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Recombination is believed to prevent genetic deterioration in sexual populations because it allows conservation of functional genotypes by removing deleterious mutations. Moreover, evidence that nonrecombining segments of a genome deteriorate is provided by genetic experiments in  Drosophila  and yeast. Y chromosomes generally do not recombine along most of their length, and thus Y chromosome genes, despite having been selectively maintained for their function, could be lost from the genome. Here we present definitive evidence that functional Y genes can be lost from the mammalian genome.  TSPY  genes must have been selectively maintained on the mammalian Y chromosome since before the radiation of eutheria, 80 million years ago, as they are found conserved on the Y chromosome in two mammalian orders: primate and artiodactyl. We have now identified  TSPY  on the rodent Y chromosome, in mouse and rat. The gene structure and expression of rat TSPY suggest that it is a functional, testis-specific gene, but the closely related mouse gene,  Tspy , has clearly become non-functional, producing only low levels of aberrantly spliced transcripts. Thus  TSPY  lost its function in the mouse lineage after its divergence from the rat lineage. So, in the case of  Tspy  at least, the absence of recombination does appear to have led to the loss of a functional gene.

Rodent Y Chromosome TSPY Gene Is Functional in Rat and Non-functional in Mouse