Data from: 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.