Data from: Phenotypic plasticity evolves at multiple biological levels in response to environmental predictability in a long-term experiment with a halotolerant microalga

Phenotypic plasticity, the change in the phenotype of a given genotype in response to its environment of development, is a ubiquitous feature of life, enabling organisms to cope with variation in their environment. Theoretical studies predict that, under stationary environmental variation, the level of plasticity should evolve to match the predictability of selection at the timing of development. However, the extent to which patterns of evolution of plasticity for more integrated traits are mirrored by their underlying molecular mechanisms remains unclear, especially in response to well-characterized selective pressures exerted by environmental predictability. Here, we used experimental evolution with the microalgae <em>Dunaliella salina</em> under controlled environmental fluctuations, to test whether the evolution of phenotypic plasticity in responses to environmental predictability (as measured by the squared autocorrelation <em>ρ</em>^<em>2</em>) occurred across biological levels, going from DNA methylation to gene expression to cell morphology. Transcriptomic analysis indicates clear effects of salinity and <em>ρ</em>^<em>2</em>×salinity interaction on gene expression, thus identifying sets of genes involved in plasticity and its evolution. These transcriptomic effects were independent of DNA methylation changes in <em>cis.</em> However we did find <em>ρ</em>^<em>2</em><em>-</em>specific responses of DNA methylation to salinity change, albeit weaker than for gene expression. Overall, we found consistent evolution of reduced plasticity in less predictable environments for DNA methylation, gene expression, and cell morphology. Our results provide the first clear empirical signature of plasticity evolution at multiple levels in response to environmental predictability, and highlight the importance of experimental evolution to address predictions from evolutionary theory, as well as investigate the molecular basis of plasticity evolution.

表型可塑性（phenotypic plasticity）指特定基因型在发育环境响应下的表型变化，是生命普遍存在的特征，使生物能够应对所处环境的变异。理论研究预测，在稳定环境变异条件下，可塑性水平应演化至匹配发育时刻选择的可预测性。然而，对于更具整合性的性状，其可塑性演化模式在多大程度上能被其潜在分子机制所反映，目前仍不清楚，尤其是在响应由环境可预测性所施加的已被充分表征的选择压力的情境中。本研究通过对盐藻（Dunaliella salina）开展受控环境波动下的实验演化，验证针对环境可预测性（以平方自相关系数ρ²衡量）的表型可塑性演化是否跨多个生物层级发生，即从DNA甲基化（DNA methylation）、基因表达到细胞形态。转录组学分析显示，盐度以及盐度与ρ²的交互作用对基因表达具有显著影响，由此鉴定出参与可塑性及其演化的基因集。这些转录组学效应与顺式（cis）作用的DNA甲基化变化无关。不过，我们确实发现了ρ²特异性的DNA甲基化对盐度变化的响应，尽管其强度弱于基因表达层面的响应。总体而言，我们在DNA甲基化、基因表达与细胞形态三个层级均发现，在可预测性更低的环境中，可塑性出现降低的一致性演化模式。本研究结果首次在多个层级上提供了响应环境可预测性的可塑性演化的明确实验证据，并凸显了实验演化方法在验证演化理论预测以及探究可塑性演化分子基础方面的重要价值。