Understanding speciation is a fundamental goal in evolutionary biology. Genomic regions of accentuated differentiation among populations often reveal patterns and mechanisms of species formation. While substantial progress has been achieved on this front for genetic variation, the contribution of epigenetic mechanisms to divergence patterns remains unclear. Here, we present evidence that DNA methylation is associated with regions exhibiting accentuated genetic differentiation between populations of Timema cristinae stick insects. We do so by integrating analyses of differentially methylated regions (DMRs) between individuals from different host-plant species with genomic sequencing. Our results reveal that DMRs exhibit accentuated genetic differentiation (FST) between populations. Strikingly, the strength of this association increases with the geographical distance between populations. We present results evaluating the contributions of mutation, reduced recombination, gene flow and selection to these divergence patterns. The overall results are consistent with a role for a balance between selection and gene flow, a finding further supported by evidence for selection in a previously-published survival field experiment. Nevertheless, details of our results suggest that selection on DMRs might be indirect and not strictly host-related. Our results establish associations between methylation and genetic change, but further work is required to clarify the exact causes of this association. Nonetheless, our results provide insight into how the interplay of epigenetic and genetic variation may influence population divergence and potentially contribute to speciation.

Epigenetic mechanisms, such as DNA methylation, can influence gene regulation and affect phenotypic variation, raising the possibility that they contribute to ecological adaptation. To being to address this issue requires high-resolution sequencing studies of natural populations to pinpoint epigenetic regions of potential ecological and evolutionary significance. However, such studies are still relatively uncommon, especially in insects, and are mainly restricted to a few model organisms. Here, we characterize patterns of DNA methylation for natural populations of Timema cristinae adapted to two host plant species (i.e., ecotypes). By integrating results from sequencing of whole transcriptomes, genomes, and methylomes, we investigate whether environmental, host, and genetic differences of these stick insects are associated with methylation levels of cytosine nucleotides in CpG context. We report an overall genome-wide methylation level for T. cristinae of ~14%, being enriched in gene bodies and impoverished in repetitive elements. Genome-wide DNA methylation variation was strongly positively correlated with genetic distance (relatedness), but also exhibited significant host-plant effects. Using methylome-environment association analysis, we pinpointed specific genomic regions that are differentially methylated between ecotypes, with these regions being enriched for genes with functions in membrane processes. The observed association between methylation variation with genetic relatedness and the ecologically-important variable of host plant suggest a potential role for epigenetic modification in T. cristinae adaptation. To substantiate such adaptive significance, future studies could test if methylation has a heritable component and the extent to which it responds to experimental manipulation in field and laboratory studies.