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Related Experiment Videos

Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions.

P G Foster1, D A Hickey

  • 1Department of Biology, University of Ottawa, Ontario, Canada.

Journal of Molecular Evolution
|March 27, 1999
PubMed
Summary

Compositional bias in DNA can skew phylogenetic analyses. This bias also affects protein sequences, leading to incorrect evolutionary trees even with advanced methods, highlighting the need for caution in protein-based phylogenetics.

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Area of Science:

  • Evolutionary Biology
  • Bioinformatics
  • Molecular Phylogenetics

Background:

  • DNA sequence compositional bias is known to impact phylogenetic analysis.
  • Protein sequence analysis is often preferred to circumvent DNA bias issues.
  • A correlation exists between nucleotide bias and amino acid composition, suggesting secondary protein bias.

Purpose of the Study:

  • To investigate if DNA compositional bias can also affect protein sequences and subsequent phylogenetic analyses.
  • To demonstrate the impact of such bias on established phylogenetic reconstruction tools.
  • To evaluate methods for mitigating bias in protein-based phylogenetics.

Main Methods:

  • Analysis of complete animal mitochondrial protein-coding sequences.
  • Application of common phylogenetic inference tools.

Related Experiment Videos

  • Testing of LogDet/paralinear transformation and removal of biased positions.
  • Examination of sequence data with significant AT/GC compositional bias.

    • Main Results:

    • Common phylogenetic tools failed to recover the correct evolutionary tree from protein-coding sequences.
    • Statistically well-supported but incorrect trees were consistently generated.
    • Neither LogDet/paralinear transform nor removal of biased sites corrected the tree topology.
    • Taxa with significant compositional bias erroneously grouped together, irrespective of true relatedness.

    Conclusions:

    • DNA compositional bias can induce protein bias, misleading phylogenetic analyses based on protein sequences.
    • Protein-based phylogenetic trees can be unreliable, especially with compositionally biased data.
    • Caution is advised in phylogenetic reconstruction using protein sequences due to potential biases.