Causes of Variation in the Rate of Molecular Evolution

The genome is an elaborate tapestry of conser- vation and change. The complex patterns of molecular evolution frustrate simple analyses and can obscure the historical narrative recorded in the genome. In addition to differences in patterns and rates of change between different regions of the genome, there are consistent differences in the tempo and mode of molecular evolution among spe- cies. In particular, the fact that species differ in their average rate of molecular evolution makes inference of evolutionary time from genetic divergence very challenging. But vari- ation in the patterns of change between lineages also gives us a rich source of evidence with which to test ideas about the causes of molecular evolutionary change. The genome is not simply a passive recorder of history, but a dynamic engine of change, both creating and responding to a species changing situation over evolutionary time. We need to develop an understanding of the influences on the rates and patterns of molecular evolution if we are to use genomic data to study evolutionary history.