The molecular basis of evolutionary change is assumed to be genetic variation. However, growing evidence suggests that epigenetic mechanisms, such as DNA methylation, may also be involved in evolutionary change. An important first step in evaluating this hypothesis is to test for the presence of epigenetic variation between natural populations living under different environmental conditions. In the current study we explored variation between populations of Darwin’s finches living in adjacent “urban” and “rural” environments on Santa Cruz Island in the Galápagos. We tested for morphological, genetic, and epigenetic differences between the urban and rural populations of each of two species of ground finches, Geospiza fortis and G. fuliginosa. Using data collected from more than 1000 birds, we found significant morphological differences between populations of G. fortis, but not G. fuliginosa. We did not find genetic differences between populations of either species, based on comparisons of copy number variation (CNV). In contrast, we did find epigenetic differences between the urban and rural populations of both species, based on DNA methylation analysis. We explored genomic features and gene associations of the differentially methylated regions (DMR), as well as their possible functional significance. In summary, our study documents local population epigenetic variation within species of Darwin’s finches.
Overall design: Red blood cell and sperm samples were collected from two species of finch (Geospiza fortis and Geospiza fuliginosa) from two different locations (rural and urban). Samples from individual birds were combined into pooled samples for sequencing. For erythrocyte samples, three pools of five individuals each were created for each site. For sperm samples, three pools of two individuals each were created for each site. The methylation characteristics of the pooled samples was estimated using a methylated DNA immunoprecipitation (MeDIP) followed by PE50 sequencing on an Illumina HiSeq 2500 platform.
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