Workflow showing the main steps applied for identifying TEs present at high frequencies in high recombination regions in the D. melanogaster genome.

LRR: TEs located at low recombination rate regions. HRR: TEs located at high recombination rate regions. Fixed: HRR TEs at frequencies > 95% in all populations. LowFreq: low frequency HRR TEs (frequencies < 10% in all samples). HighFreq: high frequency HRR TEs (frequencies < 95% in all samples and at >10% frequency in at least three samples). HighFreq TEs were further classified according to their frequency in African (AF) and/or out-of-Africa (OOA) populations: AF: TEs at high frequency only in the African population; AF-OOA: TEs at high frequency in Africa and out-of-Africa populations; OOA: TEs at high frequency in out-of-Africa populations and low frequency in the African population and NA-AF: TEs present at high frequency in out-of-Africa populations but for which we have no data for the African population.