Inferences from epigenetic information in an ecological context: A case study of DNA methylation and early-life environmental effects on zebra finches

DNA methylation (DNAm) is known to affect gene expression and has been suggested as a putative mechanism through which environmental factors can continuously shape phenotypic variation. DNAm data can be assessed using a variety of approaches, ranging from single-nucleotide resolution to the development of composite indexes, each providing unique insights. Utilizing whole-genome, longitudinal DNAm data from adult zebra finches raised in either small or large broods, we present a case study aimed at exploring how to utilize DNAm data to not only assess environmental effects on the epigenome but also to develop tools to directly measure those effects. Specifically, we (i) identified CpG sites where DNAm differed significantly between adult zebra finches raised in small and large broods, (ii) developed a phenotypic index using the methylation of the differentially methylated sites, and (iii) using an elastic net regression predicted brood size from methylation. Our findings suggest that early-life environment can lead to long-term differences in the DNAm of specific CpG sites and generate phenotypic variation. These methylation signatures can be leveraged to develop scalable tools to predict phenotypic quality and fitness outcomes as well as retroactively quantify stress.