Data from: Ancestry-specific methylation patterns in admixed offspring from an experimental coyote and gray wolf cross

Reduced fitness of admixed individuals is typically attributed to genetic
incompatibilities. Although mismatched genomes can lead to fitness
changes, in some cases the reduction in hybrid fitness is subtle. The
potential role of transcriptional regulation in admixed genomes could
provide a mechanistic explanation for these discrepancies, but evidence is
lacking for non-model organisms.Here, we explored the intersection of
genetics and gene regulation in admixed genomes derived from an
experimental cross between a western gray wolf and western coyote. We
found a significant positive association between methylation and wolf
ancestry, and identified outlier genes that have been previously
implicated in inbreeding-related, or otherwise deleterious, phenotypes. We
describe a pattern of site-specific, rather than genome-wide, methylation
driven by inter-specific hybridization. Epigenetic variation is thus
suggested to play a non-trivial role in both maintaining and combating
mismatched genotypes through putative transcriptional mechanisms. We
conclude that the regulation of gene expression is an underappreciated key
component of hybrid genome functioning, but could also act as a potential
source of novel and beneficial adaptive variation in hybrid offspring.