DOI: 10.5061/dryad.2d80m
title: Data from: Resource base influences genome-wide DNA methylation levels in wild baboons (Papio cynocephalus)

description: Variation in resource availability commonly exerts strong effects on
 fitness-related traits in wild animals. However, we know little about the
 molecular mechanisms that mediate these effects, or about their
 persistence over time. To address these questions, we profiled genome-wide
 whole blood DNA methylation levels in two sets of wild baboons: (i)
 ‘wild-feeding’ baboons that foraged naturally in a savanna environment and
 (ii) ‘Lodge’ baboons that had ready access to spatially concentrated human
 food scraps, resulting in high feeding efficiency and low daily travel
 distances. We identified 1,014 sites (0.20% of sites tested) that were
 differentially methylated between wild-feeding and Lodge baboons,
 providing the first evidence that resource availability shapes the
 epigenome in a wild mammal. Differentially methylated sites tended to
 occur in contiguous stretches (i.e., in differentially methylated regions
 or DMRs), in promoters and enhancers, and near metabolism-related genes,
 supporting their functional importance in gene regulation. In agreement,
 reporter assay experiments confirmed that methylation at the largest
 identified DMR, located in the promoter of a key glycolysis-related gene,
 was sufficient to causally drive changes in gene expression. Intriguingly,
 all dispersing males carried a consistent epigenetic signature of their
 membership in a wild-feeding group, regardless of whether males dispersed
 into or out of this group as adults. Together, our findings support a role
 for DNA methylation in mediating ecological effects on phenotypic traits
 in the wild, and emphasize the dynamic environmental sensitivity of DNA
 methylation levels across the life course.
description: total_read_countsNumber of reads mapped to a given location in the genome for a given individual. Sites included in this dataset represent the set of filtered sites we analyzed to produce our main results.methylated_read_countsNumber of methylated reads mapped to a given location in the genome for a given individual. Sites included in this dataset represent the set of filtered sites we analyzed to produce our main results.Lea_et_al_MACAU_outputThe beta (effect size), standard error, p-value, and FDR corrected value for each CpG site tested in our dataset. These are the results from a model, run in the program MACAU, testing for effects of resource base on DNA methylation levels while controlling for genetic relatedness, sex, age of the blood sample, age of the individual, and bisulfite conversion rate.counts_tables_columnsA file noting which individual appears in which column of the methylated and total read counts tables. The individual identifiers in this file are consistent with the identifiers in Table S2.cell_type_countsCounts of Basophils, Eosinophils, Neutrophils, Lymphocytes, and Monocytes obtained from blood smears. Whether an individual was a member of the Lodge group is noted (where Y=yes, the individual was a member of this group; and N=no, the individual was a member of a wild-feeding group).