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Integrated genomic and fossil evidence illuminates life's early evolution and eukaryote origin.

TLDR
The last universal common ancestor of cellular life is found to have predated the end of late heavy bombardment, and a timescale of life is derived, combining a reappraisal of the fossil material with new molecular clock analyses.
Abstract
Establishing a unified timescale for the early evolution of Earth and life is challenging and mired in controversy because of the paucity of fossil evidence, the difficulty of interpreting it and dispute over the deepest branching relationships in the tree of life. Surprisingly, it remains perhaps the only episode in the history of life where literal interpretations of the fossil record hold sway, revised with every new discovery and reinterpretation. We derive a timescale of life, combining a reappraisal of the fossil material with new molecular clock analyses. We find the last universal common ancestor of cellular life to have predated the end of late heavy bombardment (>3.9 billion years ago (Ga)). The crown clades of the two primary divisions of life, Eubacteria and Archaebacteria, emerged much later (<3.4 Ga), relegating the oldest fossil evidence for life to their stem lineages. The Great Oxidation Event significantly predates the origin of modern Cyanobacteria, indicating that oxygenic photosynthesis evolved within the cyanobacterial stem lineage. Modern eukaryotes do not constitute a primary lineage of life and emerged late in Earth’s history (<1.84 Ga), falsifying the hypothesis that the Great Oxidation Event facilitated their radiation. The symbiotic origin of mitochondria at 2.053–1.21 Ga reflects a late origin of the total-group Alphaproteobacteria to which the free living ancestor of mitochondria belonged.

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Journal ArticleDOI

The New Tree of Eukaryotes

TL;DR: The combination of traditional culturing with maturing culture-free approaches and phylogenomics should accelerate the process of completing and resolving the eukaryote Tree of Life at its deepest levels.
Journal ArticleDOI

Phylogenomics provides robust support for a two-domains tree of life

TL;DR: It is found that eukaryotes consistently originate from within the archaea in a two-domains tree when due consideration is given to the fit between model and data.
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Origin and evolution of the plant immune system

TL;DR: The ancient associations between plants and microbes as well as the evolutionary principles underlying plant-pathogen interactions are discussed and the current knowledge on the origin and evolution of key components of the plant immune system is synthesized and reviewed.
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Nonenzymatic Metabolic Reactions and Life's Origins.

TL;DR: This review discusses metabolic pathways of relevance to the origin of life in a manner accessible to chemists, and summarizes experiments suggesting several pathways might have their roots in prebiotic chemistry.
Journal ArticleDOI

A one-billion-year-old multicellular chlorophyte.

TL;DR: Filamentous macrofossils from the one-billion-year-old Nanfen Formation of northern China are interpreted as a new species of early multicellular green algae, suggesting that chlorophytes acquired macroscopic size,Multicellularity and cellular differentiation nearly a billion years ago, much earlier than previously thought.
References
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Journal Article

R: A language and environment for statistical computing.

R Core Team
- 01 Jan 2014 - 
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Journal ArticleDOI

Basic Local Alignment Search Tool

TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI

MUSCLE: multiple sequence alignment with high accuracy and high throughput

TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Journal ArticleDOI

PAML 4: Phylogenetic Analysis by Maximum Likelihood

TL;DR: PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML), which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses.
Journal ArticleDOI

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

TL;DR: TrimAl is a tool for automated alignment trimming, which is especially suited for large-scale phylogenetic analyses and can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized.
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