The revised classification of eukaryotes

By S. Adl, Alastair G. B. Simpson, Christopher E. Lane, J. Lukeš, David Bass, S. Bowser, Matthew W Brown, Fabien Burki, Micah Dunthorn, V. Hampl and 15 more. Journal of Eukaryotic Microbiology, 2012

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This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re‐introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under‐sampled areas and from environmental genomic information.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a8a227f9e94e181d92f60cfd1603792aca372b93

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Citations in the corpus

SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? (2017, background): “…rank information for Archaea and Bacteria is obtained from Bergey’s Taxonomic Outlines [10–13] and from the List of Prokaryotic Names with Standing in Nomenclature (LPSN) [14], whereas eukaryotic taxonomy is based on the consensus views of the International Society of Pro-tistologists [15, 16].”
Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications (2016, background): “However, on the basis of metagenomic and phylogenomic studies and NGS data, the classifications and nomenclatures of eukaryotes continue to be revised and organized into other supergroups such as Amoebozoa, Opsthokonta, Ecavata, Archae‐ plastida (Plantae), SAR (Stra/Alveo/Rhizaria), and Incertae sed”
Insights into Ciliary Genes and Evolution from Multi-Level Phylogenetic Profiling (2017, background): “This organelle was present in the Last Eukaryotic Common Ancestor (LECA) and has experienced a profound diversification among eukaryotes, so much so that it is commonly used as a major determinant in eukaryotic classification (Adl et al. 2012).”
Soil protistology rebooted: 30 fundamental questions to start with (2017, neutral): “These usually single-celled or colonial microorganisms are by far the most diverse eukaryotes (Adl et al., 2012) and their species-numbers might easily exceed 10 million (Global Soil Biodiversity Atlas; www.globalsoilbiodiversity.org).”
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NCBI Taxonomy: a comprehensive update on curation, resources and tools (2020, background): “(NCBI:txid2759 excluding NCBI:txid33090, NCBI:txid33208) The higher classification of the eukaryotes largely follows the Adl et al . consensus classification proposed by a large group of experts published in 2012 and revisited in 2019 (59, 65).”
The Weng'an biota and the Ediacaran radiation of multicellular eukaryotes (2014, background): “A life cycle with an endospore stage occurs convergently in many eukaryote groups [117], and cannot be used to uniquely identify Megasphaera as mesomycetozoean-like holozoans.”
High-level classification of the Fungi and a tool for evolutionary ecological analyses (2018, background): “Many taxonomists place the unicellular Rozellomycota, Microsporidia and Aphelida within Fungi (James et al. 2006a; Jones et al. 2011a, Adl et al. 2012; James and Berbee 2012 and further studies on fungal classification), but other authors indicate the monophyly of Aphelida and Rozellomycota in a…”
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks (2013, methodology): “With SILVA release 111 in 2012, ETWG implemented a phylogenetic tree-guided curated taxonomy for Eukaryota based on the consensus views of the International Society of Protistologists (26,30), which focused on the higher taxonomic levels (e.g. Opisthokonta, Stramenopiles, Excavata).”
Towards a phylogenetic classification of the Myxomycetes (2019, background): “This excludes all other fruiting members of the Amoebozoa.”
Big answers from small worlds: a user's guide for protist microcosms as a model system in ecology and evolution (2015, methodology): “Species used for protist microcosm experiments cover several major domains of life and a large part of eukaryotic phylogenetic diversity (Adl et al. 2012).”
The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy (2012, methodology): “As for the PR2 database, SILVA taxonomy for eukaryotes now offers a taxonomy based on the structure proposed by Adl et al. (12).”
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Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes (2015, background): “common algal lineages illustrates this diversity and its influence on ocean biogeochemistry: Some stramenopiles have silicate frustules of nanoscale precision (diatoms), whereas others are naked; haptophytes can be covered in ornate calcium carbonate plates (coccolithophores), whereasmany picoplankt”
Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes (2018, background): “DIAPHORETICKES ARCHAEPLASTIDA Chloroplastida Fawley, M.V., Yun, Y., & Qin, M. 2000.”