Genes located on the mammalian Y chromosome outside of the pseudoautosomal region do not recombine with those on the X and are predicted to either undergo selection for male function or gradually degenerate because of an accumulation of deleterious mutations. Here, phylogenetic analyses of X-Y homologues, Zfx and Zfy, among 26 felid species indicate two ancestral episodes of directed genetic exchange (ectopic gene conversion) from X to Y: once during the evolution of pallas cat and once in a common predecessor of ocelot lineage species. Replacement of the more rapidly evolving Y homologue with the evolutionarily constrained X copy may represent a mechanism for adaptive editing of functional genes on the nonrecombining region of the mammalian Y chromosome.T he eutherian Y chromosome is unusual because conventional recombination with the X is limited to genes within the small pseudoautosomal region. Comparative analyses of mammalian sex chromosomes suggest that the Y acquires genes through recombination with the X in the pseudoautosomal region, and that these genes subsequently undergo extensive repositioning into the nonrecombining region of the Y (NRY) via inversion and intrachromosomal translocation (1, 2). There, X-Y recombination ceases, and genes in the NRY are predicted to either become specialized for male function (3, 4) or gradually degenerate from the accumulation of deleterious mutations through processes such as Muller's ratchet (5), hitchhiking with favorable mutations at other Y genes (6), background selection (6), and insertion of retroposons (7).However, additional factors may influence the genetic composition and evolution of genes within the NRY. For example, during hominid evolution 4-5 million years ago, a major portion of the X long arm was incorporated onto the Y (8) and subsequently was repositioned into the NRY via intrachromosomal recombination between repetitive LINE (long-interspersed element) retroposons (9). This is evidence that the occasional translocation of large chromosome fragments into the NRY is possible. Another example is Zfx and Zfy, a pair of gene homologues located in the sex-specific regions of chromosomes X and Y, respectively. A sequence comparison of coding regions of these genes between rodent and primate taxa (10-12) revealed lower than expected divergence estimates between these X and Y homologues. Thus, some form of genetic exchange was indicated in the NRY.Here we address this potential evolutionary paradox by a comprehensive sequence analysis of the terminal Zn-finger exon of Zfy and Zfx in 26 species of the cat family Felidae. Unusual patterns of diversification between these homologues demonstrate a novel mechanism of genetic exchange, termed ectopic gene conversion, occurs within the nonrecombining regions of the X and Y. Because the felid phylogeny has been well established by using multiple molecular genetic markers (13-20), we were able to characterize precisely two distinct episodes of ectopic gene conversion of Zfy by Zfx during the evolution of modern-d...
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