design: Genomic DNA was extracted from males following the protocol described in Chakraborty et al. (2016). To shear the DNA, it was subjected to 10 plunges of a 21 gauge needle followed by 10 plunges of a 24 gauge needle. It was then subjected to the 20-80Kb size selection protocol on the Blue Pippin instrument (Chakraborty et al. 2016). The size distribution of genomic DNA was measured with pulse-field gel electrophoresis (Chakraborty et al. 2016). The library for D. simulans (wxd1) were generated following the standard 20 kb library protocol. All the sequencing was performed at the UCI genomics core using the P6-C4 chemistry on the RS II platform