A new view of the tree of life

@article{Hug2016ANV,
  title={A new view of the tree of life},
  author={Laura A. Hug and Brett J. Baker and Karthik Anantharaman and Christopher T. Brown and Alexander J. Probst and Cindy J. Castelle and Cristina N Butterfield and Alex W Hernsdorf and Yuki Amano and Kotaro Ise and Yohey Suzuki and Natasha K. Dudek and David A. Relman and Kari M. Finstad and Ronald Amundson and Brian C. Thomas and Jillian F. Banfield},
  journal={Nature Microbiology},
  year={2016},
  volume={1}
}
The tree of life is one of the most important organizing principles in biology1. Gene surveys suggest the existence of an enormous number of branches2, but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships3–5 or on the known, well-classified diversity of life with an emphasis on eukaryotes6. These approaches overlook the dramatic change in our understanding of life… 

Progress towards the Tree of Eukaryotes

Illuminating the first bacteria

TLDR
A new estimate is provided of the root of the bacterial tree of life, that is, the ancestor from which all bacterial species are derived, and offers glimpses into the nature of the first bacterial cells.

Lifemap: Exploring the Entire Tree of Life

TLDR
Lifemap is a tool allowing the exploration of a complete representation of the ToL in its entirety in a zoomable interface, and should help researchers in ecology and evolutionary biology in their everyday work, but may also permit the diffusion to a broader audience of the authors' current knowledge of the evolutionary relationships linking all organisms.

Lifemap: Exploring the Entire Tree of Life.

TLDR
Lifemap is a tool allowing the exploration of a complete representation of the ToL in its entirety in a zoomable interface, and should help researchers in ecology and evolutionary biology in their everyday work, but may also permit the diffusion to a broader audience of the authors' current knowledge of the evolutionary relationships linking all organisms.

The growing tree of Archaea: new perspectives on their diversity, evolution and ecology

TLDR
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.

Whole-proteome tree of life suggests a deep burst of organism diversity

TLDR
The main features of a whole-proteome ToL for 4,023 species with known complete or almost complete genome sequences on grouping and kinship among the groups at deep evolutionary levels are described.

An estimate of the deepest branches of the tree of life from ancient vertically-evolving genes

TLDR
It is shown that estimates of a reduced Archaea-Bacteria (AB) branch length result from inter-domain gene transfers and hidden paralogy in the expanded marker gene set, and that the AB branch lengths of ribosomal and non-ribosomal marker genes are statistically indistinguishable.

An estimate of the deepest branches of the tree of life from ancient vertically evolving genes

TLDR
It is shown that estimates of a reduced Archaea-Bacteria (AB) branch length result from inter-domain gene transfers and hidden paralogy in the expanded marker gene set, and that the AB branch lengths of ribosomal and non-ribosomal marker genes are statistically indistinguishable.

What is an archaeon and are the Archaea really unique?

TLDR
A case study examines multiple datasets that support contradicting conclusions about the origins and evolution of the Archaea and casts doubt on evolutionary inferences drawn solely from the analyses of a small set of core genes.

Microbial Ecology: Current Advances from Genomics, Metagenomics and Other Omics

TLDR
Traditional taxonomic classification of bacteria could be replaced with a quasispecies model because the cumulative number of new genes discovered increases with the number of genomes studied as a power law and subsequently leads to the lack of evidence for a unique core genome within closely related organisms.
...

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