Cytochrome b evolution in birds and mammals: An evaluation of the avian constraint hypothesis

Patterns of molecular evolution in birds have long been considered anomalou s. Compared with other vertebrates, birds have reduced levels of genetic di vergence between groups of similar taxonomic ranks for a variety of nuclear and mitochondrial markers. This observation led to the avian constraint hy pothesis, which identifies increased functional constraint on avian protein s as the cause for the reduction in genetic divergence. Subsequent investig ations provided additional support for the avian constraint hypothesis when rates of molecular evolution were found to be slower in birds than in mamm als in a variety of independent calibrations. It is possible to test the av ian constraint hypothesis as an explanation for this avian slowdown by comp aring DNA sequence data from protein-coding regions in birds and homologous regions in mammals. The increased selective constraints should lead to a r eduction in the proportion of amino acid replacement substitutions. To test for such a decrease, we calculated the numbers of amino acid replacement s ubstitutions per replacement site (d(N)) and silent substitutions per silen t site (d(S)) for the complete mitochondrial cytochrome b gene using 38 avi an and 43 mammalian comparisons that were phylogenetically independent. We find that d(N)/d(S) is significantly smaller in birds than in mammals. This difference cannot be explained by differences in codon bias affecting d(S) values. We suggest that the avian slowdown can be explained, at least in p art, by a decreased tolerance for amino acid substitutions in avian species relative to mammalian species.