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DEX: a consensus-based amino acid exchangeability measure for improved codon substitution modelling.

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We compared 30 amino acid distance measures for molecular evolution models. The new DEX measure, a consensus of experimental data, best predicts codon substitution patterns across diverse species.

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Area of Science:

  • Molecular Evolution
  • Genomics
  • Bioinformatics

Background:

  • Amino acid similarity is crucial for understanding molecular evolution, yet existing distance measures are underutilized due to a lack of consensus on accuracy.
  • Physicochemically similar amino acids exhibit more frequent substitutions, but quantifying these relationships for evolutionary modeling remains challenging.

Purpose of the Study:

  • To systematically compare the performance of 30 amino acid distance measures in molecular evolution models.
  • To introduce a novel, improved amino acid distance measure based on recent deep mutational scanning data.
  • To evaluate the utility of variant effect predictors versus amino acid distance measures in predicting substitution frequencies.

Main Methods:

  • Assessed 30 amino acid distance measures, including a new deep mutational scanning-derived measure, against codon substitution models.
  • Utilized alignments from diverse lineages (Streptococcus, Drosophila, mammals) and variant data (E. coli, human).
  • Employed the DISTATIS approach to construct and test consensus measures from top-performing individual measures.

Main Results:

  • Experimentally-derived amino acid distance measures, particularly the new measure and the existing experimental exchangeability (EX) measure, demonstrated the best fit to codon substitution patterns.
  • A consensus measure, named DEX, combining the new measure and EX, performed optimally across diverse datasets.
  • Site-specific variant effect predictors were less effective than amino acid distance measures for predicting mean substitution frequencies but informative for identifying highly deleterious mutations.

Conclusions:

  • The DEX measure offers an improved, general-purpose tool for molecular evolution models, outperforming existing measures in fitting substitution patterns.
  • Experimentally-derived measures are superior for capturing evolutionary substitution dynamics compared to traditional physicochemical measures.
  • While variant effect predictors have distinct applications, amino acid distance measures remain essential for large-scale evolutionary analyses.