Epigenetic changes can provide a pathway for organisms to respond to local environmental conditions by influencing gene expression.  However, we still know little about the spatial distribution of epigenetic variation in natural systems, how it relates to the distribution of genetic variation and the environmental structure of the landscape, and the processes that generate and maintain it.  Studies examining spatial patterns of genetic and epigenetic variation can provide valuable insights into how ecological and population processes contribute to epigenetic divergence across heterogeneous landscapes.  Here, we perform a comparative analysis of spatial genetic and epigenetic variation based on 8,459 single nucleotide polymorphisms (SNPs) and 8,580 single methylation variants (SMVs) from eight populations of the Puerto Rican crested anole, Anolis cristatellus, an abundant lizard in the adaptive radiations of anoles on the Greater Antilles that occupies a diverse range of habitats.  Using generalized dissimilarity modeling and multiple matrix regression, we found that genome-wide epigenetic differentiation is strongly correlated with environmental divergence, even after controlling for the underlying genetic structure.  We also detected significant associations between key environmental variables and 96 SMVs, including 42 located in promoter regions or gene bodies.  Our results suggest an environmental basis for population-level epigenetic differentiation in this system and contribute to better understanding how environmental gradients structure epigenetic variation in nature.

Environmental PC Rasters

Principal component rasters for the bioclimate data from the WorldClim database are provided in GeoTIFF format.  The extent of each raster covers the whole island of Puerto Rico.

SNP Data

SNP data are provided in structure format, with samples on two rows.

SMV Data

Single methylation variant (SMV) data are provided in CSV format.  Samples are on two rows; C calls are the first row, and T calls are the second row.  The first column is the sample number.