EEF2 analysis challenges the monophyly of Archaeplastida and Chromalveolata. PLoS One 3:e2621

Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
PLoS ONE (Impact Factor: 3.23). 02/2008; 3(7):e2621. DOI: 10.1371/journal.pone.0002621
Source: PubMed

ABSTRACT Classification 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.
This 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.
Our 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.

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    • "At some point the members of this group, which also includes the cryptophytes, haptophytes, and alveolates as well as the heterokontophytes, acquired their plastid through secondary endosymbiosis of a red alga, explained by the presence of four membranes, the outer one being continuous with the rough endoplasmic reticulum and the outer membrane of the nucleus (Keeling 2009). In recent studies of diatom genomes, however, there have been discoveries of nuclear genes of a green algal origin that are not the result of lateral gene transfer, suggesting a cryptic endosymbiont likely related to prasinophyte-like green algae in an ancestor of chromalveolates (Kim & Graham 2008). The combination of two ancient endosymbiosis events, as well as supplemental horizontal gene transfer, has provided the chromalveolates with the genetic potential to become one of "
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    • "Due to the differences in taxa sampled and ambiguous alignment, the findings of previous phylogenetic studies based on 18S rDNAs vary extensively from each other (Cavalier-Smith and Chao, 1996; Kumar and Rzhetsky, 1996; Van de Peer and De Wachter, 1997; Burki et al., 2002; Kostka et al., 2004; Nikolaev et al., 2004; Polet et al., 2004; Shalchian-Tabrizi et al., 2006; Shalchian-Tabrizi et al., 2007). Additionally because of the effects of sparse taxon sampling and heterogeneity in the sequence data, the results of the studies based on multiple proteins or protein-coding genes are also quite different from each other (Baldauf et al., 2000; Philippe et al., 2004; Harper et al., 2005; Rodríguez- Ezpeleta et al., 2005; Burki and Pawlowski, 2006; Burki et al., 2007; Hackett et al., 2007; Patron et al., 2007; Kim and Graham, 2008). Only Opisthokonta, also known as the Fungi- Metazoa group, appears in all of the studies of eukaryote interrelationships (Parfrey et al., 2006). "
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    • "It has been suggested that 100+ genes are necessary to recover " Archaeplastida " with strong support (Rodríguez-Ezpeleta et al. 2005). The Archaeplastida hypothesis is not supported in our analyses (Tables 1 and S6 and Figs. 1 and 2) or those of others (Parfrey et al. 2006; Kim and Graham 2008; Yoon et al. 2008; Hampl et al. 2009). Here, the " Archaeplastida " lineages red algae, green algae, and glaucocystophytes are never monophyletic, but instead generally form a poorly supported cluster with the secondarily photosynthetic haptophytes and cryptomonads plus other nonphotosynthetic lineages (Table 1 "
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