<p>Genome-wide variation in hybrid index (HI) in the control and heat-selection treatments.</p>

<p>HI was plotted in windows of 200 non-overlapping SNPs along the genome in <b>(A)</b> the control and <b>(B)</b> the heat-selection lines (relative differences between the lines shown in <a href="plosbiology.org/article/info:doi/10.1371/journal.pbio.3004028#pbio.3004028.s008" target="_blank">S2A Fig</a>). Different colors indicate different replicate lines. The dashed horizontal line indicates the expected <i>D. montana</i> ancestry at the start of the hybridize, evolve, and re-sequence (HER) experiment.

Vertical solid and dashed lines denote the breakpoints of the alternatively fixed chromosomal inversions between <i>D. flavomontana</i> and <i>D. montana</i>. Black segments at the bottom of the plots represent SNPs with an HI of 0, indicating no introgression from <i>D. montana</i> in any of the six control or six heat-selection lines (strong contemporary barriers). Note that the size of a segment is not proportional to a single SNP.