Toward Automatic Reconstruction of a Highly Resolved Tree of Life

@article{Ciccarelli2006TowardAR,
  title={Toward Automatic Reconstruction of a Highly Resolved Tree of Life},
  author={Francesca D. Ciccarelli and Tobias Doerks and Christian von Mering and Christopher J. Creevey and Berend Snel and Peer Bork},
  journal={Science},
  year={2006},
  volume={311},
  pages={1283 - 1287}
}
We have developed an automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains. The tree has its basis in a concatenation of 31 orthologs occurring in 191 species with sequenced genomes. It revealed interdomain discrepancies in taxonomic classification. Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing us to confirm accepted relationships and resolve disputed… 
A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life
TLDR
A novel phylogenetic approach (Nested Phylogenetic Reconstruction) in which each tree node is optimized based on the genes shared at that taxonomic level is presented, which enables the reconstruction and continuous update of highly-resolved phylogenies of sequenced organisms.
Tree of Life Based on Genome Context Networks
TLDR
This paper has devised a distance-based strategy to reconstruct a highly resolved backbone tree of life, on the basis of the genome context networks of 195 fully sequenced representative species, and demonstrates the feasibility of the reconstruction of highly resolved phylogenetic tree with extensible gene networks across all three domains of life.
Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea
TLDR
These findings provide a robust and standardized framework for multidomain phylogenetic reconstruction that can be used to evaluate inter-phylum relationships and assess uncertainty in conflicting topologies of the Tree of Life.
Estimation of phylogenetic inconsistencies in the three domains of life.
TLDR
Lateral gene transfer between distant prokaryotic species may have been more rare than previously thought, which opens the way to obtain the tree of life of bacterial and archaeal species using genomic data and the concatenation of adequate genes, in the same way as it is usually done in eukaryotes.
The eukaryotic tree of life from a global phylogenomic perspective.
  • Fabien Burki
  • Biology
    Cold Spring Harbor perspectives in biology
  • 2014
TLDR
The pros and cons of phylogenomics are discussed and the eukaryotic supergroups are reviewed in light of earlier work that laid the foundation for the current view of the tree, including the position of the root.
Ordered orthology as a tool in prokaryotic evolutionary inference
  • S. Snir
  • Biology
    Mobile genetic elements
  • 2016
TLDR
A method to infer evolutionary relationships among closely related species where the conventional evolutionary markers do not provide a strong enough signal is developed, which relies on the loss of synteny, gene order conservation among species that provides a stronger signal, sufficient to classify even strains of a given species.
Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny.
It has recently been proposed that a well-resolved Tree of Life can be achieved through concatenation of shared genes. There are, however, several difficulties with such an approach, especially in
Drawing the tree of eukaryotic life based on the analysis of 2,269 manually annotated myosins from 328 species
TLDR
This approach is expected to result in superior accuracy compared to single-gene or phylogenomic analyses because the orthology problem is resolved and a strong determinant not depending on any technical uncertainties is incorporated, the class distribution.
Integrating Markov clustering and molecular phylogenetics to reconstruct the cyanobacterial species tree from conserved protein families.
TLDR
By integrating phylogenetic data inferred for upward of 1,000 protein-coding genes common to all or most cyanobacteria, this work has reconstructed an evolutionary history of the phylum, establishing a framework for resolving key issues regarding the evolution of their metabolic and phenotypic diversity.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 80 REFERENCES
Phylogenomics and the reconstruction of the tree of life
TLDR
This work has demonstrated the power of the phylogenomics approach, which has the potential to provide answers to several fundamental evolutionary questions, but challenges for the future have also been revealed.
Phylogenetics and the Cohesion of Bacterial Genomes
TLDR
Although comparisons of complete gene inventories indicate appreciable gain and loss of genes, orthologs available for phylogenetic reconstruction are consistent with a single tree.
Phylogenetic Classification and the Universal Tree
TLDR
Molecular phylogeneticists will have failed to find the “true tree,” not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.
Universal trees based on large combined protein sequence data sets
TLDR
Combined protein universal trees are highly congruent with SSU rRNA trees in their strong support for the separate monophyly of domains as well as the early evolution of thermophilic Bacteria.
Horizontal gene transfer and phylogenetics.
The new animal phylogeny: reliability and implications.
TLDR
DNA sequence analysis dictates new interpretation of phylogenic trees and forces us to rethink the genesis of bilaterian complexity.
Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales?
TLDR
It is indicated that the placement of N. equitans in archaeal phylogenies on the basis of ribosomal protein concatenation may be strongly biased by the coupled effect of its above-average evolutionary rate and lateral gene transfers.
Towards a Genome-Based Taxonomy for Prokaryotes
TLDR
The AAI-based approach provides a means to evaluate the robustness of alternative genetic markers for phylogenetic purposes, and could contribute significantly to a genome-based taxonomy for all microbial organisms.
The New View of Animal Phylogeny
TLDR
The evidence supporting the current understanding of metazoan phylogeny is discussed on a clade by clade basis, supported by molecular and morphological data.
Detection of Seven Major Evolutionary Lineages in Cyanobacteria Based on the 16S rRNA Gene Sequence Analysis with New Sequences of Five Marine Synechococcus Strains
TLDR
Analysis of 16S rRNA gene phylogeny by the maximum-likelihood and neighbor-joining methods combined with rate homogeneous and heterogeneous models revealed seven major evolutionary lineages of the cyanobacteria, including prochlorophycean organisms.
...
1
2
3
4
5
...