Sex chromosomes are generally believed to have descended from a
pair of homologous autosomes. Suppression of recombination
between the ancestral sex chromosomes led to the genetic degeneration
of the Y chromosome1. In response, the X chromosome
may become dosage-compensated1,2. Most proposed mechanisms
for the degeneration of Y chromosomes involve the rapid fixation
of deleterious mutations on the Y1. Alternatively, Y-chromosome
degeneration might be a response to a slower rate of adaptive
evolution, caused by its lack of recombination3. Here we report
patterns of DNA polymorphism and divergence at four genes
located on the neo-sex chromosomes of Drosophila miranda. We
show that a higher rate of protein sequence evolution of the neo-
X-linked copy of Cyclin B relative to the neo-Y copy is driven by
positive selection, which is consistent with the adaptive hypothesis
for the evolution of the Y chromosome3. In contrast, the neo-
Y-linked copies of even-skipped and roundabout show an elevated
rate of protein evolution relative to their neo-X homologues,
probably reflecting the reduced effectiveness of selection against
deleterious mutations in a non-recombining genome1.Our results
provide evidence for the importance of sexual recombination for
increasing and maintaining the level of adaptation of a population
