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A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data.

D Dalevi, P Hugenholtz, L L Blackall

    International Journal of Systematic and Evolutionary Microbiology
    |April 26, 2001
    PubMed
    Summary

    Choosing reference organisms for prokaryotic evolutionary history is challenging. This study introduces a multiple-outgroup method using 16S ribosomal RNA gene (16S rDNA) data to improve phylogenetic analysis, especially for distantly related bacteria.

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    Area of Science:

    • Microbiology
    • Evolutionary Biology
    • Bioinformatics

    Background:

    • The 16S ribosomal RNA gene (16S rDNA) is a primary marker for prokaryotic phylogeny.
    • Vast numbers of 16S rDNA sequences exist, posing challenges for phylogenetic dataset construction.
    • Dataset composition significantly impacts inferred evolutionary relationships and tree topology.

    Purpose of the Study:

    • To address the dilemma of selecting reference organisms in phylogenetic analysis.
    • To propose and validate a novel multiple-outgroup approach for resolving division-level phylogenetic relationships.
    • To assess the monophyly of bacterial divisions OP9 and OP10 using the proposed method.

    Main Methods:

    • Utilizing a large dataset of 16S rDNA sequences.
    • Implementing a multiple-outgroup strategy in phylogenetic analyses.

    Related Experiment Videos

  • Conducting case studies on bacterial divisions OP9 and OP10.

    • Main Results:

    • Demonstrated that dataset composition affects phylogenetic outcomes, particularly for distantly related sequences.
    • The multiple-outgroup approach provides a robust method for inferring division-level relationships.
    • Case studies illustrated the utility of the method in evaluating the monophyly of proposed bacterial divisions.

    Conclusions:

    • The choice of reference organisms is critical for accurate prokaryotic phylogenetics.
    • A multiple-outgroup approach enhances the reliability of 16S rDNA phylogenetic analyses at the division level.
    • This method aids in clarifying the evolutionary placement of novel bacterial groups.