We have determined 1990 bp mitochondrial DNA sequence which extends from 3′ end of the cytochrome oxidase subunit I (COI) gene to 5′ end of the COIII gene from two sibling species of Drosophila, D. simulans and D. mauritiana. Analyses of the sequences and part of the NADH dehydrogenase subunit 2 gene and the COI gene together with those from D. melanogaster and D. yakuba revealed that amino-acid substitution rate of the ATPase 6 gene seems to be higher in some strains of D. melanogaster than in the other species. High level of amino-acid polymorphism in this gene was observed in D. melanogaster. Synonymous substitution rate is relatively constant in all the genes examined, suggesting that mutation rate is not higher in the ATPase 6 gene of D. melanogaster. The amino-acid substitutions found specifically in D. melanogaster are at the sites which are not conserved among mammals, yeast and E. coli. These sites of the ATPase 6 gene might lose the selective constraint in D. melanogaster, and the amino-acid substitutions can be explained by neutral mutations and random genetic drift.

Many inbred and isofemale lines derived from wild populations of Drosophila melanogaster were tested for gonadal dysgenic sterility, male recombination and snw secondary mutation. Among them, we have found strains whose dysgenic offspring show negligible sterility, and undetectable male recombination and snw mutation. They can be considered to be neutral strains in the strict sense. Such neutral strains appear to carry only defective P elements in their genomes. Taking the observations of Karess & Rubin (1984) into account, it is suggested that some defective P elements retain the function necessary for P cytotype. Cytotype determination mechanisms are discussed.

Within-line heterogeneity has been found in the mitochondrial DNA (mtDNA) in two isofemale lines of D. simulans. The co-existing types, S and M, were typical of the mtDNA in D. simulans and in D. mauritiana, respectively, their nucleotide divergence per site being ca. 2·1%. Segregation analysis confirmed that some individuals in these lines were heteroplasmic and suggested incomplete maternal inheritance of mtDNA in Drosophila. Examination of other lines of D. simulans revealed that the M type of D. mauritiana occurs at 71% in Réunion, 38% in Madagascar and 0% in Kenya. This finding and interspecific sequence comparisons of both M types indicate that D. mauritiana diverged from D. simulans probably less than 240000 years ago.

By designing 3′ ends of primers in PCR (polymerase chain reaction), a specific DNA fragment was selectively amplified in the presence of a 103-fold excess of highly homologous (sequence difference ca. 2 %) opponent DNA. This technique was applied in detecting paternal leakage of mitochondrial DNA (mtDNA) in intraspecific crosses of Drosophila simulans and interspecific crosses of Drosophila simulans and Drosophila mauritiana. The mtDNA types of their progeny were analysed by selective amplification of the paternal mtDNA fragment possessing a polymorphic restriction site and detecting its cleaved fragments. Paternal mtDNA was detected in the progeny of 14 out of 16 crosses. The present result indicates small but frequent inheritance of sperm mtDNA in Drosophila, which is supportive to our previous finding.

Mitochondrial DNA (mtDNA) variation in Drosophila simulans was studied to determine whether the cytoplasmic state of mtDNA heteroplasmy persists in natural populations in Réunion. For this purpose, 172 isofemale lines, newly collected from two local populations, were examined, among which three types of mtDNA (siII, siIII and siIII′) were found, based on the Hpa II restriction pattern. Ten of the lines were heteroplasmic for a combination of siII and siIII, as determined by autoradiography. The same type of heteroplasmy had been noted in one of the two local populations 8 years before (Satta et al. 1988). The present results suggest that the heteroplasmic state occurs recurrently in natural populations of D. simulans in Réunion.