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Global patterns of population genetic variation through time offer a window into evolutionary processes that maintain diversity. Over time, lineages may expand or contract their distribution, causing turnover in population genetic composition. At individual loci, migration, drift and selection (among other processes) may affect allele frequencies. Museum specimens of widely distributed species offer a unique window into the genetics of understudied populations and changes over time. Here, we sequenced genomes of 130 herbarium specimens and 91 new field collections of Arabidopsis thaliana and combined these with published genomes. We sought a broader view of genomic diversity across the species and to test if population genomic composition is changing through time. We documented extensive and previously uncharacterised diversity in a range of populations in Africa, populations that are under threat from anthropogenic climate change. Through time, we did not find dramatic changes in genomic composition of populations. Instead, we found a pattern of genetic change every 100 years of the same magnitude seen when comparing Eurasian populations that are 185 km apart, potentially due to a combination of drift and changing selection. We found only mixed signals of polygenic adaptation at phenology and physiology QTL. We did find that genes conserved across eudicots show altered levels of directional allele frequency change, potentially due to variable purifying and background selection. Our study highlights how museum specimens can reveal new dimensions of population diversity and show how wild populations are evolving in recent history. 

Abstract Plants respond to their environment with both short‐term, within‐generation trait plasticity, and long‐term, between‐generation evolutionary changes. However, the relative magnitude of plant responses to short‐ and long‐term changes in the environment remains poorly understood. Shifts in phenological traits can serve as harbingers for responses to environmental change, and both a plant's current and source (i.e., genotype origin) environment can affect plant phenology via plasticity and local adaptation, respectively. To assess the role of current and source environments in explaining variation in flowering phenology ofBromus tectorum, an invasive annual grass, we conducted a replicated common garden experiment using 92 genotypes collected across western North America. Replicates of each genotype were planted in two densities (low = 100 seeds/1 m², high = 100 seeds/0.04 m²) under two different temperature treatments (low = white gravel; high = black gravel; 2.1°C average difference) in a factorial design, replicated across four common garden locations in Idaho and Wyoming, USA. We tested for the effect of current environment (i.e., density treatment, temperature treatment, and common garden location), source environment (i.e., genotype source climate), and their interaction on each plant's flowering phenology. Flowering timing was strongly influenced by a plant's current environment, with plants that experienced warmer current climates and higher densities flowering earlier than those that experienced cooler current climates and lower densities. Genotypes from hot and dry source climates flowered consistently earlier than those from cool and wet source climates, even after accounting for genotype relatedness, suggesting that this genetically based climate cline is a product of natural selection. We found minimal evidence of interactions between current and source environments or genotype‐by‐environment interactions. Phenology was more sensitive to variation in the current climate than to variation in source climate. These results indicate that cheatgrass phenology reflects high levels of plasticity as well as rapid local adaptation. Both processes likely contribute to its current success as a biological invader and its capacity to respond to future environmental 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.