Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota)

Simpson, Alastair G. B.

doi:10.1099/ijs.0.02578-0

Cited by 202 publications

(283 citation statements)

References 74 publications

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“…This assumption based on the cell structure was supported also by early multigene phylogenetic analyses (Baldauf et al, 2000). Currently, the Heterolobosea is nested together with Euglenozoa, Jakobida, Parabasalia, Fornicata, Preaxostyla, Malawimonas, and Tsukubamonas within the eukaryotic supergroup Excavata (Hampl et al, 2009;Rodríguez-Ezpeleta et al, 2007;Simpson, 2003;Yabuki et al, 2011). The excavate organisms were originally defined on the basis of the structure of flagellar system and ventral feeding groove (Simpson & Patterson, 1999).…”

Section: Introductionmentioning

confidence: 85%

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Diversity of Heterolobosea

Pánek¹,

Čepička²

2012

Genetic Diversity in Microorganisms

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Section: Introductionmentioning

confidence: 85%

“…The excavate organisms were originally defined on the basis of the structure of flagellar system and ventral feeding groove (Simpson & Patterson, 1999). However, Heterolobosea have lost some of these structures (Simpson, 2003).…”

Section: Introductionmentioning

confidence: 99%

Diversity of Heterolobosea

Pánek¹,

Čepička²

2012

Genetic Diversity in Microorganisms

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“…The supergroup Excavata was proposed on the basis of shared morphological characters-a ventral feeding groove and associated cytoskeletal structures (38)(39)(40), with some additional taxa (parabasalids, euglenids, and oxymonads) linked to the group primarily through molecular studies (41)(42)(43)(44)(45). There is no solid molecular phylogenetic evidence for the monophyly of Excavata as a whole, but 3 subgroups are often individually recovered as clades: (i) Preaxostyla (Trimastix and oxymonads), (ii) Fornicata (diplomonads, retortamonads, Carpediemonas) plus Parabasalia; and (iii) an unnamed clade consisting of Euglenozoa, Heterolobosea, and Jakobida (14,20,40,42,43,(45)(46)(47)(48)(49)(50)(51)(52)(53)(54)(55).…”

mentioning

confidence: 99%

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

Hampl

Hug

Leigh

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

445

405

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Nearly all of eukaryotic diversity has been classified into 6 suprakingdom-level groups (supergroups) based on molecular and morphological/cell-biological evidence; these are Opisthokonta, Amoebozoa, Archaeplastida, Rhizaria, Chromalveolata, and Excavata. However, molecular phylogeny has not provided clear evidence that either Chromalveolata or Excavata is monophyletic, nor has it resolved the relationships among the supergroups. To establish the affinities of Excavata, which contains parasites of global importance and organisms regarded previously as primitive eukaryotes, we conducted a phylogenomic analysis of a dataset of 143 proteins and 48 taxa, including 19 excavates. Previous phylogenomic studies have not included all major subgroups of Excavata, and thus have not definitively addressed their interrelationships. The enigmatic flagellate Andalucia is sister to typical jakobids. Jakobids (including Andalucia), Euglenozoa and Heterolobosea form a major clade that we name Discoba. Analyses of the complete dataset group Discoba with the mitochondrion-lacking excavates or ''metamonads'' (diplomonads, parabasalids, and Preaxostyla), but not with the final excavate group, Malawimonas. This separation likely results from a long-branch attraction artifact. Gradual removal of rapidly-evolving taxa from the dataset leads to moderate bootstrap support (69%) for the monophyly of all Excavata, and 90% support once all metamonads are removed. Most importantly, Excavata robustly emerges between unikonts (Amoebozoa ؉ Opisthokonta) and ''megagrouping'' of Archaeplastida, Rhizaria, and chromalveolates. Our analyses indicate that Excavata forms a monophyletic suprakingdom-level group that is one of the 3 primary divisions within eukaryotes, along with unikonts and a megagroup of Archaeplastida, Rhizaria, and the chromalveolate lineages.Chromalveolata ͉ Discoba ͉ long-branch attraction

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“…There is little doubt that these sequences tend to form much longer branches in phylogenies than most later-branching taxa, but an alternative phylogenetic position is not strongly supported by molecular data. Ultrastructural considerations strongly suggest a link between these taxa and other heterotrophic flagellates collectively called the Excavata (Simpson 2003). Some of these lineages, such as the jakobid flagellates, are less divergent and do not branch basally with diplomonads and parabasalids in rooted rRNA analyses (Simpson et al 2002).…”

Section: Phylogenetic Artefactsmentioning

confidence: 99%

“…In this view, most known eukaryotes, can be placed into one of six major clades (figure 1b). The evidence for these groups ranges from improved taxonomic sampling in rRNA analyses (Rhizaria; Nikolaev et al 2004), through phylogenies based on multiple nuclear and/or mitochondrial proteins (Amoebozoa, Arisue et al 2002;Plantae, Rodriguez-Ezpeleta et al 2005), gene replacement events (Chromalveolates; Fast et al 2001;Patron et al 2004) to ultrastructural synapomorphies (Excavata; Simpson 2003). It should be noted that the evidence is not strong for many of these groups and only a few of them are recovered in (Sogin 1991;Cavalier-Smith & Chao 1996).…”

Section: Towards a Consensus Hypothesis Of Eukaryote Relationshipsmentioning

confidence: 99%

The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation

Roger

Hug

2006

Phil. Trans. R. Soc. B

162

135

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Determining the relationships among and divergence times for the major eukaryotic lineages remains one of the most important and controversial outstanding problems in evolutionary biology. The sequencing and phylogenetic analyses of ribosomal RNA (rRNA) genes led to the first nearly comprehensive phylogenies of eukaryotes in the late 1980s, and supported a view where cellular complexity was acquired during the divergence of extant unicellular eukaryote lineages. More recently, however, refinements in analytical methods coupled with the availability of many additional genes for phylogenetic analysis showed that much of the deep structure of early rRNA trees was artefactual. Recent phylogenetic analyses of a multiple genes and the discovery of important molecular and ultrastructural phylogenetic characters have resolved eukaryotic diversity into six major hypothetical groups. Yet relationships among these groups remain poorly understood because of saturation of sequence changes on the billion-year time-scale, possible rapid radiations of major lineages, phylogenetic artefacts and endosymbiotic or lateral gene transfer among eukaryotes.Estimating the divergence dates between the major eukaryote lineages using molecular analyses is even more difficult than phylogenetic estimation. Error in such analyses comes from a myriad of sources including: (i) calibration fossil dates, (ii) the assumed phylogenetic tree, (iii) the nucleotide or amino acid substitution model, (iv) substitution number (branch length) estimates, (v) the model of how rates of evolution change over the tree, (vi) error inherent in the time estimates for a given model and (vii) how multiple gene data are treated. By reanalysing datasets from recently published molecular clock studies, we show that when errors from these various sources are properly accounted for, the confidence intervals on inferred dates can be very large. Furthermore, estimated dates of divergence vary hugely depending on the methods used and their assumptions. Accurate dating of divergence times among the major eukaryote lineages will require a robust tree of eukaryotes, a much richer Proterozoic fossil record of microbial eukaryotes assignable to extant groups for calibration, more sophisticated relaxed molecular clock methods and many more genes sampled from the full diversity of microbial eukaryotes.

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Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota)

Cited by 202 publications

References 74 publications

Diversity of Heterolobosea

Diversity of Heterolobosea

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

The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation

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