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Estimating selection by comparing synonymous and substitutional changes

J M Smith1

  • 1School of Biological Sciences, University of Sussex, Brighton, United Kingdom.

Journal of Molecular Evolution
|August 1, 1994
PubMed
Summary
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A neutral mutation model explains higher amino acid substitutions between species. This finding challenges previous evidence for positive selection, especially in distantly related organisms like Neisseria.

Area of Science:

  • Evolutionary biology
  • Molecular evolution
  • Population genetics

Background:

  • Higher ratios of amino acid substitutions to synonymous changes between species often indicate positive selection.
  • This observation has been a cornerstone for inferring adaptive amino acid evolution.

Purpose of the Study:

  • To propose and test a neutral mutation model that can explain the observed patterns of substitution rates.
  • To re-evaluate the interpretation of substitution rate differences between species.

Main Methods:

  • Development of a mathematical model for neutral mutations approaching steady-state.
  • Comparative analysis of substitution rates (substitutional vs. synonymous) in Neisseria species.
  • Comparison of model predictions with empirical data.

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Main Results:

  • The neutral mutation model successfully explains the higher ratio of substitutional to synonymous changes in between-species comparisons.
  • Data from Neisseria are consistent with this neutral model, where substitutions are twice as frequent relative to synonymous changes.
  • The model's validity depends on the evolutionary distance between compared species.

Conclusions:

  • Observed differences in substitution rates between species do not solely provide evidence for positive selection.
  • Neutral evolutionary processes can generate these patterns, particularly in distantly related species.
  • Evidence for positive selection may still be valid for closely related species, as in Drosophila.