Differences among replicates with (R1, R4) and without (R2) P-element ping-pong. (A) Schematic overview of the RNA-seq samples used for identifying genes differentially expressed among samples with (green) and without (blue) P-element ping-pong. (B) Volcano plots highlighting expression differences for TEs and D. erecta transcripts between naive flies and invaded flies (generations 30 and 40). Data are shown for all three replicates (R1, R2, R4). (C) Volcano plot highlighting expression differences between replicates with and without P-element ping-pong at generations 30 and 40. (D) Overview of P-element insertions with internal deletions in the experimental populations (left). The lower left panel shows the composition of the P-element and the deleted regions of D50 and the KP-element. The DNA-binding domain (orange) and regions necessary for mobilizing the P-element (green) are indicated (Majumdar and Rio 2015). The right panel shows the frequency of the IDs (relative to all P-element insertions) in the three replicates. Note that the EP-element (red), that is, a P-element variant with deletion of a similar region than for the KP-element, is increasing in frequency in replicate 2 but not in the other replicates. (E) Population frequency of EP-element insertions and the full-length (FL) insertions of the P-element in replicate 2 at generations 40 and 48.
