Populations may respond to environmental heterogeneity via evolutionary divergence or phenotypic plasticity. While evolutionary divergence occurs through DNA sequence differences among populations, plastic divergence among populations may be generated by changes in the epigenome. Here, we present the results of a genome‐wide comparison of DNA methylation patterns and genetic structure among four populations of Eastern oyster (Crassostrea virginica) in the northern Gulf of Mexico. We used a combination of restriction site‐associated DNA sequencing (RADseq) and reduced representation bisulfite sequencing (RRBS) to explore population structure, gene‐wide averages of F_ST, and DNA methylation differences between oysters inhabiting four estuaries with unique salinity profiles. This approach identified significant population structure despite a moderately low F_ST (0.02) across the freshwater boundary of the Mississippi river, a finding that may reflect recent efforts to restore oyster stock populations. Divergence between populations in CpG methylation was greater than for divergence in F_ST, likely reflecting environmental effects on DNA methylation patterns. Assessment of CpG methylation patterns across all populations identified that only 26% of methylated DNA was intergenic; and, only 17% of all differentially methylated regions (DMRs) were within these same regions. DMRs within gene bodies between sites were associated with genes known to be involved in DNA damage repair, ion transport, and reproductive timing. Finally, when assessing the correlation between genomic variation and DNA methylation between these populations, we observed population‐specific DNA methylation profiles that were not directly associated with single nucleotide polymorphisms or broader gene‐body mean F_ST trends. Our results suggest that C. virginica may use DNA methylation to generate environmentally responsive plastic phenotypes and that there is more divergence in methylation than divergence in allele frequencies.

中文翻译：

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墨西哥北部湾东部牡蛎Crassostrea virginica的种群表观遗传差异超过遗传差异。

种群可能通过进化差异或表型可塑性来应对环境异质性。虽然进化差异是通过种群之间的DNA序列差异发生的，但种群之间的可塑性差异可能是由表观基因组的变化产生的。在这里，我们介绍了墨西哥北部墨西哥湾东部牡蛎（Crassostrea virginica）的四个种群之间全基因组DNA甲基化模式和遗传结构的比较结果。我们结合了限制性位点相关的DNA测序（RADseq）和减少的代表性亚硫酸氢盐测序（RRBS）来研究群体结构，F _ST的全基因平均值，以及居住在四个具有独特盐度分布的河口的牡蛎之间的DNA甲基化差异。尽管密西西比河淡水边界的F _ST适度较低（0.02），但该方法仍能识别出明显的种群结构，这一发现可能反映了最近为恢复牡蛎种群而进行的努力。人群之间CpG甲基化的差异大于F _ST的差异，可能反映了环境对DNA甲基化模式的影响。对所有人群的CpG甲基化模式进行评估后发现，只有26％的甲基化DNA是基因间的。而且，所有差异甲基化区域（DMR）中只有17％位于这些相同区域内。位点之间的基因体内的DMR与已知与DNA损伤修复，离子转运和生殖时间有关的基因有关。最后，在评估这些人群之间的基因组变异与DNA甲基化之间的相关性时，我们观察到了特定于人群的DNA甲基化谱，这些谱与单核苷酸多态性或更广泛的基因体平均F _ST趋势不直接相关。我们的结果表明维吉尼亚衣原体 可能使用DNA甲基化产生对环境敏感的塑料表型，并且甲基化的差异大于等位基因频率的差异。