In Drosophila melanogaster, the multiply repeated genes encoding 18S and 28S rRNA are located on the X and Y chromosomes. A large percentage of these repeats are interrupted in the 28S region by insertions of two types. We compared the restriction patterns from a subcloned wild-type Oregon R strain to those of spontaneous and ethyl methanesulfonate-induced bobbed mutants. Bobbed mutations were found to be deficiencies that modffied the organization of the rDNA locus. Genes without insertions were deleted about twice as often as genes with type I insertions. Type II insertion genes were not decreased in number, except in the mutant having the most bobbed phenotype. Reversion to wild type was associated with an increase in gene copy number, affecting exclusively genes without insertions. One hypothesis which explains these results is the partial clustering of genes by type. The initial deletion could then be due either to an unequal crossover or to loss of material without exchange. Some of our findings indicated that deletion may be associated with an amplification phenomenon, the magnitude of which would be dependent on the amount of clustering of specific gene types at the locus.Drosophila melanogaster rDNA, i.e., genes coding for 18S and 28S rRNA, is located in the X and Y heterochromatic regions. Wild-type loci contain from 150 to 250 tandemly arranged repeats. Partial deficiencies of rDNA are known as bobbed mutations, which result in a phenotype characterized by small bristles, abdominal etching, and developmental delay (26). Many 28S rDNA genes are interrupted by insertions (11,12,24,35,38). The insertions are of two types (INS-I and INS-I1). They share no homology in size or sequence (6,37) and are inserted at different positions, being 51 base pairs (bp) apart within the gene (27, 28). INS-I ribosomal genes occur only on the X chromosome, with inserts ranging from 0.5 to 6.5 kilobases (kb) and with a major size class of 5.5 kb. A 0.5-kb sequence homology is found at the right end of all these insertions (36). Type I insertion sequences are also found outside rDNA (4) and are probably derived from rDNA by transposition. INS-II sequences occur exclusively in rDNA but on both the X and Y chromosomes. They range in size from 1.5 to 4 kb, with a major size class of 3.4 kb. Both types of INS genes are transcribed at a very low level, and little, if any, rRNA is produced by a splicing mechanism (15,17,19,20).rDNA restriction patterns vary from one wild-type strain to another. Differences also exist between X chromosomes of various Oregon R wild-type strain subclones, as well as between X and Y chromosomes from a given subclone (9). This is due to variation in numbers and lengths of insertions, as well as to heterogeneity in nontranscribed spacer lengths (6, 37). The evolution of tandemly arranged repetitive sequences implicates the existence of both a source of heterogeneity (new genes) and a means to achieve homogeneity (multiplication of a given unit). Mutations could be involved in the creation of new genes,...