Contrasting patterns of molecular evolution of the genes on the new and old sex chromosomes of Drosophila miranda

In organisms with chromosomal sex determination, sex is determined by a set of dimorphic sex chromosomes that are thought to have evolved from a set o f originally homologous chromosomes. The chromosome inherited only through the heterogametic sex (the Y chromosome in the case of male heterogamety) o ften exhibits loss of genetic activity for most of the genes carried on its homolog and is hence referred to as degenerate. The process by which the p roto-li chromosome loses its genetic activity has long been the subject of much speculation. We present a DNA sequence variation analysis of marker ge nes on the evolving sex chromosomes (neo-sex chromosomes) of Drosophila mir anda. Due to its relatively recent origin, the neo-Y chromosome of this spe cies is presumed to be still experiencing the forces responsible for the lo ss of its genetic activity. Indeed, several previous studies have confirmed the presence of some active loci on this chromosome. The genes on the neo- Y chromosome surveyed in the current study show generally lower levels of v ariation compared with their counterparts on the neo-X chromosome or an X-l inked gene. This is in accord with a reduced effective population size of t he neo-Y chromosome. Interestingly, the rate of replacement nucleotide subs titutions for the neo-Y linked genes is significantly higher than that fur the neo-X linked genes. This is not expected under a model where the faster evolution of the X chromosome is postulated to be the main force driving t he degeneration of the Y chromosome.