NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE58334 Query DataSets for GSE58334
Status Public on Jun 10, 2014
Title Epigenetics and the Evolution of Darwin’s Finches
Platform organism Taeniopygia guttata
Sample organisms Geospiza fortis; Geospiza fuliginosa; Geospiza scandens; Platyspiza crassirostris; Camarhynchus parvulus
Experiment type Methylation profiling by genome tiling array
Genome variation profiling by genome tiling array
Summary The prevailing theory for the molecular basis of evolution involves genetic mutations that ultimately generate the heritable phenotypic variation on which natural selection acts. However, epigenetic transgenerational inheritance of phenotypic variation may also play an important role in evolutionary change. A growing number of studies have demonstrated the presence of epigenetic inheritance in a variety of different organisms that can persist for hundreds of generations. The possibility that epigenetic changes could accumulate over macroevolutionary time has been considered, but not yet seldom been tested empirically. The current study was designed to compare epigenetic changes among several closely related species of Darwin’s finches, a well-known example of adaptive radiation. Erythrocyte DNA was obtained from five species of sympatric Darwin's finches that vary in phylogenetic relatedness. Genome wide alterations in genetic mutations using copy number variation (CNV) were compared to epigenetic alterations associated with differential DNA methylation regions (epimutations). Epimutations were more common than genetic CNV mutations among the five species; furthermore, the number of epimutations increased monotonically with phylogenetic distance. Interestingly, the number of genetic CNV mutations did not consistently increase with phylogenetic distance. The number, chromosomal locations, regional clustering, and lack of overlap of epimutations and genetic mutations suggests that epigenetic changes are distinct and that they correlate with the evolutionary history of Darwin’s finches. The potential functional significance of the epimutations was explored by comparing their locations on the genome to the location of evolutionarily important genes and cellular pathways in birds. Specific epimutations were associated with genes related to the bone morphogenic protein (BMP), toll receptor, and melanogenesis signaling pathways. Species- specific epimutations were significantly over-represented in these pathways. Since environmental factors are known to rapidly alter heritable changes in the epigenome, it is possible that epigenetic changes have played a contributing role in the molecular basis of the evolution of Darwin's finches.
 
Overall design Erythrocyte DNA was obtained from five species of sympatric Darwin's finches that vary in phylogenetic relatedness. Genome wide alterations in genetic mutations using copy number variation (CNV) were compared to epigenetic alterations associated with differential DNA methylation regions (epimutations).
 
Contributor(s) Skinner MK, Gurerrero-Bosagna C, Haque MM, Nilsson EE, Koop JA, Knutie SA, Clayton DH
Citation(s) 25062919
Submission date Jun 09, 2014
Last update date Sep 09, 2014
Contact name Michael K Skinner
E-mail(s) skinner@mail.wsu.edu
Organization name WSU
Department SBS
Street address Abelson 507
City Pullman
State/province WA
ZIP/Postal code 99163
Country USA
 
Platforms (2)
GPL18772 NimbleGen_Zebra Finch_4.2M array_v3.1
GPL18790 NimbleGen_Zebra Finch_720k_v5.0 tiling array [100713_Tguttata_MS_CGH]
Samples (24)
GSM1407363 CRA2/FOR2_1 (MeDip)
GSM1407364 FUL2/FOR2 _1 (MeDip)
GSM1407365 CRA1/FOR1_1 (MeDip)
Relations
BioProject PRJNA252020

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE58334_RAW.tar 4.3 Gb (http)(custom) TAR (of GFF, PAIR, TXT)
GSE58334_RegionsCombined_CRA_final.csv.gz 115.6 Kb (ftp)(http) CSV
GSE58334_RegionsCombined_FUL_final.csv.gz 128.5 Kb (ftp)(http) CSV
GSE58334_RegionsCombined_PAR_final.csv.gz 68.5 Kb (ftp)(http) CSV
GSE58334_RegionsCombined_SCA_final.csv.gz 37.0 Kb (ftp)(http) CSV
GSE58334_Regions_of_Loss_Gain_Finch_CRA.csv.gz 183.5 Kb (ftp)(http) CSV
GSE58334_Regions_of_Loss_Gain_Finch_FUL.csv.gz 16.0 Kb (ftp)(http) CSV
GSE58334_Regions_of_Loss_Gain_Finch_PAR.csv.gz 15.0 Kb (ftp)(http) CSV
GSE58334_Regions_of_Loss_Gain_Finch_SCA.csv.gz 476.9 Kb (ftp)(http) CSV
Raw data provided as supplementary file
Processed data are available on Series record
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap