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Series GSE87825 Query DataSets for GSE87825
Status Public on Jan 07, 2017
Title Epigenetic variation between urban and rural populations of Darwin’s finches
Organisms Geospiza fortis; Geospiza fuliginosa
Experiment type Methylation profiling by high throughput sequencing
Summary 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.
Contributor(s) McNew SM, Beck D, Sadler-Riggleman I, Knutie SA, Koop JA, Clayton DH, Skinner MK
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Submission date Oct 11, 2016
Last update date May 15, 2019
Contact name Michael K Skinner
Organization name WSU
Department SBS
Street address Abelson 507
City Pullman
State/province WA
ZIP/Postal code 99163
Country USA
Platforms (2)
GPL22544 Illumina HiSeq 2500 (Geospiza fortis)
GPL22545 Illumina HiSeq 2500 (Geospiza fuliginosa)
Samples (24)
GSM2341389 FB1
GSM2341390 FB2
GSM2341391 FB3
BioProject PRJNA347828
SRA SRP091389

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Supplementary file Size Download File type/resource
GSE87825_allForRBC.results.csv.gz 473.0 Mb (ftp)(http) CSV
GSE87825_allForSperm.results.csv.gz 406.8 Mb (ftp)(http) CSV
GSE87825_allFulRBC.results.csv.gz 423.7 Mb (ftp)(http) CSV
GSE87825_allFulSperm.results.csv.gz 484.1 Mb (ftp)(http) CSV
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