Evolutionary History of Chordate <i>PAX</i> Genes: Dynamics of Change in a Complex Gene Family

<div><p>Paired box (<i>PAX</i>) genes are transcription factors that play important roles in embryonic development. Although the <i>PAX</i> gene family occurs in animals only, it is widely distributed. Among the vertebrates, its 9 genes appear to be the product of complete duplication of an original set of 4 genes, followed by an additional partial duplication. Although some studies of <i>PAX</i> genes have been conducted, no comprehensive survey of these genes across the entire taxonomic unit has yet been attempted. In this study, we conducted a detailed comparison of <i>PAX</i> sequences from 188 chordates, which revealed restricted variation. The absence of <i>PAX4</i> and <i>PAX8</i> among some species of reptiles and birds was notable; however, all 9 genes were present in all 74 mammalian genomes investigated. A search for signatures of selection indicated that all genes are subject to purifying selection, with a possible constraint relaxation in <i>PAX4</i>, <i>PAX7</i>, and <i>PAX8</i>. This result indicates asymmetric evolution of <i>PAX</i> family genes, which can be associated with the emergence of adaptive novelties in the chordate evolutionary trajectory.</p>