Abstract
BackgroundClassification of eukaryotes provides a fundamental phylogenetic framework for ecological, medical, and industrial research. In recent years eukaryotes have been classified into six major supergroups: Amoebozoa, Archaeplastida, Chromalveolata, Excavata, Opisthokonta, and Rhizaria. According to this supergroup classification, Archaeplastida and Chromalveolata each arose from a single plastid-generating endosymbiotic event involving a cyanobacterium (Archaeplastida) or red alga (Chromalveolata). Although the plastids within members of the Archaeplastida and Chromalveolata share some features, no nucleocytoplasmic synapomorphies supporting these supergroups are currently known.Methodology/Principal FindingsThis study was designed to test the validity of the Archaeplastida and Chromalveolata through the analysis of nucleus-encoded eukaryotic translation elongation factor 2 (EEF2) and cytosolic heat-shock protein of 70 kDa (HSP70) sequences generated from the glaucophyte Cyanophora paradoxa, the cryptophytes Goniomonas truncata and Guillardia theta, the katablepharid Leucocryptos marina, the rhizarian Thaumatomonas sp. and the green alga Mesostigma viride. The HSP70 phylogeny was largely unresolved except for certain well-established groups. In contrast, EEF2 phylogeny recovered many well-established eukaryotic groups and, most interestingly, revealed a well-supported clade composed of cryptophytes, katablepharids, haptophytes, rhodophytes, and Viridiplantae (green algae and land plants). This clade is further supported by the presence of a two amino acid signature within EEF2, which appears to have arisen from amino acid replacement before the common origin of these eukaryotic groups.Conclusions/SignificanceOur EEF2 analysis strongly refutes the monophyly of the Archaeplastida and the Chromalveolata, adding to a growing body of evidence that limits the utility of these supergroups. In view of EEF2 phylogeny and other morphological evidence, we discuss the possibility of an alternative eukaryotic supergroup.
Highlights
Eukaryotes constitute one of the three domains of life, distinguished from bacteria and archaebacteria by their greater molecular, cellular, and reproductive complexity
eukaryotic translation elongation factor 2 (EEF2) and cytosolic heat-shock protein of 70 kDa (HSP70) analyses EEF2 phylogenetic trees inferred from maximum likelihood (RAxML, PhyloBayes) and distance (FastME) methods were more or less similar, some deep branching patterns that had low bootstrap support, differed
A number of well-established eukaryotic groups, including rhodophytes, alveolates, opisthokonts, euglenozoans, and Viridiplantae were recovered with .90% bootstrap support and high posterior probabilities (Figure 1)
Summary
Eukaryotes constitute one of the three domains of life, distinguished from bacteria and archaebacteria by their greater molecular, cellular, and reproductive complexity. Eukaryotes have been grouped into only two major clades— unikonts and bikonts–based largely on a single gene fusion event, under the assumption that parallel fusions would be improbable [4,5,6]. Other recent authors have classified eukaryotes into 5 or 6 major supergroups: Amoebozoa, Opisthokonta, Archaeplastida (or Plantae), Chromalveolata, Rhizaria, and Excavata, with the first two grouped as ‘unikonts’ by some authors [10,11,12]. In recent years eukaryotes have been classified into six major supergroups: Amoebozoa, Archaeplastida, Chromalveolata, Excavata, Opisthokonta, and Rhizaria. According to this supergroup classification, Archaeplastida and Chromalveolata each arose from a single plastid-generating endosymbiotic event involving a cyanobacterium (Archaeplastida) or red alga (Chromalveolata). The plastids within members of the Archaeplastida and Chromalveolata share some features, no nucleocytoplasmic synapomorphies supporting these supergroups are currently known
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