Do methylation changes drive the adaptation to altered light environment in guppies?

Guppy populations have been propagated under altered light conditions for ~20 generations resulting in diverging sexually selected phenotypic adaptations. The genotypic changes in the guppy populations have been identified, however the degree to which epigenetic changes contribute to the phenotypic divergences was completely unknown. To investigate the degree to which DNA methylation changes are responsible for creating the adaptations which have arisen in this experimental evolution research, the methylome of the guppy populations were sequenced. Once the data was processed and its quality confirmed, a differential methylation analysis was performed on multiple levels and using two different bioinformatics tools, methylkit and dmrseq. An enrichment analysis was performed to gain greater insight into the alterations of specific biological functions. The dmrseq based differential methylation analysis yielded no significant results whereas the methylkit based differential methylation analysis yielded thousands. The enrichment analysis using Cluster Profiler identified many significantly enriched and notable results. The results of this project suggest that methylation changes contribute to phenotypic adaptations in guppy populations which have been bred under altered light conditions. This provides evidence that methylation changes have the potential to contribute to short scale evolution in vertebrates.