The Y chromosome, inherited without meiotic recombination from father to son, carries relatively few genes in most species. This is consistent with predictions from evolutionary theory that nonrecombining chromosomes lack variation and degenerate rapidly. However, recent work has suggested a dynamic role for the Y chromosome in gene regulation, a finding with important implications for spermatogenesis and male fitness. We studied Y chromosomes from two populations of Drosophila melanogaster that had previously been shown to have major effects on the thermal tolerance of spermatogenesis. We show that these Y chromosomes differentially modify the expression of hundreds of autosomal and X-linked genes.Genes showing Y-linked regulatory variation (YRV) also show an association with immune response and pheromone detection. Indeed, genes located proximal to the euchromatin-heterochromatin boundary of the X chromosome appear particularly responsive to Y-linked variation, including a substantial number of odorant-binding genes. Furthermore, the data show significant regulatory interactions between the Y chromosome and the genetic background of autosomes and X chromosome. Altogether, our findings support the view that interpopulation, Y-linked regulatory polymorphisms can differentially modulate the expression of many genes important to male fitness, and they also point to complex interactions between the Y chromosome and genetic background affecting global gene expression.T HE Y chromosome is transmitted without sexual recombination from father to son. In the Y chromosome, as in other nonrecombining regions, complete linkage between genes results in the accumulation of deleterious alleles and the loss of genetic diversity due to the evolutionary processes of Muller's ratchet, background selection, and genetic hitchhiking (Bull 1983;Rice 1987;Charlesworth and Charlesworth 2000;Bachtrog et al. 2008). Consistent with theory, the Y chromosome of Drosophila melanogaster carries only 13 known protein-coding genes (Carvalho et al. 2001;Carvalho and Clark 2005;Koerich et al. 2008;Vibranovski et al. 2008;Krsticevic et al. 2010), whereas .5000 genes would be expected from typical gene densities in euchromatic regions.Six of the 13 genes discovered on the Y chromosome are male fertility factors that either encode structural components of spermatogenesis or regulate spermatogenesis-specific processes such as individualization (Carvalho et al. 2000(Carvalho et al. , 2009. Spermatogenesis in Drosophila males is extremely sensitive to heat, with males becoming sterile anywhere from 23°in heatsensitive species to 31°in heat-tolerant species (Chakir et al. 2002;David et al. 2005). In D. melanogaster, Rohmer et al. (2004) found that differences between Y chromosome lineages from tropical and temperate regions are responsible for much of the variation in thermal sensitivity of spermatogenesis. Since spermatogenesis is essential for male fitness, we expect a Y chromosome effect on thermal sensitivity to translate into effects on mal...