Abstract
Gene and genome duplication play an important role in the evolution of gene functions. Compared to an individual duplicated gene, gene clusters attract more attention, especially regarding their associations with innovation and adaptation. Here, we report, for the first time, the expansion of a gene family specific to teleost fishes, apolipoprotein D (ApoD) gene family. The only ApoD gene in the ancestor was expanded in two clusters via genome duplication and tandem gene duplication in teleost fishes, with a rather dynamic evolutionary pattern. Based on comparative genomic and transcriptomic analyses, protein 3D structure simulation, evolutionary rate detection and genome structure detection, subfunctionalization and neofunctionalization after duplication were observed both at the protein and expression levels, especially for lineage-specific duplicated genes that were under positive selection. Orthologous genes in the same physical order exhibited conserved expression patterns but became more specialized with the increasing number of duplicates. Different ApoD genes were expressed in tissues related to sexual selection and adaptation. This was particularly true for cichlid fishes, whose paralogues in different clusters showed high expression in anal fin pigmentation patterns (sexual selection related traits) and the lower pharyngeal jaw (related to feeding strategy), the two novelties famous for adaptive radiation of cichlid fishes. Interestingly, ApoD clusters are located at the breaking point of genome rearrangement. Since genome rearrangement can capture locally adapted genes or antagonous sex determining genes to protect them from introgression by reducing recombination, it can promote divergence and reproductive isolation. This further suggests the importance of the expansion of ApoD genes for speciation and adaptation in teleost fishes, especially for cichlid fishes.