Epigenomics of natural populations: A comparison of effect size and financial costs of sample pooling

In this study, we explore the effects of in vitro library pooling on DNA methylation signatures by using a study system of two invasive freshwater bivalves under pollution treatments. The aims of this study were to: 1) test whether epigenetic signatures of the same samples from in vitro pooled and individual libraries are equivalent; 2) explore differential methylation in response to pollution in the two invasive bivalves.As an empirical dataset, we generated whole-genome methylation data from two invasive freshwater mollusc species (Corbicula fluminea and Dreissena polymorpha) from Lake Maggiore, Italy. For each species, we considered two treatment groups based on water quality (polluted and non-polluted) to compare population-specific methylation data. We found that in vitro pooling effectively captures the global treatment-level differences but there are large differences in the specifics of which loci are deemed to be significantly differentially methylated.