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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
This summary is machine-generated.

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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.

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.