Archaeal “Dark Matter” and the Origin of Eukaryotes
Tom A. Williams,T. Martin Embley +1 more
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TLDR
It is shown that a recent analysis incorporating new genomes from uncultivated Archaea recovered a strongly supported three domains tree, consistent with a number of recent studies in which improved archaeal sampling and better phylogenetic models agree in supporting the eocyte tree over the three domains hypothesis.Abstract:
Current hypotheses about the history of cellular life are mainly based on analyses of cultivated organisms, but these represent only a small fraction of extant biodiversity. The sequencing of new environmental lineages therefore provides an opportunity to test, revise, or reject existing ideas about the tree of life and the origin of eukaryotes. According to the textbook three domains hypothesis, the eukaryotes emerge as the sister group to a monophyletic Archaea. However, recent analyses incorporating better phylogenetic models and an improved sampling of the archaeal domain have generally supported the competing eocyte hypothesis, in which core genes of eukaryotic cells originated from within the Archaea, with important implications for eukaryogenesis. Given this trend, it was surprising that a recent analysis incorporating new genomes from uncultivated Archaea recovered a strongly supported three domains tree. Here, we show that this result was due in part to the use of a poorly fitting phylogenetic model and also to the inclusion by an automated pipeline of genes of putative bacterial origin rather than nucleocytosolic versions for some of the eukaryotes analyzed. When these issues were resolved, analyses including the new archaeal lineages placed core eukaryotic genes within the Archaea. These results are consistent with a number of recent studies in which improved archaeal sampling and better phylogenetic models agree in supporting the eocyte tree over the three domains hypothesis.read more
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Endosymbiosis and Eukaryotic Cell Evolution.
TL;DR: Modern views on endosymbiotic theory in a historical context are framed, highlighting the transformative role DNA sequencing played in solving early problems in eukaryotic cell evolution, and posing key unanswered questions emerging from the age of comparative genomics.
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Endosymbiotic theories for eukaryote origin
TL;DR: A survey of endosymbiotic theories for theorigin of eukaryotes and mitochondria, and for the origin of the eukARYotic nucleus, summarizing the essentials of each and contrasting some of their predictions to the observations is compiled.
Journal ArticleDOI
Archaea and the origin of eukaryotes
TL;DR: A brief history of the changing shape of the tree of life is outlined and how the recent discovery of a myriad of diverse archaeal lineages has changed the authors' understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes is examined.
Journal ArticleDOI
Endosymbiotic theory for organelle origins
TL;DR: Protein import is the strongest evidence the authors have for the single origin of chloroplasts and mitochondria and is probably also the strongestevidence they have to sort out the number and nature of secondary endosymbiotic events that have occurred in evolution involving the red plastid lineage.
Journal ArticleDOI
The Growing Tree of Archaea: New Perspectives on Their Diversity, Evolution and Ecology
TL;DR: The archaeal tree is being rapidly filled up with new branches constituting phyla, classes and orders, generating novel challenges for high-rank systematics, and providing key information for dissecting the origin of this domain, the evolutionary trajectories that have shaped its current diversity, and its relationships with Bacteria and Eukarya.
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