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Cellular autoradiography was used to measure relative rates of chromosomal RNA synthesis and to examine the regulatory phenomenon of X-linked dosage compensation in Drosophila Miranda, a species containing two distinct, nonhomologous X chromosomes (X' and X2). The XI chromosome was found to be dosage-compensated, since the rate of RNA synthesis along the single XI chromosome in males equaled that of both XI chromosomes in females. Unlike other sex chromosomes that have been studied, the more recently evolved X2 heterochromosome exhibited regional differences in transcriptional activity when males and females were compared. The distal 10% of the X2 was not dosage-compensated, whereas the majority of an interior segment, representing 30% of the X2 chromosome's length, was found to be dosage-compensated. Our data are consistent with the idea that the evolution of X2 dosage compensation has paralleled the differentiation of the X2 sex chromosome. In addition, gene rearrangement seems to have accompanied the acquisition of a dosage-compensatory mechanism in the X2. The phenomenon of dosage compensation in Drosophila has been examined in a number of species within the genus. In all cases it appears as if a regulatory system modulates the amount of X chromosome gene products formed in such a way that males with one X chromosome and females with two X chromosomes have equal amounts of product. An X-linked gene is therefore twice as active in males as in females (1). The mechanism occurs at the level of transcription (2) and is dependent upon the activity of one or more autosomal genes (3-6). Xlinked genes need not be located on the X chromosome to be dosage-compensated, since (a) X chromosome genes translocated to autosomes still exhibit compensation (7-11) and (b) autosomal regions inserted into the X do not exhibit compensation (12, 13). Therefore, the regulatory elements responsible for dosage compensation are probably interspersed along the X chromosomes.As an approach toward understanding the evolution of dosage-compensatory mechanisms, we have examined a Drosophila species that has recently undergone evolutionary differentiation of its sex chromosomes. Drosophila miranda, which exhibits a unique sex-chromosome constitution, is a morphologically similar, reproductively compatible sibling species of D. pseudoobscura (14). D. miranda has two chromosomes (X' and X2), each of which exists in a single copy in males and in two copies in females (15). Both arms of the XI chromosome are homologous to the X chromosome arms of D. pseudoobscura, whereas the X2 is largely homologous to the autosomal third chromosome of D. pseudoobscura (15). The X2 evolved as a consequence of a Y-3 chromosomal fusion in the D. miranda lineage (16). Ancestral males are presumed to have had one copy of the new Y-3 fusion chromosome and one copy of the "free" third chromosome, whereas females had two copies of the latter. Eventually, most third chromosome genes on the new Y degenerated, and the "free" third chromosome gradually differenti...