Evaluating Support for the Current Classification of Eukaryotic Diversity

Abstract

Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the four eukaryotic groups within the five-kingdom classification-plants, animals, fungi, and protists-have been transformed through numerous permutations into the current system of six ''supergroups.'' The intent of the supergroup classification system is to unite microbial and macroscopic eukaryotes based on phylogenetic inference. This supergroup approach is increasing in popularity in the literature and is appearing in introductory biology textbooks. We evaluate the stability and support for the current six-supergroup classification of eukaryotes based on molecular genealogies. We assess three aspects of each supergroup: (1) the stability of its taxonomy, (2) the support for monophyly (single evolutionary origin) in molecular analyses targeting a supergroup, and (3) the support for monophyly when a supergroup is included as an out-group in phylogenetic studies targeting other taxa. Our analysis demonstrates that supergroup taxonomies are unstable and that support for groups varies tremendously, indicating that the current classification scheme of eukaryotes is likely premature. We highlight several trends contributing to the instability and discuss the requirements for establishing robust clades within the eukaryotic tree of life.Citation: Parfrey LW, Barbero E, Lasser E, Dunthorn M, Evaluating support for the current classification of eukaryotic diversity. PLoS Genet 2(12): e220.

Multigene phylogenies of clonal Spumella-like strains, a cryptic heterotrophic nanoflagellate, isolated from different geographical regions

“…The reasoning for such multigene phylogenies is that a larger number of characters improves phylogenetic accuracy and resolution when the number of alignable and informative nucleotides in single-gene analyses is too limited or the rates of sequence evolution are too different (Poe & Swofford, 1999). This approach has been successful in minimizing difficulties based on single protein-coding gene evolution in plants (Bowe et al, 2000;Karol et al, 2001;Mallatt & Winchell, 2002), animals (Mallatt & Winchell, 2002), various groups of algae (Gontcharov et al, 2004;HoefEmden et al, 2002;Nozaki et al, 2000) and the radiation of eukaryotes (Baldauf et al, 2000;Parfrey et al, 2006). The combination of seven different genes seems to minimize any potential bias in phylogenetic reconstruction of Spumellalike strains that is caused by single genes in single taxa.…”

Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii

“…Green algae are a large group of eukaryotic organisms comprising ;8000 photosynthetic species that include the direct ancestors of land plants (Norton et al, 1996;Parfrey et al, 2006). Unicellular algae have served as models for many fundamental cellular processes, including flagellar assembly, motility, DNA methylation, photosynthesis, chloroplast biogenesis, metabolism, and sex determination (Harris, 2001).…”

Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”

“…With some caveats, solid molecular phylogenetic evidence supports the monophyly of each of Rhizaria, Archaeplastida, Opisthokonta, and Amoebozoa (16,18,(29)(30)(31)(32)(33)(34). However, the monophyly of both the Chromalveolata and the Excavata remains controversial (34), with recent evidence indicating that some, but not all, of the chromalveolate lineages are most closely related to Rhizaria (20,22,35). Of critical importance to both the placement of the root, and to the overall classification of eukaryotes, the branching order among the 6 supergroups remains obscure.…”