Phylogenomics and the reconstruction of the tree of life

@article{Delsuc2005PhylogenomicsAT,
  title={Phylogenomics and the reconstruction of the tree of life},
  author={Fr{\'e}d{\'e}ric Delsuc and Henner Brinkmann and Herv{\'e} Philippe},
  journal={Nature Reviews Genetics},
  year={2005},
  volume={6},
  pages={361-375}
}
As more complete genomes are sequenced, phylogenetic analysis is entering a new era — that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms on the basis of the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to several fundamental evolutionary questions. However, challenges for the future have also been revealed. The very nature of the evolutionary… 
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.
3 Phylogenomics for the Study of Fungal Biology
TLDR
An overview of how different phylogenomic approaches can be used to address the study of fungal biology is provided, including the establishment of the phylogenetic position of a newly sequenced species, the detection of past evolutionary events shaping a given genome, or the prediction of putative functions of uncharacterized proteins.
Advances in phylogenomics.
TLDR
The mechanism, speed, accuracy, applicable range, and their application of these methods are summarized and the prospects of phylogenomics and challenges that it is faced with are discussed.
Histories of molecules: Reconciling the past.
The New Tree of Eukaryotes.
Phylogeny and Evolution
TLDR
Two major cellular systems of parasitological relevance, mitochondrion-related organelles and endocytic systems, will be explored, highlighting where considering the genomics and molecular cell biology of parasites in the context of their emergence from free-living relatives have helped us to better understand organelle evolution.
Phylogenomics, Protein Family Evolution, and the Tree of Life: An Integrated Approach between Molecular Evolution and Computational Intelligence
TLDR
The application of phylogenomics (phylogenetics and genomics) is focused on to improve functional prediction of genes and gene products, to understand the evolution of protein families, and to resolve phylogenetic relationships of organisms.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 246 REFERENCES
Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species
TLDR
The study of the dependence of the genomes' tree accuracy on the number of exons used, demonstrated that an unexpectedly larger number of characters are necessary to obtain robust phylogenies.
A phylogenomic approach to microbial evolution.
TLDR
The complete set of phylogenetic trees derived from the proteome of an organism as the phylome is defined and the term phylogenetic connection as a concept that describes the relative relationships between taxa in a tree is introduced.
Rooting the Eukaryote Tree by Using a Derived Gene Fusion
TLDR
It is shown that all eukaryote groups ancestrally with two cilia (bikonts) are evolutionarily derived and the root lies between bIKonts and opisthokonts (animals, Fungi, Choanozoa).
Horizontal gene transfer and phylogenetics.
Genome-scale approaches to resolving incongruence in molecular phylogenies
TLDR
The results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies, and have important implications for resolving branches of the tree of life.
Whole genome-based phylogenetic analysis of free-living microorganisms.
TLDR
A phylogenetic 'tree of life' has been constructed based on the observed presence and absence of families of protein-encoding genes observed in 11 complete genomes of free-living microorganisms, indicating a single robust underlying evolutionary history for these organisms.
From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria
TLDR
The analysis indicates that single-copy orthologous genes are resistant to horizontal transfer, even in ancient bacterial groups subject to high rates of LGT, thus establishing a foundation for reconstructing the evolutionary transitions that underlie diversity in genome content and organization.
A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history.
TLDR
An attempt to use a supertree method to build the phylogenetic tree of 45 organisms, with special focus on bacterial phylogeny, by performing a phylogenetic study of congruence of tree topologies, which allows the identification of a core of genes supporting similar species phylogeny.
Genome trees and the tree of life.
...
1
2
3
4
5
...