Gene and genome duplication in animal evolution

Abstract

Gene and genome duplications have an important role in evolution as a mechanism that creates novel genetic material. Paralogues created by duplication can diversify in function and contribute to the complexity of genetic networks, especially in the context of the gene regulation and signalling pathways that control animal development. Clusters of related genes that have arisen by tandem duplication illustrate the role of regulatory elements in preserving synteny by constraining gene neighbourhoods. Whole genome duplications have occurred on the stems of lineages characterised by the evolution of novel structures, adaptations to different environments, and species diversity. Here, I aim to understand how gene and genome duplications have impacted specific developmental gene families and processes throughout animal evolution with a comparative genomics approach. I make use of genomic resources from phylogenetically informative lineages, including new genomes of early-branching chordates, spiralians, and ecdysozoans. I have examined the impact of the vertebrate two rounds of whole genome duplication on chordate muscle development including the highly conserved family of myogenic regulatory factors and muscle gene expression. I have also investigated the evolution of homeobox gene families, with a focus on clusters of genes found across bilaterians, and specifically focus on the Hox cluster. With phylogenetic and synteny analyses, I found that a tandem duplication underpins the origin of two vertebrate muscle gene types. I examined the impact of whole genome duplication on a diversity of genes encoding proteins in a highly conserved signalling pathway in muscle, and I surveyed and revised the hypotheses for the evolution of homeobox genes across the bilaterians. In doing so, I have also generated a large resource of genomic annotations and protein sequences to facilitate functional studies in the future. These findings not only have identified certain duplications that have underpinned certain known instances of subfunctionalisation among paralogues, but also indicate gene families to target for future study.