Epigenetic variation between urban and rural populations of Darwin’s finches

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-1025-9) contains supplementary material, which is available to authorized users.

Avian ecological epigenetics: pitfalls and promises

“…This difference in methylation between bold and shy types was not found in a forest population (Riyahi et al 2015). A later study found differences in DNA methylation levels and morphological features between rural and urban populations of Darwin's finches (Geospiza fortis and Geospiza fuliginosa) (McNew et al 2017). In contrast to genetic variation (Bonduriansky and Day 2009;Ledon-Rettig et al 2013;Price et al 2003), epigenetic variation may enable organisms to adjust their phenotype to match novel environments, or provide them with the ability to quickly respond to a changing environment (Jablonka and Lamb 2007;Tammen et al 2013).…”

Genome‐wide variation in DNA methylation is associated with stress resilience and plumage brightness in a wild bird

“…In our population, both plumage brightness and negative feedback predict stress resilience (Taff et al, , ; Zimmer et al, ), but the two traits are only weakly correlated, further supporting the idea that they might contribute to variation in resilience through different mechanisms. Most prior studies that use a similar MeDIP approach have also focused on categorical traits that might be expected to have large‐scale consequences on methylation throughout the genome, such as urban versus rural populations (McNew et al, ), sister species (Skinner et al, ) and rearing conditions (Pertille et al, ). To our knowledge, no other studies to date have used MeDIP to examine differences in glucocorticoid regulation.…”

“…The level of fragmentation and total length of our assembly are similar to the 45 avian genomes published by Zhang et al (), albeit with a slightly shorter scaffold N50. One of these genomes was used by McNew et al () in a MeDIP analysis comparing rural and urban Geospiza fortis individuals. The average and standard deviation for comparable statistics from the Zhang et al () genomes is 1.1 ± 0.1 Gb in length, with N50s of 21.2 ± 7.7 Kb (contig) and 1.7 ± 2.4 Mb (scaffold).…”

“…The average and standard deviation for comparable statistics from the Zhang et al () genomes is 1.1 ± 0.1 Gb in length, with N50s of 21.2 ± 7.7 Kb (contig) and 1.7 ± 2.4 Mb (scaffold). The statistics for the Geospiza fortis genome used by McNew et al () are as follows: length 1.07 Gbp, 30 kb contig N50 and 5.2 mb scaffold N50. To assess completeness, we searched for 4,915 single‐copy vertebrate loci using busco version 3.0.2 (Simão et al, ).…”

“…We prepared libraries from each of the 24 samples after immunoprecipitation. Because the final product of the immunoprecipitation is single‐stranded DNA, we used the NEBNext ® Ultra™ RNA Library Prep Kit for Illumina, starting at step 1.4 to create double‐stranded DNA and using 13 μl of the eluted DNA from the immunoprecipitation as the starting input (as in McNew et al, ). The rest of the library preparation was completed exactly as described in the manufacturer's protocol.…”