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Testing for covarion-like evolution in protein sequences.

Huai-Chun Wang1, Matthew Spencer, Edward Susko

  • 1Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada. hcwang@mathstat.dal.ca

Molecular Biology and Evolution
|October 24, 2006
PubMed
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The covarion hypothesis explains changing evolutionary rates at molecular sites. A new general model improves upon existing methods by allowing rates to switch between variable and invariable states, better fitting complex evolutionary data.

Area of Science:

  • Molecular Evolution
  • Phylogenetics
  • Computational Biology

Background:

  • The covarion hypothesis posits that selective pressures change over time, leading to variable evolutionary rates across phylogenetic tree branches.
  • Existing Markov models for the covarion process include Huelsenbeck's (2002) model with discrete gamma distribution and Galtier's (2001) model with unrestricted rate class switching.

Purpose of the Study:

  • To propose and implement a general covarion model integrating features of previous models.
  • To allow evolutionary rates to switch between variable and invariable states and among different variable rates.
  • To evaluate the performance of the general covarion model against simpler models using empirical protein data.

Main Methods:

  • Implementation of three covarion models (Huelsenbeck's, Galtier's, and the general model) within a maximum likelihood framework.

Related Experiment Videos

  • Application of these models to 23 diverse protein sequence data sets.
  • Comparative analysis of model fit using likelihood scores.

    • Main Results:

    • All three covarion models demonstrated significant improvements in fit compared to a model without site-specific rate variation.
    • The proposed general covarion model provided a superior fit to the data in most cases compared to the simpler covarion models.
    • These findings underscore the intricate nature of modeling the covarion process.

    Conclusions:

    • The general covarion model offers a more robust approach to modeling molecular evolution with changing rates.
    • This model has potential applications in phylogenetic tree topology comparisons, molecular dating, and studying protein adaptation.
    • The study highlights the importance of complex models for accurately capturing evolutionary dynamics.