Phylogenetic association mapping (PAM) can unravel the genetic basis of species differences, however, successful reports are still scarce. Here we correlated gene copy-number differences across 47 Brassicaceae species to two variable traits, leaf shape and mutation rates. This revealed a previously described gene required for complex leaf shapes, and a significant association between CG?TG mutations and CHROMOMETHLYASE 3. Species without CMT3 lack gene-body methylation and show reduced mutation rates most likely due to lower mutability of non-methylated cytosines. This coincidence implies an evolutionary trade-off between functional gene body methylation and low mutation rates and demonstrates the huge potential of PAM.