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Nematode small subunit phylogeny correlates with alignment parameters.

Ashleigh B Smythe1, Michael J Sanderson, Steven A Nadler

  • 1Department of Nematology, University of California, One Shields Avenue, Davis, California 95616, USA. smythea@si.edu

Systematic Biology
|March 10, 2007
PubMed
Summary

Nematode small subunit ribosomal RNA (SSU rRNA) phylogenies are sensitive to alignment parameters. Removing ambiguous regions reduces this bias, leading to more reliable evolutionary trees for Nematoda.

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Area of Science:

  • Molecular evolution
  • Phylogenetics
  • Bioinformatics

Background:

  • Nuclear small subunit (SSU) ribosomal RNA (rRNA) sequences are increasingly used for nematode phylogeny construction.
  • Alignment of these sequences is crucial but has received limited attention.
  • Understanding alignment sensitivity is vital for accurate phylogenetic inference.

Purpose of the Study:

  • To investigate the impact of alignment parameters on nematode SSU rRNA phylogenies.
  • To assess the effect of removing alignment-ambiguous regions on phylogenetic stability.
  • To determine how alignment choices influence evolutionary tree construction for nematodes.

Main Methods:

  • Generated ten alignments using CLUSTAL W with varying parameters.
  • Created reduced alignments by removing ambiguous regions and culled alignments from these regions.

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  • Performed phylogenetic analyses using maximum parsimony, neighbor-joining, and bootstrap methods.
  • Compared resulting phylogenies using the symmetric difference metric (SymD).

    • Main Results:

    • Phylogenetic trees from full and culled alignments showed significant correlation with alignment parameters.
    • Reduced alignments exhibited less correlation, indicating bias reduction.
    • Majority-rule consensus trees from full alignments were sensitive to alignment parameters, unlike those from reduced or culled alignments.

    Conclusions:

    • Alignment parameter choice can bias nematode SSU rRNA phylogenies.
    • Removing alignment-ambiguous regions mitigates this bias, improving phylogenetic reliability.
    • Conservative phylogenetic hypotheses for Nematoda are achievable through careful alignment and data curation.