TESTING THE COVARION HYPOTHESIS OF MOLECULAR EVOLUTION

The covarion hypothesis of molecular evolution states that the fixatio n of mutations may alter the probability that any given position will fix the next change. Tests of this hypothesis using the divergence of real sequences are compromised because models of rate variation among sites (e.g., the gamma version of the one-parameter equation) predict sequence divergence values similar to those for the covarion process. This study therefore focuses on the extent to which the varied and unv aried codons of two well-diverged taxa are the same, because fewer are expected by the covarion hypothesis than by the gamma model. The data for these tests are the protein sequences of Cu, Zn superoxide dismut ase (SOD) for mammals and plants. Simulation analyses show that the co varion hypothesis makes better predictions about the frequencies of va ried and unhit positions in common between these two taxa than does th e gamma version of the one-parameter model. Furthermore, the analysis of SOD tertiary structure demonstrates that mammal and plant variabili ties are distributed differently on the protein. These results support the conclusions that the variable and invariable codons of mammal and plant SODs are different and that the covarion model explains the evo lution of this protein better than the gamma version of the one-parame ter process. Unlike other models, the covarion hypothesis accounts for rate fluctuations among positions over time, which is an important pa rameter of molecular evolution.