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 -