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Related Experiment Videos

Bacterial molecular phylogeny using supertree approach.

V Daubin1, M Gouy, G Perrière

  • 1Laboratoire de Biometrie et Biologie Eolutive, UMR CNRS 5558, Universite Claude Bernard - Lyon 1, 43 bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France. daubin@biomserv.univ-lyon1.fr

Genome Informatics. International Conference on Genome Informatics
|January 16, 2002
PubMed
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A novel supertree method resolves prokaryotic phylogeny using gene family trees, challenging the thermophilic origin hypothesis and the complexity hypothesis for core genes.

Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Complete genome sequences offer potential for clarifying organismal phylogeny, but efficient data utilization remains a challenge.
  • Existing methods like gene presence/absence coding or sequence concatenation have limitations in capturing phylogenetic information and evolutionary rates.
  • Building consensus trees is hindered by the limited number of shared genes across diverse organisms.

Purpose of the Study:

  • To develop and apply a new supertree construction method for robust phylogenetic analysis of completely sequenced genomes.
  • To investigate the phylogenetic relationships of 33 prokaryotes and four eukaryotes using a large dataset of gene family trees.
  • To test key hypotheses regarding the origin of life and the nature of core genes in prokaryotes.

Main Methods:

Related Experiment Videos

  • Utilized a supertree approach to integrate information from hundreds of gene family trees.
  • Constructed a robust supertree representing the phylogeny of 33 prokaryotes and four eukaryotes.
  • Analyzed orthologous gene families from completely sequenced genomes.

Main Results:

  • Generated a robust supertree demonstrating the feasibility of prokaryotic species phylogeny.
  • Challenged the hypothesis of a thermophilic origin for bacteria and present-day life.
  • Results support a core gene set with rare lateral transfers but question the complexity hypothesis regarding informational processes.

Conclusions:

  • Supertree construction from gene family trees provides a powerful method for robust phylogenetic inference.
  • The study provides evidence against a thermophilic origin of life, suggesting alternative evolutionary scenarios.
  • The findings necessitate a re-evaluation of the role of core genes and the complexity hypothesis in prokaryotic evolution.