Distribution of the studied accessions and TE polymorphism frequencies.

Panel A: Map showing the geographical distribution of the accessions used in the current study. The phylogenetic tree illustrates the phylogeny between the five genetic clades. This panel was made based on the data and results published by Stritt et al. [38] and Minadakis et al. [39]. Panel B: Observed (blue) and simulated (gray) XtX values of TE polymorphisms in B. distachyon. Dotted lines show the 2.5% and 97.5% quantiles of the simulated XtX values. Panel C-G: Folded site frequency spectrum of TE polymorphisms and synonymous SNPs in all clades. C: A_East; D: A_Italia; E: B_West; F: B_East; G: C.

ANCOVA predicting the number of fixed TE polymorphisms per clade in candidate regions under positive selection.

ANCOVA predicting the allele frequency of TE polymorphisms per clade in candidate regions under positive selection.

Age-adjusted SFS of retrotransposons.

The top row shows the age-adjusted SFS of all retrotransposons (colored), non-synonymous SNPs (light gray) and high effect SNPs (dark gray) in the four derived clades. The bottom row shows the age-adjusted SFS of retrotransposons based on their distance to the next gene in the four derived clades. The X axes show the age range of the mutations in each bin, and the age range of each bin was chosen so that each bin represents the same number of retrotransposon observations in the top row. The different columns show the four derived clades: A: A_East; B: A_Italia; C: B_West; D: B_East. Boxplots are based on 100 estimations of Δ frequency. Significant deviations of Δ frequency estimates from 0 in the age-adjusted SFS of retrotransposons are shown with asterisks (one-side Wilcoxon tests, Bonferroni corrected p value < 0.01: ***).

Relative age difference ((mutation age in simulations – observed mutation age)/maximum absolute age difference) between simulated and observed data in the last bin of the age-adjusted SFS. A: 25% quantile; B: 50% quantile; C: 75% quantile.