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.混血个体的适合度（fitness）降低通常归因于遗传不相容性（genetic incompatibilities）。尽管基因组不匹配可引发适合度改变，但部分案例中杂交适合度的下降幅度较为细微。转录调控（transcriptional regulation）在混血基因组中的潜在作用，或可为这类差异提供机制性解释，但目前针对非模式生物的相关证据仍较为匮乏。本研究针对西部灰狼与西部郊狼的实验杂交后代所构建的混血基因组，探讨了遗传学与基因调控的交叉关联。我们发现甲基化（methylation）水平与灰狼祖先组分间存在显著正相关关系，并鉴定出此前被报道与近交相关或存在其他有害表型的离群基因。我们揭示了一种由种间杂交驱动的、位点特异性而非全基因组范围的甲基化模式。据此表明，表观遗传变异（epigenetic variation）可通过潜在的转录机制，在维持与拮抗不匹配基因型两方面发挥不可忽视的作用。综上，基因表达调控是杂交基因组功能中一个长期被低估的关键组分，同时也可能成为杂交后代产生新颖且有益的适应性变异的潜在来源。