Johnson Kevin M, Kelly Morgan W
Department of Biological Sciences Louisiana State University Baton Rouge LA USA.
Evol Appl. 2020 Jan 7;13(5):945-959. doi: 10.1111/eva.12912. eCollection 2020 May.
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 () 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 , and DNA methylation differences between oysters inhabiting four estuaries with unique salinity profiles. This approach identified significant population structure despite a moderately low (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 , 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 trends. Our results suggest that may use DNA methylation to generate environmentally responsive plastic phenotypes and that there is more divergence in methylation than divergence in allele frequencies.
种群可能通过进化分歧或表型可塑性对环境异质性做出反应。虽然进化分歧是通过种群间的DNA序列差异发生的，但种群间的可塑性分歧可能由表观基因组的变化产生。在这里，我们展示了墨西哥湾北部四个东部牡蛎（）种群之间DNA甲基化模式和遗传结构的全基因组比较结果。我们结合使用限制性位点相关DNA测序（RADseq）和简化代表性亚硫酸氢盐测序（RRBS）来探索种群结构、全基因范围内的平均值，以及栖息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。尽管在密西西比河的淡水边界处的基因流（0.02）适度较低，但这种方法仍确定了显著的种群结构，这一发现可能反映了最近恢复牡蛎种群数量的努力。种群间CpG甲基化的差异大于基因流的差异，这可能反映了环境对DNA甲基化模式的影响。对所有种群的CpG甲基化模式评估发现，只有26%的甲基化DNA是基因间的；并且，所有差异甲基化区域（DMRs）中只有17%位于这些相同区域内。不同位点基因体内的DMRs与已知参与DNA损伤修复、离子运输和繁殖时间的基因相关。最后，当评估这些种群之间基因组变异与DNA甲基化之间的相关性时，我们观察到了种群特异性的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基因流趋势没有直接关联。我们的结果表明，可能利用DNA甲基化来产生对环境有响应的可塑性表型，并且甲基化的差异比等位基因频率的差异更大。
