Dissecting plant responses to the environment is key to understanding whether and how plants adapt to anthropogenic climate change. Stomata, plants’ pores for gas exchange, are expected to decrease in density following increased CO₂ concentrations, a trend already observed in multiple plant species. However, it is unclear whether such responses are based on genetic changes and evolutionary adaptation. Here we make use of extensive knowledge of 43 genes in the stomatal development pathway and newly generated genome information of 191 Arabidopsis thaliana historical herbarium specimens collected over 193 years to directly link genetic variation with climate change. While we find that the essential transcription factors SPCH, MUTE and FAMA, central to stomatal development, are under strong evolutionary constraints, several regulators of stomatal development show signs of local adaptation in contemporary samples from different geographic regions. We then develop a functional score based on known effects of gene knock-out on stomatal development that recovers a classic pattern of stomatal density decrease over the past centuries, suggesting a genetic component contributing to this change. This approach combining historical genomics with functional experimental knowledge could allow further investigations of how different, even in historical samples unmeasurable, cellular plant phenotypes may have already responded to climate change through adaptive evolution.

剖析植物对环境的反应是了解植物是否以及如何适应人为气候变化的关键。气孔是植物进行气体交换的孔隙，随着CO ₂浓度的增加，气孔的密度预计会降低，这一趋势已经在多种植物物种中观察到。然而，目前尚不清楚这种反应是否基于遗传变化和进化适应。在这里，我们利用气孔发育途径中 43 个基因的广泛知识以及 193 年来收集的 191 个拟南芥历史植物标本的新生成的基因组信息，将遗传变异与气候变化直接联系起来。虽然我们发现气孔发育的核心转录因子 SPCH、MUTE 和 FAMA 受到强烈的进化限制，但气孔发育的几个调节因子在来自不同地理区域的当代样本中显示出局部适应的迹象。然后，我们根据基因敲除对气孔发育的已知影响开发了一个功能评分，该评分恢复了过去几个世纪气孔密度下降的经典模式，表明导致这种变化的遗传成分。这种将历史基因组学与功能实验知识相结合的方法可以进一步研究即使在不可测量的历史样本中，细胞植物表型可能已经通过适应性进化对气候变化做出了何种不同的反应。