The proteins of linked genes evolve at similar rates

Much more variation in the rate of protein evolution occurs than is expected by chance1. But why some proteins evolve rapidly but others slowly is poorly resolved. It was proposed, for example, that essential genes might evolve slower than dispensable ones2, but this is not the case3; and despite earlier claims4, rates of evolution do not correlate with amino-acid composition5. A few patterns have been found: proteins involved in antagonistic co-evolution (for example, immune genes3,6, parasite antigens7 and reproductive conflict genes8,9,10) tend to be rapidly evolving, and there is a correlation between the rate of protein evolution and the mutation rate of the gene1,11,12. Here we report a new highly statistically significant predictor of a protein's rate of evolution, and show that linked genes have similar rates of protein evolution. There is also a weaker similarity of rates of silent site evolution (see ref. 13), which appears to be, in part, a consequence of the similarity in rates of protein evolution. The similarity in rates of protein evolution is not a consequence of underlying mutational patterns. A pronounced negative correlation between the rate of protein evolution and a covariant of the recombination rate indicates that rates of protein evolution possibly reflect, in part, the local strength of stabilizing selection.