Rooting the Eukaryotic Tree with Mitochondrial and Bacterial Proteins

Derelle, Romain; Lang, B. Franz

doi:10.1093/molbev/msr295

Cited by 123 publications

(144 citation statements)

References 68 publications

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“…Opisthokonts and Amoebozoa are often united in a larger supergroup called the unikonts (Cavalier-Smith 2002) or, more recently, Amorphea (Adl et al 2012), which is supported by a gene duplication/fusion Cavalier-Smith 2002, 2003) as well as singlegene phylogenies (e.g., Baldauf and Palmer 1993) and phylogenomics (Rodriguez-Ezpeleta et al 2007a;Hampl et al 2009;Brown et al 2012;Derelle and Lang 2012). Amorphea also contains protist lineages of unclear placement, such as the apusomonads, ancryomonads, and breviate amoebae.…”

Section: Amoebozoamentioning

confidence: 99%

The Eukaryotic Tree of Life from a Global Phylogenomic Perspective

Burki

2014

Cold Spring Harbor Perspectives in Biology

286

262

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Molecular phylogenetics has revolutionized our knowledge of the eukaryotic tree of life. With the advent of genomics, a new discipline of phylogenetics has emerged: phylogenomics. This method uses large alignments of tens to hundreds of genes to reconstruct evolutionary histories. This approach has led to the resolution of ancient and contentious relationships, notably between the building blocks of the tree (the supergroups), and allowed to place in the tree enigmatic yet important protist lineages for understanding eukaryote evolution. Here, I discuss the pros and cons of phylogenomics and review the eukaryotic supergroups in light of earlier work that laid the foundation for the current view of the tree, including the position of the root. I conclude by presenting a picture of eukaryote evolution, summarizing the most recent progress in assembling the global tree.

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Section: Amoebozoamentioning

confidence: 99%

The Eukaryotic Tree of Life from a Global Phylogenomic Perspective

Burki

2014

Cold Spring Harbor Perspectives in Biology

286

262

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“…The reconstruction of evolutionary gains/losses of given TFs types in each node and ancestral states has been inferred using Dollo parsimony. The phylogenetic framework was taken from up-to-date eukaryote phylogenomic studies (71)(72)(73)(74)(75). DBDs gains are shown in green and lineage-specific DBDs secondary losses are shown in red boxes.…”

Section: Phylostratigraphic Analysis Of Tfome Expression In Multicellmentioning

confidence: 99%

Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages

Mendoza

Sebé-Pedrós

Šestak

et al. 2013

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

185

209

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Transcription factors (TFs) are the main players in transcriptional regulation in eukaryotes. However, it remains unclear what role TFs played in the origin of all of the different eukaryotic multicellular lineages. In this paper, we explore how the origin of TF repertoires shaped eukaryotic evolution and, in particular, their role into the emergence of multicellular lineages. We traced the origin and expansion of all known TFs through the eukaryotic tree of life, using the broadest possible taxon sampling and an updated phylogenetic background. Our results show that the most complex multicellular lineages (i.e., those with embryonic development, Metazoa and Embryophyta) have the most complex TF repertoires, and that these repertoires were assembled in a stepwise manner. We also show that a significant part of the metazoan and embryophyte TF toolkits evolved earlier, in their respective unicellular ancestors. To gain insights into the role of TFs in the development of both embryophytes and metazoans, we analyzed TF expression patterns throughout their ontogeny. The expression patterns observed in both groups recapitulate those of the whole transcriptome, but reveal some important differences. Our comparative genomics and expression data reshape our view on how TFs contributed to eukaryotic evolution and reveal the importance of TFs to the origins of multicellularity and embryonic development.phylotypic stage | Holozoa | LECA T ranscription factors (TFs) are proteins that bind to DNA in a sequence-specific manner (1) and enhance or repress gene expression (2-4). In response to a broad range of stimuli, TFs coordinate many important biological processes, from cell cycle progression and physiological responses, to cell differentiation and development (5, 6). Thus, TFs have a central role in the transcriptional regulation of all cellular organisms, being present in all branches of the tree of life (bacteria, archaea, and eukaryotes). There appears to be a correlation between elaborate regulation of gene expression and the complexity of organisms (7), such that the amount (as a proportion of an organism's total gene content) and diversity of TF proteins is expected to be directly correlated with this complexity (8). Indeed, TFs play a crucial role in multicellular eukaryotes. For example, TFs are the master regulators of embryonic development in embryophytes and metazoans (9), and analyses of their embryonic transcriptional profiles support the presence of a phylotypic stage in both lineages (10-14). These studies have also shown that evolutionarily younger genes tend to be expressed at earlier and later stages of development, whereas the transcriptomes of the middle stages (the phylotypic stage) are dominated by ancient genes (10, 13). It remains to be investigated how the evolutionary age and the expression patterns of the different TFs shift throughout the ontogeny of these lineages and whether TF expression profiles correlate with the general transcriptome profiles.Previous studies have analyzed the evolutionary ...

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“…Another challenge inherent to dating ancient events in eukaryotic evolution is the current uncertainty regarding the location of the root Cavalier-Smith 2002, 2003a,b;Cavalier-Smith 2010;Derelle and Lang 2012;Katz et al 2012). Tackling this question is made especially difficult by the absence of closely related outgroups to eukaryotes.…”

Section: The Eukaryotic Tree Of Lifementioning

confidence: 99%

On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks

Eme

Sharpe

Brown

et al. 2014

Cold Spring Harbor Perspectives in Biology

209

152

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Our understanding of the phylogenetic relationships among eukaryotic lineages has improved dramatically over the few past decades thanks to the development of sophisticated phylogenetic methods and models of evolution, in combination with the increasing availability of sequence data for a variety of eukaryotic lineages. Concurrently, efforts have been made to infer the age of major evolutionary events along the tree of eukaryotes using fossilcalibrated molecular clock-based methods. Here, we review the progress and pitfalls in estimating the age of the last eukaryotic common ancestor (LECA) and major lineages. After reviewing previous attempts to date deep eukaryote divergences, we present the results of a Bayesian relaxed-molecular clock analysis of a large dataset (159 proteins, 85 taxa) using 19 fossil calibrations. We show that for major eukaryote groups estimated dates of divergence, as well as their credible intervals, are heavily influenced by the relaxed molecular clock models and methods used, and by the nature and treatment of fossil calibrations. Whereas the estimated age of LECA varied widely, ranging from 1007 (943-1102) Ma to 1898 (1655 -2094) Ma, all analyses suggested that the eukaryotic supergroups subsequently diverged rapidly (i.e., within 300 Ma of LECA). The extreme variability of these and previously published analyses preclude definitive conclusions regarding the age of major eukaryote clades at this time. As more reliable fossil data on eukaryotes from the Proterozoic become available and improvements are made in relaxed molecular clock modeling, we may be able to date the age of extant eukaryotes more precisely.

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Rooting the Eukaryotic Tree with Mitochondrial and Bacterial Proteins

Cited by 123 publications

References 68 publications

The Eukaryotic Tree of Life from a Global Phylogenomic Perspective

The Eukaryotic Tree of Life from a Global Phylogenomic Perspective

Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages

On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks

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