Linking DNA methylation to localised genetic differentiation in Timema cristinae stick insects

Understanding speciation is a fundamental goal in evolutionary biology. Genome scans of genetic differentiation (FST) have become a cornerstone of speciation research, helping identify genomic regions likely involved in population divergence and speciation. While such studies have advanced our understanding, the relationship between epigenetic mechanisms and genetic differentiation 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 often show greater FST than expected by chance. Strikingly, the magnitude of this accentuation of FST in DMRs 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 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 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.