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Abstract 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 CO₂concentrations, 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 191Arabidopsis thalianahistorical 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. 

ABSTRACT It is unclear how plants respond to increasing temperatures. Leaf heat tolerance (LHT) is often at its upper limit in tropical forests, suggesting that climate change might negatively impact these forests. We hypothesized that intraspecific variation in LHT might be associated with changes in the soil microbiome, which might also respond to climate. We hypothesized that warming would increase LHT through changes in the soil microbiome: we combined an in situ tropical warming experiment with a shade house experiment in Puerto Rico. The shade house experiment consisted of growing seedlings ofGuarea guidonia, a dominant forest species, under different soil microbiome treatments (reduced arbuscular mycorrhizal fungi, reduced plant pathogens, reduced microbes, and unaltered) and soil inoculum from the field experiment. Heat tolerance was determined using chlorophyll fluorescence (F_V/F_m) on individual seedlings in the field and on groups of seedlings (per pot) in the shade house. We sequenced soil fungal DNA to analyze the impacts of the treatments on the soil microbiome. In the field, seedlings from ambient temperature plots showed higherF_V/F_mvalues under high temperatures (0.648 at 46°C and 0.067 at 52°C) than seedlings from the warming plots (0.535 at 46°C and 0.031 at 52°C). In the shade house, the soil microbiome treatments significantly influenced the fungal community composition and LHT (T_critandF_V/F_m). Reduction in fungal pathogen abundance and diversity alteredF_V/F_mbeforeT₅₀for seedlings grown with soil inoculum from the warming plots but afterT₅₀for seedlings grown with soil inoculum from the ambient plots. Our findings emphasize that the soil microbiome plays an important role in modulating the impacts of climate change on plants. Understanding and harnessing this relationship might be vital for mitigating the effects of warming on forests, emphasizing the need for further research on microbial responses to climate change. 

Summary Phenotypic and genomic diversity inArabidopsis thalianamay be associated with adaptation along its wide elevational range, but it is unclear whether elevational clines are consistent among different mountain ranges.We took a multi‐regional view of selection associated with elevation. In a diverse panel of ecotypes, we measured plant traits under alpine stressors (low CO₂partial pressure, high light, and night freezing) and conducted genome‐wide association studies.We found evidence of contrasting locally adaptive regional clines. Western Mediterranean ecotypes showed low water use efficiency (WUE)/early flowering at low elevations to high WUE/late flowering at high elevations. Central Asian ecotypes showed the opposite pattern. We mapped different candidate genes for each region, and some quantitative trait loci (QTL) showed elevational and climatic clines likely maintained by selection. Consistent with regional heterogeneity, trait and QTL clines were evident at regional scales (c. 2000 km) but disappeared globally. Antioxidants and pigmentation rarely showed elevational clines. High elevation east African ecotypes might have higher antioxidant activity under night freezing.Physiological and genomic elevational clines in different regions can be unique, underlining the complexity of local adaptation in widely distributed species, while hindering global trait–environment or genome–environment associations. To tackle the mechanisms of range‐wide local adaptation, regional approaches are thus warranted. 

Host–parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple cropSorghum bicolor(L.) Moench and its association with the parasitic weedStriga hermonthica(Delile) Benth., a major constraint to food security in Africa. We hypothesize that geographic selection mosaics across gradients of parasite occurrence maintain genetic diversity in sorghum landrace resistance. Suggesting a role in local adaptation to parasite pressure, multiple independent loss-of-function alleles at sorghumLOW GERMINATION STIMULANT 1 (LGS1)are broadly distributed among African landraces and geographically associated withS. hermonthicaoccurrence. However, low frequency of these alleles withinS. hermonthica-prone regions and their absence elsewhere implicate potential trade-offs restricting their fixation.LGS1is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and below-ground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with trade-offs, we find signatures of balancing selection surroundingLGS1and other candidates from analysis of genome-wide associations with parasite distribution. Experiments with CRISPR–Cas9-edited sorghum further indicate that the benefit ofLGS1-mediated resistance strongly depends on parasite genotype and abiotic environment and comes at the cost of reduced photosystem gene expression. Our study demonstrates long-term maintenance of diversity in host resistance genes across smallholder agroecosystems, providing a valuable comparison to both industrial farming systems and natural communities.