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Universal trees based on large combined protein sequence data sets.

J R Brown1, C J Douady, M J Italia

  • 1Anti-Microbial Bioinformatics Group, GlaxoSmithKline,1250 South Collegeville Road, UP1345 P.O. Box 5089, Collegeville, Pennsylvania 19426-0989, USA. James_R_Brown@gsk.com

Nature Genetics
|June 30, 2001
PubMed
Summary
This summary is machine-generated.

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Universal trees of life, reconstructed using combined protein data, strongly support separate domains (Archaea, Bacteria, Eucarya). This research clarifies the early evolution of thermophilic Bacteria.

Area of Science:

  • * Molecular Biology
  • * Evolutionary Biology
  • * Bioinformatics

Background:

  • * Small-subunit ribosomal RNA (SSU rRNA) trees traditionally support distinct domains of life: Archaea, Bacteria, and Eucarya.
  • * Protein-based phylogenetic trees have challenged this view, suggesting intermixing between domains, possibly due to horizontal gene transfer or signal degradation.
  • * Reconciling these conflicting tree topologies is crucial for understanding universal evolutionary history.

Purpose of the Study:

  • * To construct robust universal phylogenetic trees using large alignments of conserved orthologous proteins.
  • * To investigate the monophyly of the three domains of life and the placement of early bacterial lineages.
  • * To assess the impact of potential horizontal gene transfer on phylogenetic reconstructions.

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Main Methods:

  • * Construction of large, combined alignments of 23 orthologous proteins from 45 species across all domains.
  • * Generation of universal phylogenetic trees using these combined protein data sets.
  • * Analysis of tree topologies, including the impact of removing potential horizontally transferred genes.

Main Results:

  • * Combined protein data strongly support the monophyly of the Archaea, Bacteria, and Eucarya domains.
  • * Initial analyses placed spirochaetes as the earliest derived bacterial group.
  • * Removing nine protein data sets, suspected of horizontal gene transfer, shifted the earliest bacterial lineage to thermophiles, aligning with SSU rRNA tree findings.

Conclusions:

  • * Combined protein analyses provide robust support for the distinct evolutionary paths of Archaea, Bacteria, and Eucarya.
  • * The early evolution of thermophilic Bacteria is supported by phylogenetic trees constructed with careful consideration of horizontal gene transfer.
  • * These findings reinforce the congruence between SSU rRNA and protein-based universal tree reconstructions.