Endocrine and epigenetic flexibility in an African starling

This dataset for the manuscript \"Endocrine and epigenetic flexibility in an African starling\" includes methylation input files derived from Superb starling Reduced Representation Bisulfite Sequencing (RRBS) libraries, and sample collection variables. It includes code for Bismark alignment of bisulfite data, for Metilene differentially methylated region (DMR) analysis (with actual data and randomized sample header runs), CGmapTools variant calling, GEMMA relatedness matrix generation, an R lme4qtl generalized linear mixed model for CpG methylation sites, and bedtools intersection of significant DMRs and CpG sites with genome regions of interest.
, , # Data from: Endocrine and epigenetic flexibility in an African

Dataset DOI: [10.5061/dryad.t4b8gtjff](https://doi.org/10.5061/dryad.t4b8gtjff)

## Description of the data and file structure

Superb starlings were captured across three sites in central Kenya with a gradient of rainfall, and kept in aviaries in the moderate rainfall savanna site. Baseline and stress-induced corticosterone levels were measured by ELISA assay at initial capture, and at 3 and 6 month timepoints in captivity (Table S1 of associated manuscript RSTB-2025-0027.R1). Reduced representation bisulfite sequencing (RRBS) libraries were sequenced for each individual. This data includes sequence processing, methylation analysis, variant calling and relatedness matrix generation.

### Files and variables

#### File: Rubenstein_Solomon_dryad_v2.zip

Zip file with subfolders for each analysis.

**1) alignments_metilene_lme4qtl_run_code_SNP_calling** 

includes raw sequence file trimming trimming_raw_sequencer_fq_files.tx..., , **Changes after Oct 21, 2025:** 

Added Lindner et al. citation from in press manuscript associated with this dataset to readme and to the specific portions of the lme4qtl_R_code.txt that were adapted and modified.