| Summary: | <p>Abstract</p> <p>Backgound</p> <p>The <it>RPS4</it> gene codifies for ribosomal protein S4, a very well-conserved protein present in all kingdoms. In primates, <it>RPS4</it> is codified by two functional genes located on both sex chromosomes: the <it>RPS4X </it>and <it>RPS4Y </it>genes. In humans, <it>RPS4Y </it>is duplicated and the Y chromosome therefore carries a third functional paralog: <it>RPS4Y2</it>, which presents a testis-specific expression pattern.</p> <p>Results</p> <p>DNA sequence analysis of the intronic and cDNA regions of <it>RPS4Y </it>genes from species covering the entire primate phylogeny showed that the duplication event leading to the second Y-linked copy occurred after the divergence of New World monkeys, about 35 million years ago. Maximum likelihood analyses of the synonymous and non-synonymous substitutions revealed that positive selection was acting on <it>RPS4Y2 </it>gene in the human lineage, which represents the first evidence of positive selection on a ribosomal protein gene. Putative positive amino acid replacements affected the three domains of the protein: one of these changes is located in the KOW protein domain and affects the unique invariable position of this motif, and might thus have a dramatic effect on the protein function.</p> <p>Conclusion</p> <p>Here, we shed new light on the evolutionary history of <it>RPS4Y </it>gene family, especially on that of <it>RPS4Y2</it>. The results point that the <it>RPS4Y1 </it>gene might be maintained to compensate gene dosage between sexes, while <it>RPS4Y2 </it>might have acquired a new function, at least in the lineage leading to humans.</p>
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