Data from: Genome-wide signature of local adaptation linked to variable CpG methylation in oak populations

It has long been known that adaptive evolution can occur through genetic
mutations in DNA sequence, but it is unclear whether adaptive evolution
can occur through analogous epigenetic mechanisms, such as through DNA
methylation. If epigenetic variation contributes directly to evolution,
species under threat of disease, invasive competition, climate change or
other stresses would have greater stores of variation from which to draw.
We looked for evidence of natural selection acting on variably methylated
DNA sites using population genomic analysis across three climatologically
distinct populations of valley oaks. We found patterns of genetic and
epigenetic differentiations that indicate local adaptation is operating on
large portions of the oak genome. While CHG methyl polymorphisms are not
playing a significant role and would make poor targets for natural
selection, our findings suggest that CpG methyl polymorphisms as a whole
are involved in local adaptation, either directly or through linkage to
regions under selection.