Making inference about the functional properties of a genomic region from patterns of substitution rates requires calibration to adjust for complexity in the mutation spectra. Rates of substitution are demonstrably heterogeneous across the genome in mammals and between mammal lineages. We have several projects underway that aim to dissect the causes of these important patterns. These efforts are focussed on the properties of DNA that make it particularly prone to mutation, and the influence of DNA replication/DNA repair systems. Of particular interest is the modified nucleotide mC (5-methyl-cytosine), which plays a critical role in mammal developmental biology and also exhibits a very high mutation rate. Published outcomes of this work demonstrate the striking influence of mC on genomic diversity, and reveal a cost to methylation of the protein coding gene BRCA1.