Closely related species often use the same genes to adapt to similar environments. However, we know little about why such genes possess increased adaptive potential and whether this is conserved across deeper evolutionary lineages. Adaptation to climate presents a natural laboratory to test these ideas, as even distantly related species must contend with similar stresses. Here, we re-analyse genomic data from thousands of individuals from 25 plant species as diverged as lodgepole pine and Arabidopsis (~300 Myr). We test for genetic repeatability based on within-species associations between allele frequencies in genes and variation in 21 climate variables. Our results demonstrate significant statistical evidence for genetic repeatability across deep time that is not expected under randomness, identifying a suite of 108 gene families (orthogroups) and gene functions that repeatedly drive local adaptation to climate. This set includes many orthogroups with well-known functions in abiotic stress response. Using gene co-expression networks to quantify pleiotropy, we find that orthogroups with stronger evidence for repeatability exhibit greater network centrality and broader expression across tissues (higher pleiotropy), contrary to the ‘cost of complexity’ theory. These gene families may be important in helping wild and crop species cope with future climate change, representing important candidates for future study.

密切相关的物种通常使用相同的基因来适应相似的环境。然而，对于为什么这些基因具有更高的适应潜力以及这在更深的进化谱系中是否是保守的，我们知之甚少。对气候的适应提供了一个天然的实验室来测试这些想法，因为即使是远亲物种也必须与类似的压力作斗争。在这里，我们重新分析了来自 25 种植物物种的数千个个体的基因组数据，这些植物物种分为黑松和拟南芥 （~300 Myr）。我们根据基因等位基因频率和 21 个气候变量变异之间的物种内关联来测试遗传可重复性。我们的结果证明了在随机性下无法预料的深时间遗传可重复性的重要统计证据，确定了一套 108 个基因家族（直系群）和反复驱动局部适应气候的基因功能。这组包括许多在非生物胁迫反应中具有众所周知功能的正交群。使用基因共表达网络来量化多效性，我们发现具有更强可重复性证据的直系群表现出更大的网络中心性和更广泛的跨组织表达（更高的多效性），这与“复杂性成本”理论相反。这些基因家族可能在帮助野生和农作物物种应对未来的气候变化方面发挥重要作用，是未来研究的重要候选者。