The Arabidopsis thaliana population has been exposed to unexperienced biotic and abiotic stresses as a result of range expansion or environmental change. To obtain a global picture of the genetic adaptations in the population history of A. thaliana, we constructed a database of the phenotypic-adaptations (p-adaptations) and gene expression-adaptations (e-adaptations). We analysed the dynamics of the allele frequencies at the 23,880 QTLs of 174 traits and 8,618 eQTLs of 1,829 genes with respect to the total SNPs in the genomes, and identified 650 p-adaptations and 3,925 e-adaptations (FDR=0.05). The population underwent large scale p-adaptations and e-adaptations along four lineages, the eastward migration to Central Asia and South Siberia, Russia, the northward migration to Sweden, the migration to Azerbaijan, and the migration of the German population to the United States. Extremely cold winters and short summers prolonged seed dormancy, and expanded the root system architecture. Low temperatures prolonged the growing season and low light intensity required the increased chloroplast activity. The subtropical and humid environment enhanced phytohormone signaling pathways in response to the biotic and abiotic stresses. Exposure to heavy metals selected for alleles underlying low heavy metal uptake from soil, lower growth rate, lower resistance to bacteria, and higher expression of photosynthetic genes were selected. The database of p-adaptations and e-adaptations, which complements studies focusing on specific aspects of adaptation, may be useful for future studies to understand the biological adaptations of A. thaliana throughout its population history.

During the history of range expansion, the populations encounter with variety of environments. They respond to the local environments by modifying the mutually interacting traits. Therefore, to understand the whole life history of the populations, it is ideal to capture the history of their range expansion with reference to the series of surrounding environments and to infer the coadaptation of the multiple traits. Toward this end, we provide an exploratory analysis based on the features of populations: site frequency spectra of populations, population-specific FST, association between genes and environments, positive selections on traits mapped on the admixture graph, and GWAS results. Correspondence analysis of genes, environments, and traits provides a bird’s-eye view of the history of population differentiation and range expansion and various types of environmental selections at the times. Principal component analysis of the estimated trait-specific polygenic adaptations mapped on the admixture graph enables to understand the coadaptation of multiple traits. The potential usefulness was confirmed by analyzing a public dataset of wild poplar in northwestern America. In response to the northern cold temperature and longer daylength, the populations increased the photosynthetic activity and nutrient use efficiency at the expense of the risk of pathogen invasion, and in response to warm temperature, they increased the growth. At higher altitude, they shifted the maximum activity to earlier period in spring to reduce the activity in dry summer. The R codes for our representation method and simulations of population colonization used in this study are available as supplementary script.