We present data that demonstrate that three MR elements isolated from wild populations of Drosophila melanogaster on two continents can cause large deletions of the X chromosome in males. The deleted chromosomes, termed mini-X chromosomes, are induced at a frequency of =1:4000 in chromosomes that are initially free of P elements. In situ hybridizations using a cloned P sequence as a probe fail to reveal any sequences homologous to the nomadic P family at the deletion breakpoints. Genetic analysis of 12 such mini-X chromosomes also reveals that there are no "hotspots" of chromosome breakage and that there must have been a minimum of three distinct distal breakpoints and five different proximal breakpoints in the formation of these deleted chromosomes. In fact all 12 proximal and 12 distal breakpoints may well be unique. Our data show that MR elements generate essentially random breaks along the X chromosome. We emphasize that we find no involvement of P sequences in the chromosome breakage process, consonant with the notion that MR elements exert their influence on processes involved in mitotic crossing-over.Two major properties have been assigned to MR (mutationrecombination) elements that are widespread in natural populations (1)(2)(3). These elements generate elevated levels of mitotic crossing-over in premeiotic germ cells of both males and females (4-6) and also act as mutators by mostly facilitating the integration of P elements at various loci (7,8). It is also known that two MR-bearing chromosomes inherited patroclinously are no more potent than a single one in terms of mutator activity (9). Furthermore, mapping of two second chromosome MR elements from sources as diverse as Haifa, Israel and Texas reveals very similar chromosomal locations in a short interval of <1 map unit (10, 11). In addition, cytogenetic analyses have revealed that MR elements can generate deletions of up to several contiguous gene loci in the regions including the loci of lethal giant larva (12), net (12), cinnabar (12, 13), black (12), purple (12), light (6), scarlet, and peach (M.M.G., unpublished data). They can also generate translocations and duplications (13). In some cases tandem duplications of at least four polytene chromosome divisions have been induced by MR on an X chromosome initially free of P elements (M.M.G., unpublished data). MR elements thus provide a genetic basis for the phenomena associated with the P-M system of "hybrid dysgenesis" (8,(14)(15)(16). It has also been claimed that MR factors and P factors are indistinguishable (16), and some studies have been predicated on this assumption (6).We now report that MR elements can regularly produce massive deletions of most of the euchromatic part of the X chromosome at comparatively high frequencies in X chromosomes that are originally free of P elements. The deletion events, of the order of 15 million base pairs, are detected through the recovery offree X-chromosome duplications that retain the centromere and telomere but have most of the interstitial euchr...