Diversity, nomenclature, and taxonomy of protists.

  title={Diversity, nomenclature, and taxonomy of protists.},
  author={Sina M Adl and Brian S. Leander and Alastair G. B. Simpson and John M. Archibald and O. Roger Anderson and David Bass and Samuel S. Bowser and Guy Brugerolle and Mark A. Farmer and Sergey A. Karpov and Martin Kolisko and Christopher E. Lane and D. Jean Lodge and David G. Mann and Ralf Meisterfeld and Leonel Mendoza and {\O}jvind Moestrup and Sharon E Mozley-Standridge and Alexey V Smirnov and Frederick W. Spiegel},
  journal={Systematic biology},
  volume={56 4},
the origin of echolocation and flight in bats. Nature 403:188– 192. van Rheede, T., T. Bastiaans, D. N. Boone, S. B. Hedges, W. W. de Jong, and O. Madsen. 2006. The platypus in its place: nuclear genes and indels confirm the sister group relation of monotremes and therians. Mol. Biol. Evol. 23:587–597. Waddell, P. J., H. Kishino, and R. Ota. 2001. A phylogenetic foundation for comparative mammalian genomics. Genome Informatics 12:141– 154. Waddell, P. J., N. Okada, and M. Hasegawa. 1999… 

Tables from this paper

Protist Evolution and Phylogeny
A new higher level classification of eukaryotes combining the results of microscopic and various ‘omics’ studies has been proposed, and important part of protist diversity has been uncovered by environmental DNA study.
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.
A time-calibrated multi-gene phylogeny provides insights into the evolution, taxonomy and DNA barcoding of the Pinnularia gibba group (Bacillariophyta)
The phylogenetic analysis was used to assess marker resolution for DNA barcoding, showing that the proposed diatom barcode markers rbcL and V4 SSU rDNA can distinguish closely related (pseudo)cryptic species of the P. gibba group.
Untangling the Phylogeny of Amoeboid Protists 1
This review describes the taxonomic composition of both supergroups and presents their small subunit rDNA‐based phylogeny, highlighting the interest of Amoebozoa and Rhizaria for understanding eukaryotic evolution and suggesting that resolving their phylogenies will be among the main challenges for future phylogenomic analyses.
Identification of a Divergent Environmental DNA Sequence Clade Using the Phylogeny of Gregarine Parasites (Apicomplexa) from Crustacean Hosts
An expanded molecular phylogenetic context enabled us to establish a major clade of intestinal gregarine parasites and infer the cellular identities of several previously unidentified environmental SSU rDNA sequences, including several sequences that have formerly been discussed broadly in the literature as a suspected “novel” lineage of eukaryotes.
Linking Biological and Geological Data on Dinoflagellates Using the Genus Spiniferites as an Example: The Implications of Species Concepts, Taxonomy and Dual Nomenclature
The background of dual nomenclature is examined and the implications of new advances in molecular phylogeny for dual taxonomy are discussed, as well as briefly review earlier attempts to unite cyst/fossil and motile-/living-based nomenClatures.
DNA Barcoding of Apicomplexa: Mitochondrial Evolution across the Phylum
The mt COI locus is recommended as a suitable DNA barcoding target for coccidian parasites of veterinary and zoonotic importance and Mitochondrial COI sequences were concluded to be better species-level markers than the widely used nu 18S rDNA locus; mtCOI sequences had utility in both diagnostic and phylogenetic studies.
Morphology and Phylogenetic Position of Two New Gregarine Species (Apicomplexa: Eugregarinorida) Parasitizing the Lubber Grasshopper Taeniopoda centurio (Drury, 1770) (Insecta: Orthoptera: Romaleidae) in Mexico
Two new eugregarine species from the gut of the host are described: Amoebogregarina taeniopoda n.
Ecological Differentiation of Cryptic Species within an Asexual Protist Morphospecies: A Case Study of Filamentous Green Alga Klebsormidium (Streptophyta)
It is considered that the permanent existence of genetically and ecologically well‐defined cryptic species is enabled by the mechanism of selective sweep.


Species Names in the PhyloCode: the approach adopted by the International Society for Phylogenetic Nomenclature.
Gene trees and species trees are not the same, and Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions are recommended.
Naming taxa from cladograms: a cautionary tale.
  • A. Dubois
  • Biology
    Molecular phylogenetics and evolution
  • 2007
The Diversity of Eukaryotes
This catalog includes all known major elements of the comprehensive evolutionary tree of protists and eukaryotes and introduces the concept of “extended in‐group” to refer to in‐groups and the most proximate sister group and to assist in identifying the hierarchical location of taxa.
Biogeography and dispersal of micro-organisms: a review emphasizing protists
This review summarizes data on the biogeography and dispersal of bacteria, microfungi and selected protists, such as dinoflagellates, chrysophytes, testate amoebae, and ciliates. Furthermore, it
The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes
A molecular survey of small subunit ribosomal RNA genes in water and sediment samples of two ponds shows that protist diversity is very high, and suggests that, contrary to current ideas, the diversity of freshwater protists is far from being completely described.
By deriving the principles and methods of his approach from the tenet of common descent, Hennig granted the concept of evolution a position in taxonomy.
A Comparison of Phylogenetic Nomenclature with the Current System: A Botanical Case Study
The family Lamiaceae was used as a case study to compare the current system of nomenclature with a phylogenetic alternative proposed by de Queiroz and Gauthier (1992), and the recommendation that the principle of exhaustive subsidiary taxa be abandoned is endorsed.
The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists
This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists, and proposes a scheme that is based on nameless ranked systematics.
Species names in phylogenetic nomenclature.
Here, 13 methods for naming species in the context of phylogenetic nomenclature are contrasted with each other and with Linnaean binomials and a fundamental dichotomy among the proposed methods distinguishes those that retain the entire binomial of a preexisting species name fromThose that retain only the specific epithet.
Classifying species versus naming clades
The February 2004 issue of Taxon included two articles and an opinion piece that either (Jorgensen, 2004) opposed development of the PhyloCode or (Barkley & al., 2004a, b) argued that it was unnecessary to meet the needs of phylogenetic classification.