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The Revised Classification of Eukaryotes
This revision of the classification of eukaryotes retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees.
Swarm v2: highly-scalable and high-resolution amplicon clustering
Swarm v2 has two important novel features: a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and the new fastidious option that reduces under-grouping by grafting low abundant OTUs onto larger ones.
The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy
The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists.
Swarm: robust and fast clustering method for amplicon-based studies
Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to…
Eukaryotic plankton diversity in the sunlit ocean
Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies.
Patterns of Rare and Abundant Marine Microbial Eukaryotes
CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms
A group of protist experts proposes a two-step DNA barcoding approach, comprising a universal eukaryotic pre-barcode followed by group-specific barcodes, to unveil the hidden biodiversity of…
Evaluating Support for the Current Classification of Eukaryotic Diversity
It is demonstrated that supergroup taxonomies are unstable and that support for groups varies tremendously, indicating that the current classification scheme of eukaryotes is likely premature.
Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes
It is confirmed that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista, and suggested primer sets for DNA sequences from environmental samples that are effective for each clade are provided.
Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing.
This extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date.