High-level classification of the Fungi and a tool for evolutionary ecological analyses

By Leho Tedersoo, S. Sánchez-Ramírez, Urmas Kõljalg, M. Bahram, Markus Döring, D. Schigel, T. May, Martin Ryberg, Kessy Abarenkov. Fungal diversity, 2018

581 citations recorded by the source corpus.

High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum- and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomophthoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example of testing evolutionary ecological hypotheses based on a global soil fungal data set.

Subfields: Cell Biology, Pharmacology, Plant Science

View Paper: https://www.semanticscholar.org/paper/791870b5aac0fe246f39ed9a4af7fdb247b05529

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Citations in the corpus

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes (2018, background): “…and Aleoshin 2014 [Cryptomycota M. D. M. Jones & T. A. Richards 2011; Rozellomycota Doweld 2013; Rozellosporidia Karpov et al. 2017; Rozellomycotina Tedersoo et al. 2018] (R) Unicellular, holocarpic, zoospores single-celled with a single posterior cilium; cysts with chitin cell wall; endobiotic…”
Roles of Arbuscular Mycorrhizal Fungi on Plant Growth and Performance: Importance in Biotic and Abiotic Stressed Regulation (2020, background): “AMF are classified as a member of subkingdom Mucoromyceta and the phylum Glomeromycota including three classes (Glomeromycetes, Archaeosporomycetes, and Paraglomeromycetes [4]).”
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications (2018, background): “There is no generally agreed upon, up-to-date system for fungal classification, although a synthesis was recently published (23).”
Outline of Fungi and fungus-like taxa (2020, methodology): “Wijayawardene et al. (2018b) provided a detailed classification system (from phyla to genera) for basal clades of Fungi, agreeing with Tedersoo et al. (2018).”
Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics (2021, background): “Molecular phylogenetics has provided an entirely new pathway to classify and delimit organisms, from the highest taxonomic levels down to infraspecies, particularly in Fungi and fungus-like organisms (Hibbett et al. 2007; Printzen 2010; Lumbsch and Leavitt 2011; Lücking et al. 2017a; Tedersoo et al.”
NCBI Taxonomy: a comprehensive update on curation, resources and tools (2020, background): “Currently, the NCBI classification contains nine phyla based on genome comparisons (56) but up to 16 are accepted in the literature (57, 58).”
New scientific discoveries: Plants and fungi (2020, background): “K E Y W O R D S DNA versus morphology, extinction before scientific discovery, properties of new species, rates of discovery of plants and fungi four new phyla of fungi were named in 2018, taking the total to 18 (Tedersoo et al., 2018).”