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…
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References
SHOWING 1-10 OF 246 REFERENCES
Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species
- BiologyISMB/ECCB
- 2004
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.
Molecular phylogenetics: state-of-the-art methods for looking into the past.
- BiologyTrends in genetics : TIG
- 2001
A phylogenomic approach to microbial evolution.
- BiologyNucleic acids research
- 2001
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
- BiologyScience
- 2002
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).
Genome-scale approaches to resolving incongruence in molecular phylogenies
- BiologyNature
- 2003
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.
- BiologyNucleic acids research
- 1999
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
- BiologyPLoS biology
- 2003
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.
- BiologyGenome research
- 2002
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.