Sampling sites and phylogenetic relationship among surveyed species.

(a) Sampling locations of wild sunflower populations studied in the present study, and (b) phylogenetic relationship of the four (sub-)species. Numbered brackets represent the six pairwise comparisons performed in this study.

The range of environmental and phenotypic variation in the studied species. Variation in environment (a) and phenotype (b) for the studied species, along the two largest axes of a Principle component analysis (PCA). Violin plots show two examples of variation in environment (Hargreaves reference evapotranspiration index; Eref) and phenotype (Days to Flower; DTF) within and among the taxa (c,d).

Signatures of association for Number of Frost-Free Days (NFFD) in the four taxa on chromosome 15 (A) and genome-wide (B). Panel A shows Windows of Repeated Association (WRAs; coloured bars) for comparisons between the focal species, H. annuus, and each of the other 3 taxa, with the haploblocks in H. annuus shaded in violet and the regions with significant PicMin hits as vertical orange lines. Panel B shows the value of the top candidate index for each of the 1000 windows with the strongest signatures of association in at least one species (∼top 2% of genome-wide windows). Rows are ordered using hierarchical clustering to group windows with similar patterns across multiple species, illustrating the extent of overlap/non-overlap in the windows with strongest signatures in each species (i.e., position in the figure does not reflect chromosomal position).

Relationship between maximum Similarity in Phenotype-Environment Correlation (SIPEC) and number of Clusters of Repeated Association (CRAs). SIPEC was calculated for each phenotypic PCA axis with the maximum taken across the axes that cumulatively explain 95% of the phenotypic variance, for each environment. Each panel includes both a linear model fit to the data within the panel (coloured lines), and a linear model fit to all data simultaneously (black lines) for comparison. Note that because environmental variables are correlated, these points are not independent and therefore represent a source of pseudoreplication, preventing formal statistical tests of this relationship.

Enrichment of signatures of repeated association within genomic regions harbouring a haploblock in one of the two compared lineages. Each panel shows the proportion of top candidate windows that fall within haploblocks for windows with significant signatures of repeated association by the null-W test (WRAs) vs. those with non-significant signatures (non-WRAs). Comparisons of H. petiolaris petiolaris vs. H. petiolaris fallax are omitted as they share segregating haploblocks. Each point corresponds to the results for a single phenotype or environment, with dark shading used for cases where the deviation from random for the contingency table is significant by a permutation test (p < 0.05), and lighter shading indicating a non-significant result. Note that because many environmental variables and phenotypes are correlated with each-other, these points are not independent and therefore represent a source of pseudoreplication, preventing formal statistical tests of the overall relationship within each panel.