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Archaeal "dark matter" and the origin of eukaryotes.

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.

SUBMITTER: Williams TA

PROVIDER: S-EPMC3971582 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature

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Archaeal "dark matter" and the origin of eukaryotes.

Williams Tom A TA Embley T Martin TM

Genome biology and evolution 20140301 3

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 incorp ...[more]

PMID: 24532674

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Project description:In the late 20th century, cosmology became a precision science. Now, at the beginning of the next century, the parameters describing how our universe evolved from the Big Bang are generally known to a few percent. One key parameter is the total mass density of the universe. Normal matter constitutes only a small fraction of the total mass density. Observations suggest this additional mass, the dark matter, is cold (that is, moving nonrelativistically in the early universe) and interacts feebly if at all with normal matter and radiation. There's no known such elementary particle, so the strong presumption is the dark matter consists of particle relics of a new kind left over from the Big Bang. One of the most important questions in science is the nature of this dark matter. One attractive particle dark-matter candidate is the axion. The axion is a hypothetical elementary particle arising in a simple and elegant extension to the standard model of particle physics that nulls otherwise observable CP-violating effects (where CP is the product of charge reversal C and parity inversion P) in quantum chromo dynamics (QCD). A light axion of mass 10(-(6-3)) eV (the invisible axion) would couple extraordinarily weakly to normal matter and radiation and would therefore be extremely difficult to detect in the laboratory. However, such an axion is a compelling dark-matter candidate and is therefore a target of a number of searches. Compared with other particle dark-matter candidates, the plausible range of axion dark-matter couplings and masses is narrowly constrained. This focused search range allows for definitive searches, where a nonobservation would seriously impugn the dark-matter QCD-axion hypothesis. Axion searches use a wide range of technologies, and the experiment sensitivities are now reaching likely dark-matter axion couplings and masses. This article is a selective overview of the current generation of sensitive axion searches. Not all techniques and experiments are discussed, but I hope to give a sense of the current experimental landscape of the search for dark-matter axions.

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Archaeal "dark matter" and the origin of eukaryotes.

Publications

Archaeal "dark matter" and the origin of eukaryotes.

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