The taxon hypothesis paradigm—on the unambiguous detection and communication of taxa

U Kõljalg, HR Nilsson, D Schigel, L Tedersoo… - Microorganisms, 2020 - mdpi.com
Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction,
identification, and communication of taxa as datasets. Defining taxa as datasets of …

The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered

K Abarenkov, RH Nilsson, KH Larsson… - Nucleic Acids …, 2024 - academic.oup.com
Abstract UNITE (https://unite. ut. ee) is a web-based database and sequence management
environment for molecular identification of eukaryotes. It targets the nuclear ribosomal …

The intellectual content of taxonomy: a comment on DNA taxonomy

D Lipscomb, N Platnick, Q Wheeler - Trends in Ecology & Evolution, 2003 - cell.com
Tautz et al.[1] propose to 'solve'the lack of adequate classifications and effective
identification tools (the socalled 'taxonomic impediment') by replacing existing classifications …

Taxonomy: renaissance or Tower of Babel?

J Mallet, K Willmott - Trends in Ecology & Evolution, 2003 - cell.com
Taxonomy, the science of naming and classifying organisms, is the original bioinformatics
and a fundamental basis for all biology. Yet over the past few decades, teaching and funding …

Considerations and consequences of allowing DNA sequence data as types of fungal taxa

JC Zamora, M Svensson, R Kirschner, I Olariaga… - IMA fungus, 2018 - Springer
Nomenclatural type definitions are one of the most important concepts in biological
nomenclature. Being physical objects that can be re-studied by other researchers, types …

Tightening the requirements for species diagnoses would help integrate DNA-based descriptions in taxonomic practice

FE Rheindt, P Bouchard, RL Pyle… - PLoS …, 2023 - journals.plos.org
Modern advances in DNA sequencing hold the promise of facilitating descriptions of new
organisms at ever finer precision but have come with challenges as the major Codes of …

Genome-based microbial taxonomy coming of age

P Hugenholtz, A Skarshewski… - Cold Spring Harbor …, 2016 - cshperspectives.cshlp.org
Reconstructing the complete evolutionary history of extant life on our planet will be one of
the most fundamental accomplishments of scientific endeavor, akin to the completion of the …

Systematic identification of gene families for use as “markers” for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major …

D Wu, G Jospin, JA Eisen - PloS one, 2013 - journals.plos.org
With the astonishing rate that genomic and metagenomic sequence data sets are
accumulating, there are many reasons to constrain the data analyses. One approach to such …

Defining DNA-based operational taxonomic units for microbial-eukaryote ecology

DA Caron, PD Countway, P Savai… - Applied and …, 2009 - Am Soc Microbiol
ABSTRACT DNA sequence information has increasingly been used in ecological research
on microbial eukaryotes. Sequence-based approaches have included studies of the total …

Formal description of sequence-based voucherless Fungi: promises and pitfalls, and how to resolve them

R Lücking, DL Hawksworth - IMA fungus, 2018 - Springer
There is urgent need for a formal nomenclature of sequence-based, voucherless Fungi,
given that environmental sequencing has accumulated more than one billion fungal ITS …