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Testing the covarion hypothesis of molecular evolution

M M Miyamoto¹, W M Fitch

¹Department of Zoology, University of Florida, Gainesville 32611, USA.

Molecular Biology and Evolution

|May 1, 1995

Summary

The covarion hypothesis better explains molecular evolution than the gamma model by accounting for changing mutation rates at specific sites. Analysis of Cu, Zn superoxide dismutase (SOD) in mammals and plants supports this finding.

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Area of Science:

Molecular Evolution
Biophysics

Background:

The covarion hypothesis posits that mutation fixation probabilities change over time.
Testing this hypothesis with sequence divergence is challenging due to similar predictions from rate variation models like the gamma distribution.
Previous models did not adequately account for rate fluctuations among sites over evolutionary time.

Purpose of the Study:

To differentiate between the covarion hypothesis and the gamma model of molecular evolution.
To investigate the conservation and variation patterns in Cu, Zn superoxide dismutase (SOD) protein sequences between mammals and plants.

Main Methods:

Comparative analysis of varied and unvaried codons in mammalian and plant SOD protein sequences.
Simulation analyses to compare covarion and gamma model predictions.
Examination of SOD tertiary structure to assess variability distribution.

Main Results:

The covarion hypothesis provided a better prediction of shared varied and unvaried codon frequencies between mammals and plants than the gamma model.
Mammalian and plant SOD protein structures exhibit different patterns of variability.
The analysis revealed distinct sets of variable and invariable codons in mammal and plant SODs.

Conclusions:

The covarion model offers a superior explanation for the evolution of Cu, Zn superoxide dismutase compared to the gamma model.
The covarion hypothesis's ability to incorporate rate fluctuations over time is crucial for understanding molecular evolution.
Variable and invariable codons in mammal and plant SODs are not conserved, supporting the covarion model.

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