Article

The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nat Rev Microbiol 8:743-752

Institut Pasteur, Department of Microbiology, Paris, France.
Nature Reviews Microbiology (Impact Factor: 23.57). 10/2010; 8(10):743-52. DOI: 10.1038/nrmicro2426
Source: PubMed

ABSTRACT

The origin of eukaryotes and their evolutionary relationship with the Archaea is a major biological question and the subject of intense debate. In the context of the classical view of the universal tree of life, the Archaea and the Eukarya have a common ancestor, the nature of which remains undetermined. Alternative views propose instead that the Eukarya evolved directly from a bona fide archaeal lineage. Several recent large-scale phylogenomic studies using an array of approaches are divided in supporting either one or the other scenario, despite analysing largely overlapping data sets of universal genes. We examine the reasons for such a lack of consensus and consider how alternative approaches may enable progress in answering this fascinating and as-yet-unresolved question.

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    • "Most notably, other phylogenetic markers supported different relationships in the early branches of the tree, especially among bacterial (or archaeal) phyla and between Archaea and Eukarya (Brown and Doolittle 1997). With the development of genome sequencing, the combination of genetic markers to resolve deep relationships in the tree of life became popular (Delsuc et al. 2005), but again led only to ephemeral conclusions: different so-called " phylogenomic " studies identified very different numbers of phylogenetic markers potentially informative to infer the tree of life (with variations among studies from 14 to .50 genes), each combination of these markers pleading for different trees, and different phylogenetic methods yielded conflicting signals (see review inGribaldo et al. 2010). Metagenomic studies are now bringing new incentive to these approaches by providing genomic sequences for previously unknown organisms, which turn out to be key to resolve, for instance, the relationships between Eukarya and Archaea (Spang et al. 2015). "
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    ABSTRACT: Microbes acquire DNA from a variety of sources. The last decades, which have seen the development of genome sequencing, have revealed that horizontal gene transfer has been a major evolutionary force that has constantly reshaped genomes throughout evolution. However, because the history of life must ultimately be deduced from gene phylogenies, the lack of methods to account for horizontal gene transfer has thrown into confusion the very concept of the tree of life. As a result, many questions remain open, but emerging methodological developments promise to use information conveyed by horizontal gene transfer that remains unexploited today.
    Full-text · Article · Jan 2016 · Cold Spring Harbor perspectives in biology
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    • "However, at least since Reanney (1974) it has been questioned which direction the change occurred—akaryotes to eukaryotes, eukaryotes to akaryotes, or were both forms equally old? The question as to whether eukaryotes are oldest has been raised quite a few times (Carlile 1982; Blake 1983; Forterre 1994; Jeffares et al. 1998; Brinkmann and Philippe 1999; Caetano-Anollés 2002; de Duve 2007; Desmond et al. 2011; Gribaldo et al. 2010) and this 'protoeukaryote' question has never been satisfactorily addressed by advocates of the alternative 'akaryotes old' viewpoint. And they might be correct—but we need to evaluate all the ideas scientifically. "
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    ABSTRACT: The Last Eukaryote Common Ancestor (LECA) appears to have the genetics required for meiosis, mitosis, nucleus and nuclear substructures, an exon/intron gene structure, spliceosomes, many centres of DNA replication, etc. (and including mitochondria). Most of these features are not generally explained by models for the origin of the Eukaryotic cell based on the fusion of an Archeon and a Bacterium. We find that the term 'prokaryote' is ambiguous and the non-phylogenetic term akaryote should be used in its place because we do not yet know the direction of evolution between eukaryotes and akaryotes. We use the term 'protoeukaryote' for the hypothetical stem group ancestral eukaryote that took up a bacterium as an endosymbiont that formed the mitochondrion. It is easier to make detailed models with a eukaryote to an akaryote transition, rather than vice versa. So we really are at a phylogenetic impasse in not being confident about the direction of change between eukaryotes and akaryotes.
    Full-text · Article · Sep 2014 · Journal of Molecular Evolution
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    • "Yet, the plethora of phylogenetic studies that has tried to resolve this conundrum has thus far failed to reach consensus, prompting some to even speak of a " phylogenomic impasse " (Gribaldo et al. 2010). Clearly, the phylogenomic approaches taken to resolve these deep evolutionary relationships have to be performed with great care as they are prone to all sorts of biases and artifacts (Delsuc et al. 2005; Gribaldo et al. 2010). Some of those, such as compositional bias and varying evolutionary rates (heterotachy ), are inherent in the nature of biological sequence data. "
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    ABSTRACT: The origin of the eukaryotic cell can be regarded as one of the hallmarks in the history of life on our planet. The apparent genomic chimerism in eukaryotic genomes is currently best explained by invoking a cellular fusion at the root of the eukaryotes that involves one archaeal and one or more bacterial components. Here, we use a phylogenomics approach to reevaluate the evolutionary affiliation between Archaea and eukaryotes, and provide further support for scenarios in which the nuclear lineage in eukaryotes emerged from within the archaeal radiation, displaying a strong phylogenetic affiliation with, or even within, the archaeal TACK superphylum. Further taxonomic sampling of archaeal genomes in this superphylum will certainly provide a better resolution in the events that have been instrumental for the emergence of the eukaryotic lineage.
    Full-text · Article · Jul 2014 · Cold Spring Harbor perspectives in biology
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