Fig. 3

Species-specific peaks may be poised for evolution. A, B Boxplots of raw model outputs in the head (A) and testis (B) from the model trained on D. melanogaster data. D. melanogaster-specific peaks on 3L (purple) have significantly lower model outputs than conserved peaks overall (magenta); their orthologous non-peak sequences (orange) from D. simulans and D. yakuba have significantly higher model outputs than non-peaks overall (green). The species-specific peaks have modestly higher model outputs than their orthologous non-peaks. The phylogeny is not to scale. One-sided Mann–Whitney U tests; ***: p < 1E − 10; **: p < 0.001; *: p < 0.05. C, D As A and B, except using the D. simulans model, the D. simulans 3L peak (magenta) and non-peak examples (green), D. simulans-specific peaks (blue), and their orthologous non-peak sequences from D. melanogaster and D. yakuba (orange). E, F As A and B, except using the D. yakuba model, the D. yakuba 3L peak (magenta) and non-peak examples (green), D. yakuba-specific peaks (blue) and their orthologous non-peak sequences from D. melanogaster and D. simulans (orange)