Ecological epigenetics in Timema cristinae stick insects:On the patterns, mechanisms and ecological consequences of DNA methylation in the wild

Epigenetic factors can contribute to phenotypic diversity and to ecological processes. For instance, DNA methylation can influence gene regulation, and thus phenotypic plasticity. However, little is yet known about how and why methylation varies in the wild. In this dissertation, I build on this knowledge by combining ecological, genetic and DNA methylation data from natural and experimental populations of the stick insect Timema cristinae. This species is an important system to ecological genetics studies, which provides good starting point for the investigation of the patterns, drivers, and the possible ecological consequences of natural methylation variation. I obtained methylation data using whole-genome bisulfite sequencing (BS-seq) and genetic data from restriction site associated DNA sequencing (RAD-seq). From a population survey, I found natural methylation variation in T. cristinae (1) is characteristic of “Hemimetabola” insects; (2) is structured in geographical space; and (3) is strongly correlated to genetic variation. In addition, an experiment simulating a host shift was carried out to test for the direct effects of host plant species on T. cristinae methylation levels. In both the population survey and in the experiment, binomial mixed models were used to perform a methylome scan in search of candidate single methylation polymorphisms (SMPs) associated with host plant use. This analysis is analogous to genome-wide analysis studies, but applied to methylation levels. They use genetic data to estimate random effects arising from relatedness. The results suggest (4) an association between methylation levels and host plant in specific regions and that (5) some of them could be responsive to host shift treatment. Finally, the model suggested (6) significant mean heritability of methylation status, estimated based on the genetic relatedness. My results collectively indicate methylation variation could be ecologically relevant to T. cristinae, and adds to the general understanding of the importance of epigenetic variation.