Fig. 3

Evidence of positive selection centered on the PtFT2 locus. a Patterns of normalized iHS scores (y-axes) across the ~ 700-kbp genomic region (x-axis) around the PtFT2 gene (vertical light gray bar). The dashed horizontal lines indicate the threshold of positive selection signal (|iHS| > 2). The red dot indicates the SNP (Potra001246:25256) showing the strongest signal of local adaptation. b A high concentration of significant |iHS| signals was found in the ~ 700-kbp region surrounding PtFT2 (marked as red line) compared to the genome-wide distribution (based on dividing the genome into non-overlapping windows of 700 kbp). The dashed lines represent the 95% and 99% quantiles, respectively. c Allele frequencies of the most strongly associated SNP Potra001246:25256 for the 12 original populations of the SwAsp collection. d The decay of extended haplotype homozygosity (EHH) of the derived (blue) and ancestral (red) alleles for the SNP Potra001246:25256. e The extent of the three most common haplotypes at Potra001246:25256. Rare recombinant haplotypes were pooled and are displayed in gray. f Joint inference of allele age and selection coefficient for the region surrounding PtFT2