Methods to generate Drosophila in vivo cybrid lines. (A) Repeated backcrossing. The chosen mtDNA variant is added during the first cross where the virgin females from the mtDNA donor strain are crossed with the males of the nuclear donor strain. Virgin females of the following progeny are crossed again with the males of the nuclear donor strain. This will be repeated for >15 generations, after which the cybrid progeny contain the wanted mtDNA variant on a nuclear background that in theory is the same as the one in the nuclear donor strain. This method also has the potential to reveal possible mito-nuclear epistasis during the course of the backcrossing. (B) Balancer chromosome method. Drosophila males do not go through recombination, whereas in females the recombination can be controlled with the balancer chromosomes which do not recombine with the normal chromosome homologs during meiotic prophase. The presence of balancer chromosomes in the progeny can be recognized by the dominant marker mutations that the balancers carry, e.g., mutations affecting eye shape, body color, or wing morphology. If the progeny do not have the balancer, it has the normal homolog of the wanted chromosome. Three (labeled here a,a,a or b,b,b) of the four D. melanogaster chromosomes can be replaced to contain the genetic content of the wanted nuclear donor strain by using the balancer chromosome method. The mtDNA from the maternal donor strain is introgressed to the strain during the first cross and the chromosome content is replaced chromosome at a time by using the correct progeny of the previous cross. For clarity, chromosomes 2 and 3 have not been marked to the cross where the X(a) is replaced with the X(b).