Data from: Genome-wide epigenetic isolation by environment in a widespread Anolis lizard

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.