Phylogenomic Approach to the Evolutionary Dynamics of Gene Duplication in Birds

New genes are thought to arise primarily through a process of gene duplication. Genes that are homologous as a result of divergence across lineages via speciation are said to be orthologous , whereas genes that are homologous as a result of gene duplication are paralogous (Li, 2006). Paralogous genes that are functionally redundant and selectively nearly neutral can result in one copy being mutated into a functionless sequence called a pseudogene, or they can be deleted altogether. On the other hand, some duplicated genes can be beneficial from their time of origin because of dosage effects (Kondrashov et al., 2002) and may ultimately be important for speciation. In Passeriformes (perching birds) this may be the case for growth hormone (GH) paralogs, which have undergone differential selection since their divergence (Yuri et al., 2008). In a process called subfunctionalization , each paralog adopts partial function of their ancestral gene (Nowak et al., 1997; Lynch and Force, 2000). Changes in gene expression immediately following duplication as a result of