Abstract
BackgroundThe 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 rapid adaptation to new environments. 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.ResultsIn the current study we explored variation between populations of Darwin’s finches, which comprise one of the best-studied examples of adaptive radiation. We tested for morphological, genetic, and epigenetic differences between adjacent “urban” and “rural” populations of each of two species of ground finches, Geospiza fortis and G. fuliginosa, on Santa Cruz Island in the Galápagos. 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 large size copy number variation (CNV) genetic differences between populations of either species. However, other genetic variants were not investigated. In contrast, we did find dramatic 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 DNA methylated regions (DMR), as well as their possible functional significance.ConclusionsIn summary, our study documents local population epigenetic variation within each of two species of Darwin’s finches.
Highlights
IntroductionGrowing evidence suggests that epigenetic mechanisms, such as DNA methylation, may be involved in rapid adaptation to new environments
The molecular basis of evolutionary change is assumed to be genetic variation
Urbanization is associated with a shift in the distribution of beak size in G. fortis: beak size is strongly bimodal at the rural site, whereas bimodality has decreased at the urban site concurrently with human population growth [35]
Summary
Growing evidence suggests that epigenetic mechanisms, such as DNA methylation, may be involved in rapid adaptation to new environments. Studies of the molecular basis of evolutionary change have focused almost exclusively on genetic mechanisms. Recent work suggests that heritable modifications to gene expression and function, independent of changes to DNA sequence, may be involved in the evolution of phenotypes [1,2,3]. Methylation can be induced by the environment and affect gene expression and phenotypic traits without changing the DNA sequence itself [5,6,7,8]. Some patterns of methylation are Environmentally-induced epimutations may be a component of the adaptive radiation of closely related species to new environments [17]. The results of this study suggest that epigenetic changes accumulate over macroevolutionary time and further suggest that epigenetic changes may contribute to the evolution of adaptive phenotypes
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