irja
AU - Suija, Ave
AU - Savchenko, Anton
AU - Yatsiuk, Iryna
AU - Adojaan, Kristjan
AU - Ivanov, Filipp
AU - Piirmann, Timo
AU - Pöhönen, Raivo
AU - Zirk, Allan
AU - Abarenkov, Kessy
PY - 2020
Y1 - 2020
N2 - 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.
AB - 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.
KW - microbial species
KW - taxonomy
KW - DNA taxonomy
KW - biodiversity informatics
KW - discovery of species
KW - taxon hypotheses
KW - species hypotheses
KW - metabarcoding
KW - IDENTIFICATION
KW - BARCODE
KW - SEARCH
KW - SYSTEM
U2 - 10.3390/microorganisms8121910
DO - 10.3390/microorganisms8121910
M3 - Journal article
C2 - 33266327
VL - 8
JO - Microorganisms
JF - Microorganisms
SN - 2076-2607
IS - 12
M1 - 1910
ER -
ID: 256162009