Crossing schemes to clone X and Y chromosomes X Y Congo, CS, Z53, Mass Congo, CS, Z53, Mass Y × DX Y Y Y × × Y Y DX Y × × Y Y DX Y × × Y Y DX Y × × Y Y Y DX × × Supplementary figure 1. To make iso-X and iso-Y lines from the four populations we made use of the fact that there is no recombination in male Drosophila melanogaster and some genetic tools that are available for this species. Each unit in the figure represents a genotype and the bars and letters within each genotype depicts the different chromosomes (top pair – X and Y chromosome, second and third pair – the two major autosomes, fourth pair – the fourth dot chromosome). All blue chromosomes came from the LHM population, red chromosomes came from one of the four target populations (Congo, CS, Mass-1 or Z-53), DX stands for an attached X-chromosome (C(1)DX y,f) that segregates as one unit, the long green bar is a translocation between the two major chromosomes T(2;3) marked with the dominate visible marker apterous-Xasta (apXa) and the pink chromosome is marked with the dominant visible marker cubitus interuptus-Dominant (ciD). All crosses were conducted in a manner that precludes hybrid dysgenisis.