Long-Branch Attraction and the rDNA Model of Early Eukaryotic Evolution

Stiller, John W.; Hall, Benjamin D.

doi:10.1093/oxfordjournals.molbev.a026217

Cited by 138 publications

(87 citation statements)

References 43 publications

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“…Recently, tiny relict mitochondrial organelles have been identified in Giardia (Tovar et al, 2003). Furthermore, it has become clear that the basal portions of eukaryotic molecular phylogenies may be structured by analysis artefacts, rather than by true historical signal (Philippe & Adoutte, 1998;Hirt et al, 1999;Stiller & Hall, 1999;Philippe et al, 2000). The deeply diverged position of diplomonads is now seriously in question.…”

Section: The Excavate Hypothesismentioning

confidence: 99%

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

Simpson

2003

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

199

264

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Section: The Excavate Hypothesismentioning

confidence: 99%

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

Simpson

2003

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

199

264

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“…However, in this case, it is reasonable to treat them as independent, at least at a high taxonomic level. One reason is that the tree is not yet known with great confidence at a high taxonomic level (e.g., Philippe and Adoutte 1998;Katz 1999;Stiller and Hall 1999;Taylor 1999). Another is that divergences are separated in most cases by enormous stretches of time, allowing many opportunities for gains and losses of parts in most lineages.…”

Section: A Test Of the Hypothesismentioning

confidence: 99%

A Complexity Drain on Cells in the Evolution of Multicellularity

McShea¹

2002

Evolution

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Abstract. A hypothesis has been advanced recently predicting that, in evolution, as higher-level entities arise from associations of lower-level organisms, and as these entities acquire the ability to feed, reproduce, defend themselves, and so on, the lower-level organisms will tend to lose much of their internal complexity (McShea 2001a). In other words, in hierarchical transitions, there is a drain on numbers of part types at the lower level. One possible rationale is that the transfer of functional demands to the higher level renders many part types at the lower level useless, and thus their loss in evolution is favored by selection for economy. Here, a test is conducted at the cell level, comparing numbers of part types in free-living eukaryotic cells (protists) and the cells of metazoans and land plants. Differences are significant and consistent with the hypothesis, suggesting that tests at other hierarchical levels may be worthwhile. Hierarchical transitions occur when a group of organisms combine to form a higher-level entity (Spencer 1904;Campbell 1958;Simon 1962;Pattee 1970;Eldredge and Salthe 1984;Salthe 1985Salthe , 1993Buss 1987;Bonner 1988;Maynard Smith 1988;Wimsatt 1994;Maynard Smith and Szathmáry 1995;McShea 1996 McShea , 2001bPettersson 1996;Valentine and May 1996;Michod 1999). In the history of life, salient examples include the origin of the eukaryotic cell from symbiotic associations of prokaryotic cells, of multicellular individuals from clones of free-living eukaryotic cells, and of colonies from associations of multicellular individuals. A hypothesis has been advanced recently that predicts that, as such transitions occur, and as the new higher-level entities acquire the ability to feed, reproduce, defend themselves, and so on, their component organisms will tend to lose many of these functional capabilities and therefore will tend to lose many of their internal parts (McShea 2001a). More precisely, the expectation is that the component organisms will tend to lose part types at the next hierarchical level down (Fig. 1). (Technical understandings of the terms part and level will be offered shortly; for present purposes, colloquial meanings suffice.)Concretely, the hypothesis predicts that the cells of multicellular organisms will have fewer part types than freeliving eukaryotic cells, that is, nonparasitic protists (hereafter simply protists; sensu Patterson 1999). At a higher level, in colonial marine invertebrates and social insects, the multicellular individuals (e.g., polyps, zooids) that constitute the more individuated colonies-that is, those in which coloniality is more highly developed (Boardman and Cheetham 1973)-should have fewer part types, on average, than those of their less colonial or solitary relatives (Beklemishev 1969). And at a lower level, the former prokaryotes that today function as organelles in eukaryotic cells (e.g., mitochondria, plastids) should have fewer part types than free-living prokaryotes.Attention to hierarchical level is crucial. A considerable body of e...

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“…[1][2][3][4][5]. This approach suffered from lack of resolution (stochastic error) because of the low number of informative sites and systematic error in tree estimation caused by model violations such as compositional heterogeneity among sequences, and problems related to long-branch attraction (LBA) (6)(7)(8)(9)(10)(11). Worse, in some cases single genes had been transferred laterally between the lineages under examination (12).…”

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.

443

404

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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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Long-Branch Attraction and the rDNA Model of Early Eukaryotic Evolution

Cited by 138 publications

References 43 publications

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

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

A Complexity Drain on Cells in the Evolution of Multicellularity

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

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