Data from: The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves

• Main Authors: Janowitz Koch, Ilana, Creek, Michelle M., Thompson, Michael J., Deere-Machemer, Kerry A., Wang, Jun, Duarte, Lionel, Gnanadesikan, Gitanjali E., McCoy, Eskender L., Rubbi, Liudmilla, Stahler, Daniel R., Pellegrini, Matteo, Ostrander, Elaine A., Wayne, Robert K., Sinsheimer, Janet S., VonHoldt, Bridgett M., Clark, Michelle M.
• Format: Dataset
• Language: unknown
• Published: Dryad Digital Repository 2019
• Subjects: Domestication; Methylation; Genome Regulation; Canid; Life sciences; medicine and health care; psy; envir; Canis lupus
• Online Access: https://doi.org/10.5061/dryad.q2g6h

The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits observed in domesticated species. Here, we explored methylation differences from >24 000 cytosines distributed across the genomes of the domesticated dog (Canis familiaris) and the grey wolf (Canis lupus). PCA and model-based cluster analyses identified two primary groups, domestic vs. wild canids. A scan for significantly differentially methylated sites (DMSs) revealed species-specific patterns at 68 sites after correcting for cell heterogeneity, with weak yet significant hypermethylation typical of purebred dogs when compared to wolves (59% and 58%, P 66%) of differentially methylated regions contained or were associated with repetitive elements, indicative of a genotype-mediated trend. However, DMSs were also often linked to functionally relevant genes (e.g. neurotransmitters). Finally, we utilized known genealogical relationships among Yellowstone wolves to survey transmission stability of methylation marks, from which we found a substantial fraction that demonstrated high heritability (both H2 and h2 > 0.99). These analyses provide a unique epigenetic insight into the molecular consequences of recent selection and radiation of our most ancient domesticated companion, the dog. These findings suggest selection has acted on methylation patterns, providing a new genomic perspective on phenotypic diversification in domesticated species. GO gene lists_NeutralityThe gene IDs that were used for the GO analyses for the Neutrality results.EWAsher_GOA list of our genes used for GO analyses (from the list of 68 outliers) with the background list that we used in the second tab.Epigenotype_FilesEpigenotype variant files used for ADMIXTURE, dendrograms, and PCAEpigenotype_File.xlsxBS-Seeker_Log_FilesBS-Seeker results log files ...