Mitochondrial DNA extracted from an isofemale strain of Drosophila mauritiana (subgroup melanogaster) appeared to be heterogeneous in size. A short genome [S; 18,500 base pairs (bp)] and a longer one (L; 19,000 bp) coexist in the preparation. The additional 500 bp have been located within the A+T-rich region. Hpa I digest patterns suggest that the S genome may carry a duplication of a 500-bp sequence including an Hpa I site and that the L genome may carry a triplication of the same sequence. At the 30th generation of the isofemale strain, 60 female genotypes were examined individually. Half of the flies were pure either for the S or the L DNA. The remaining 50% exhibited various degrees of heteroplasmy for the two DNA types. Among metazoan animals, this D. mauritiana strain offers an exceptional situation with regard to the number of individuals heterogeneous for mtDNA and the relative stability of heteroplasmy through generations.In metazoan animals, the lack of mitochondrial mutants is compensated by the use of restriction endonucleases to study the heredity and the evolution of mitochondrial DNA. Three general features of animal mitochondrial genetics emerge from different analyses (1). (i) mtDNA is maternally inherited: the first evidences from interspecific hybridization experiments (2, 3) have been confirmed later by intraspecific crosses. (ii) Sequence differences are frequent between individuals within the same species and even within the same population (4-8). (iii) From the existence of interindividual differences, a heteroplasmic transitory phase might be expected; however, for each individual the mtDNA always appears as a molecular clone (6-10): the mtDNA is homogeneous for a given organ, and the DNA molecules are identical from one organ to another within an individual (4, 11). This last observation suggests a rapid purification of the mitochondrial genome.Drosophila mtDNA exhibits these general properties (12-14). In the course of a sequence variability study within the melanogaster subgroup of Drosophila, we analyzed numerous isofemale strains. As For physical mapping, mitochondria were isolated either from embryos, from virgin eggs, or from adult flies. mtDNA was purified on CsCl gradients. If necessary, a second purification was carried out on CsCI/4',6-diamidino-2-phenylindol-2.HCl (DAPI) gradients. Cleavage sites of nine restriction endonucleases were mapped by analysis of partial and complete single digests and of double digests. The digestion fragments were separated by vertical electrophoresis on 1% agarose or 4.5% acrylamide slab gels. HindIII/A phage and HindII/4X174 phage DNA digests were used as molecular weight standards for calibration. After electrophoresis the gels were stained by standard procedures with ethidium bromide and then photographed under short wave UV light.For individual mitochondrial genotype comparison, it was not possible to get from a single fly enough DNA for a slab gel analysis; so we used the progeny of each female fly under study. About 30 generations...