Rising atmospheric CO2 concentration is a key driver of enhanced global greening, thought to account for up to 70% of increased global vegetation in recent decades. CO2 fertilization effects have further profound implications for ecosystems, food security and biosphere‐atmosphere feedbacks. However, it is also possible that current trends will not continue, due to ecosystem level constraints and as plants acclimate to future CO2 concentrations. Future predictions of plant response to rising [CO2] are often validated using single‐generation short‐term FACE (Free Air CO2 Enrichment) experiments but whether this accurately represents vegetation response over decades is unclear. The role of transgenerational plasticity and adaptation in the multigenerational response has yet to be elucidated. Here, we propose that naturally occurring high CO2 springs provide a proxy to quantify the multigenerational and long‐term impacts of rising [CO2] in herbaceous and woody species respectively, such that plasticity, transgenerational effects and genetic adaptation can be quantified together in these systems. In this first meta‐analysis of responses to elevated [CO2] at natural CO2 springs, we show that the magnitude and direction of change in eight of nine functional plant traits are consistent between spring and FACE experiments. We found increased photosynthesis (49.8% in spring experiments, comparable to 32.1% in FACE experiments) and leaf starch (58.6% spring, 84.3% FACE), decreased stomatal conductance (gs, 27.2% spring, 21.1% FACE), leaf nitrogen content (6.3% spring, 13.3% FACE) and Specific Leaf Area (SLA, 9.7% spring, 6.0% FACE). These findings not only validate the use of these sites for studying multigenerational plant response to elevated [CO2], but additionally suggest that long‐term positive photosynthetic response to rising [CO2] are likely to continue as predicted by single‐generation exposure FACE experiments.

Unravelling plant responses to rising atmospheric CO2 concentration ([CO2]) has largely focussed on plastic functional attributes to single generation [CO2] exposure. Quantifying the consequences of long‐term, decadal multigenerational exposure to elevated [CO2] and the genetic changes that may underpin evolutionary mechanisms with [CO2] as a driver remain largely unexplored. Here, we investigated both plastic and evolutionary plant responses to elevated [CO2] by applying multi‐omic technologies using populations of Plantago lanceolata L., grown in naturally high [CO2] for many generations in a CO2 spring. Seed from populations at the CO2 spring and an adjacent control site (ambient [CO2]) were grown in a common environment for one generation, and then offspring were grown in ambient or elevated [CO2] growth chambers. Low overall genetic differentiation between the CO2 spring and control site populations was found, with evidence of weak selection in exons. We identified evolutionary divergence in the DNA methylation profiles of populations derived from the spring relative to the control population, providing the first evidence that plant methylomes may respond to elevated [CO2] over multiple generations. In contrast, growth at elevated [CO2] for a single generation induced limited methylome remodelling (an order of magnitude fewer differential methylation events than observed between populations), although some of this appeared to be stably transgenerationally inherited. In all, 59 regions of the genome were identified where transcripts exhibiting differential expression (associated with single generation or long‐term natural exposure to elevated [CO2]) co‐located with sites of differential methylation or with single nucleotide polymorphisms exhibiting significant inter‐population divergence. This included genes in pathways known to respond to elevated [CO2], such as nitrogen use efficiency and stomatal patterning. This study provides the first indication that DNA methylation may contribute to plant adaptation to future atmospheric [CO2] and identifies several areas of the genome that are targets for future study.

Adaptive genetic diversity in crop wild relatives (CWRs) can be exploited to develop improved crops with higher yield and resilience if phylogenetic relationships between crops and their CWRs are resolved. This further allows accurate quantification of genome-wide introgression and determination of regions of the genome under selection. Using broad sampling of CWRs and whole genome sequencing we further demonstrate the relationships among two economically valuable and morphologically diverse Brassica crop species, their CWRs and their putative wild progenitors. Complex genetic relationships and extensive genomic introgression between CWRs and Brassica crops were revealed. Some wild B. oleracea populations have admixed feral origins, some domesticated taxa in both crop species are of hybrid origin, while wild B. rapa is genetically indistinct from turnips. The extensive genomic introgression we reveal could result in false identification of selection signatures during domestication using traditional comparative approaches used previously, therefore we adopted a single population approach to study selection during domestication. We used this to explore examples of parallel phenotypic selection in the two crop groups and highlight promising candidate genes for future investigation. Our analysis defines the complex genetic relationships between Brassica crops and their diverse CWRs, revealing extensive cross-species gene flow with implications for both crop domestication and evolutionary diversification more generally.