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Phylogenetic classification and the universal tree.

W F Doolittle1

  • 1Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada. ford@is.dal.ca

Science (New York, N.Y.)
|June 26, 1999
PubMed
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Molecular phylogeneticists created a universal tree of life using gene sequences. However, widespread lateral gene transfer challenges the idea of a single tree, suggesting life's history is more complex than a hierarchy.

Area of Science:

  • Evolutionary Biology
  • Molecular Phylogenetics
  • Genomics

Background:

  • Molecular phylogeneticists have used nucleotide sequences of ribosomal RNAs and proteins to construct a "universal tree of life."
  • This tree has served as the foundation for a "natural" hierarchical classification of all living organisms.
  • Recent findings have introduced uncertainties regarding the accuracy of some early branches of this tree.

Purpose of the Study:

  • To evaluate the impact of evidence suggesting widespread gene acquisition from multiple sources on the concept of a universal tree of life.
  • To determine if a hierarchical classification based on molecular sequences remains valid in light of extensive chimerism and lateral gene transfer.

Main Methods:

  • Comparative analyses of nucleotide sequences of genes encoding ribosomal RNAs and proteins.

Related Experiment Videos

  • Assessment of evidence for chimerism and lateral gene transfer across archaeal, bacterial, and inferred ancestral eukaryotic genomes.

    • Main Results:

    • Evidence indicates that most archaeal and bacterial genomes, as well as the inferred ancestral eukaryotic nuclear genome, contain genes from multiple sources.
    • Lateral gene transfer and chimerism appear to be significant factors, not trivial in extent or limited to specific gene categories.
    • The history of life may not be accurately representable as a single, hierarchical tree.

    Conclusions:

    • A strictly hierarchical "natural" classification based on a universal tree of life may not be achievable due to extensive lateral gene transfer.
    • The "true tree" of life may be elusive not due to methodological flaws but because the evolutionary history is not strictly treelike.
    • Molecular sequence-based taxonomies remain indispensable tools for biological classification and understanding evolutionary processes.