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

Dataset DOI: 10.5061/dryad.nk98sf85p

## Description of the data and file structure

DNA was extracted from zebra finch blood samples. Enzymatic Methyl-sequencing was used to quantify whole genome methylation. 

### Files and variables

Raw data can be found in [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1108628](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1108628). Bioinformatics pipeline from raw sequencing data to .cov.gz methylation files can be found in [https://zenodo.org/records/12074859](https://zenodo.org/records/12074859)

### File descriptions

**R-Script:** *PhilTrans_DNAm_BroodSize_R1.R*

R code, including all plots and statistical analyses presented in the case study

*Cov_ZF_2023_MalesnoW.rds*

* StartPosition: position of the site
* Endposition: position of site (“StartPosition” and “Endpositio...,