Epigenetic variation reflects dynamic habitat conditions in a rare floodplain herb

Variation of DNA-methylation is thought to play an important role for rapid adjustments of plant populations to dynamic environmental conditions, thus compensating for the relatively slow response time of genetic adaptations. However, genetic and epigenetic variation of wild plant populations has not yet been directly compared in fast changing environments. Here we surveyed populations of Viola elatior from two adjacent habitat types along a successional gradient characterized by strong differences in light availability. Using AFLP and MSAP analyses we found relatively low levels of genetic (H’gen=0.19) and epigenetic (H’epi=0.23) diversity and high genetic (ϕST=0.72) and epigenetic (ϕST=0.51) population differentiation. Diversity and, respectively, differentiation were significantly correlated, suggesting that epigenetic variation partly depends on the same driving forces as genetic variation. Correlation based genome scans detected comparable levels of genetic (17.0%) and epigenetic (14.2%) outlier markers associated with site specific light availability. However, as revealed by separate differentiation based genome scans for AFLP, only few genetic markers seemed to be actually under positive selection (0-4.5%). Moreover, PCoA and Mantel tests showed that overall epigenetic variation was more closely related to habitat conditions, indicating that environmentally-induced methylation changes may lead to convergence of populations experiencing similar habitat conditions and may thus play a major role for the transient and/or heritable adjustment to changing environments. Additionally, using a new MSAP scoring approach, we found that mainly the unmethylated (ϕST=0.60) and CG-methylated states (ϕST=0.46) of epiloci contributed to population differentiation and putative habitat related adaptation, whereas CHG-hemimethylated states (ϕST=0.21) only played a marginal role.

DNA甲基化（DNA-methylation）变异被认为在植物种群快速适应动态环境条件的过程中发挥关键作用，可弥补遗传适应响应速度相对缓慢的不足。然而，目前尚未在快速变化的环境中对野生植物种群的遗传与表观遗传变异开展直接比较研究。本研究针对沿演替梯度分布、光照条件差异显著的两种相邻生境类型的高堇菜（Viola elatior）种群展开调查。通过扩增片段长度多态性（AFLP）与甲基化敏感扩增多态性（MSAP）分析，本研究发现种群的遗传（H’gen=0.19）与表观遗传（H’epi=0.23）多样性水平相对较低，而群体遗传（ϕST=0.72）与表观遗传（ϕST=0.51）分化程度较高。多样性与分化程度分别呈显著相关，这表明表观遗传变异在一定程度上与遗传变异共享相同的驱动因素。基于相关性的基因组扫描检测到与位点特异性光照条件相关的遗传异常位点标记（17.0%）与表观遗传异常位点标记（14.2%）水平相当。然而，针对AFLP的独立分化基因组扫描结果显示，实际处于正向选择的遗传标记仅占极少数（0~4.5%）。此外，主坐标分析（PCoA）与曼特尔检验（Mantel test）结果显示，整体表观遗传变异与生境条件的关联更为紧密，这表明环境诱导的甲基化变化可使经历相似生境条件的种群趋于表型一致，进而在种群对变化环境的短期和/或可遗传适应中发挥核心作用。另外，通过采用新型MSAP评分方法，本研究发现表观遗传位点（epiloci）主要以未甲基化（ϕST=0.60）与CG甲基化（ϕST=0.46）状态参与群体分化及潜在的生境适应性演化，而CHG半甲基化（ϕST=0.21）状态仅发挥微弱作用。