Data from: Characterizing genomic variation of Arabidopsis thaliana: the roles of geography and climate

Arabidopsis thaliana inhabits diverse climates and exhibits varied
phenology across its range. Although A. thaliana is an extremely-well
studied model species, the relationship between geography, growing season
climate and its genetic variation is poorly characterized. We used
redundancy analysis (RDA) to quantify the association of genomic variation
[214,051 single nucleotide polymorphisms (SNPs)] with geography and
climate among 1,003 accessions collected from 447 locations in Eurasia. We
identified climate variables most correlated with genomic variation, which
may be important selective gradients related to local adaptation across
the species range. Climate variation among sites of origin explained
slightly more genomic variation than geographical distance. Large-scale
spatial gradients and early spring temperatures explained the most genomic
variation, while growing season and summer conditions explained the most
after controlling for spatial structure. SNP variation in Scandinavia
showed the greatest climate structure among regions, possibly because of
relatively consistent phenology and life history of populations in this
region. Climate variation explained more variation among non-synonymous
SNPs than expected by chance, suggesting that much of the climatic
structure of SNP correlations is due to changes in coding sequence that
may underlie local adaptation.