Reduced representation sequencing of Drosophila simulans balancer chromosome crossed to Drosophila mauritiana

To determine whether a new balancer chromosome on Chromosome arm 2L of D. simulans blocks recombination, D. simulans flies carrying the balancer were backcrossed to D. mauritiana and then hybrid females carrying the balancer chromosome were repeatedly backcrossed to D. mauritiana males. Reduced representation sequencing of single individuals from generation ten was performed and genomewide ancestry was estimated for each sample.