<p>Inversion breakpoints of alternatively fixed inversions between <i>D. montana</i> and <i>D. flavomontana</i> pools.</p>

<p>Illumina paired-end re-sequencing data of both species were mapped against <i>D. flavomontana</i> reference genome, and the data is illustrated with Integrative Genomics Viewer (IGV) [<a href="plosbiology.org/article/info:doi/10.1371/journal.pbio.3004028#pbio.3004028.ref082" target="_blank">82</a>]. Due to inversion differences between the species, <i>D. montana</i> reads are split, the insert size of its paired reads deviates from the expected (red reads), and paired reads are in reversed orientation (blue and turquoise reads).

Note that not all X inversion breakpoints exhibit reversed orientation due to the complex overlap of these inversions (see <a href="plosbiology.org/article/info:doi/10.1371/journal.pbio.3004028#pbio.3004028.s001" target="_blank">S1 Table</a>). Since chromosome 4 of the <i>D. flavomontana</i> reference genome was scaffolded, the presence of the inversion on chromosome 4 was verified by mapping both species to the <i>Drosophila lummei</i> reference genome (breakpoints 1,568,294 and 15,689,984 in the <i>D. lummei</i> genome equal to 23,745,872 and 7,855,585 in the <i>D. flavomontana</i> genome, respectively; <a href="plosbiology.org/article/info:doi/10.1371/journal.pbio.3004028#pbio.3004028.s001" target="_blank">S1 Table</a>), as described in Poikela and colleagues [<a href="plosbiology.org/article/info:doi/10.1371/journal.pbio.3004028#pbio.3004028.ref050" target="_blank">50</a>].