Data from: Fine-scale population epigenetic structure in relation to gastro-intestinal parasite load in red grouse (Lagopus lagopus scotica)

Epigenetic modification of cytosine methylation states can be elicited by environmental stresses and may be a key process affecting phenotypic plasticity and adaptation. Parasites are potent stressors with profound physiological and ecological effects on their host, but there is little understanding in how parasites may influence host methylation states. Here, we estimate epigenetic diversity and differentiation among 21 populations of red grouse (Lagopus lagopus scotica) in north-east Scotland, and test for association of gastro-intestinal parasite load (caecal nematode Trichostrongylus tenuis) with hepatic genome-wide and locus-specific methylation states. Following methylation-sensitive AFLP (MSAP), 129 bands, representing 73 methylation-susceptible and 56 non-methylated epiloci, were scored across 234 individuals. The populations differed significantly in genome-wide methylation levels and were also significantly epigenetically (FST = 0.0227; p < 0.001) and genetically (FST = 0.0058; p < 0.001) differentiated. Parasite load was not associated with either genome-wide methylation levels or epigenetic differentiation. Instead, we found eight disproportionately differentiated epilocus-specific methylation states (FST -outliers) using bayescan software and significant positive and negative association of 35 methylation states with parasite load from bespoke generalised estimating equations (GEE), simple logistic regression (sam) and Bayesian environmental analysis (bayenv). Following Sanger sequencing, genome mapping and geneontology (go) annotation, some of these epiloci were linked to genes involved in regulation of cell cycle, signalling, metabolism, immune system and notably rRNA methylation, histone acetylation and small RNAs. These findings demonstrate an epigenetic signature of parasite load in populations of a wild bird and suggest intriguing physiological effects of parasite-associated cytosine methylation.

Raw presence/absence scores of MSAP bands: This file contains the raw scores of 129 MSAP bands scored across 234 red grouse individuals. Use this file as input for the R package "msap" to do basic methylation analyses.
msap_raw_scores.csv:

Transformed MSAP scores and morphological data: This file contains 303 epiloci that were generated by transforming 129 MSAP bands into binary loci. The file also provides morphological data in order to do regression analyses.
msap_transformed_scores.txt

Nomenclature for MSAP bands and corresponding epiloci: Contains identifiers for each MSAP band and each corresponding epilocus alongside represented methylation state (unmethylated, hemimethylated, fully methylated)
locus_ids.txt

Pairwise geographic distances: Contains a matrix with pairwise geographic distances among the 21 study populations.
geo_distances.txt

Complete R analysis script: Contains R code for analysing the input files using "msap" and custom logistic regressions.
R_analysis.r

Readme: Details file contents

This work is licensed under a CC0 1.0 Universal (CC0 1.0) Public Domain Dedication license.