Interrogation of chromatin modifications, such as DNA methylation, has
potential to improve forecasting and conservation of marine ecosystems.
The standard method for assaying DNA methylation (Whole Genome Bisulfite
Sequencing), however, is too costly to apply at the scales required for
ecological research. Here we evaluate different methods for measuring
DNA methylation for ecological epigenetics. We compare Whole Genome
Bisulfite Sequencing (WGBS) with Methylated CpG Binding Domain
Sequencing (MBD-seq), and a modified version of MethylRAD we term
methylation-dependent Restriction site-Associated DNA sequencing
(mdRAD). We evaluate these three assays in measuring variation in
methylation across the genome, between genotypes, and between polyp
types in the reef-building coral Acropora millepora. We find that all
three assays measure absolute methylation levels similarly, with tight
correlations for methylation of gene bodies (gbM), as well as exons and
1Kb windows. Correlations for differential gbM between genotypes were
weaker, but still concurrent across assays. We detected little to no
reproducible differences in gbM between polyp types. We conclude that
MBD-seq and mdRAD are reliable cost-effective alternatives to WGBS.
Moreover, the considerably lower sequencing effort required for mdRAD to
produce comparable methylation estimates makes it particularly useful
for ecological epigenetics.