DNA methylation differences between stick insect ecotypes

Abstract

Epigenetic mechanisms, such as DNA methylation, can influence gene regulation and affect phenotypic variation, raising the possibility that they contribute to ecological adaptation. Beginning 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 the CpG context. We report an overall genome‐wide methylation level for T. cristinae of ~14%, with methylation 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 and genetic relatedness, and with the ecologically important variable of host plant, suggests a potential role for epigenetic modification in T. cristinae adaptation. To substantiate such adaptive significance, future studies could test whether methylation can be transmitted across generations and the extent to which it responds to experimental manipulation in field and laboratory studies.

The contribution of epigenetic variation to evolution in crows

“…Furthermore, as our primary interest is on DNA methylation divergence between taxa, integrating two metrics of taxonomic divergence (i.e., parental comparisons in two experiments and hybrid index in another) will identify sites verifiably corresponding to taxonomic divergence. While financial constraints may cause our study to miss small-effect DNA methylation loci due to sample size limitations, our sample size within each experiment matches those in other WGBS [72][73][74][75][76] and RRBS [77][78][79][80][81] studies. Our multiexperimentally validated approach offers a novel framework to assess both inter-experimental batch effects and repeatability in a conservative framework, and our preferred approach in contrast to an approach which maximizes DMP discovery at the cost of false positives.…”

Complementary genetic and epigenetic changes facilitate rapid adaptation to multiple global change stressors

“…The interaction between plasticity and adaptation is an integral component underlying resilience, or lack thereof, of populations to rapidly changing environments. While authors have studied how these components interact during adaptation across natural environmental gradients ( 10, 21, 22 ), limited work has focused on how epigenetic and genetic changes might drive phenotypic responses during evolutionary rescue from global change. Our results show that epigenetic and genetic changes are negatively related and affect unique regions of the genome (Fig.…”