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The ability to raise an immune response is essential for all life. Despite this, the evolution of immune systems is poorly understood, as immune genes confound many bioinformatic analyses. This is driven by the rapid rates at which immune genes evolve due to the incessant arms race between host and pathogen often causing standard phylogenetic approaches to fail to accurately model the evolutionary history of immune gene families. Many phylogenetic lessons have been learned since the dawn of the phylogenomics era however, and genome sequences of non-model organisms have now been assembled, permitting improved immune gene detection and hence taxon sampling. In this thesis, I have paired sophisticated phylogenomic tools, including outgroup-free rooting methods, and substitution models that account for structural and functional constraints on protein evolution, with new genome and transcriptome sequence data from taxa that allow inference of the ancestral immune state in vertebrates and animals. Using this approach, I have managed to identify the origins of several key immune genes and families. My results support ancestral complexity in the genes that regulate the functioning of vertebrate adaptive immune systems. My findings also support the presence of a complement system, a front-line innate immune defence, in the ancestor of all animals. I show that this system later underwent a period of major remodelling early in vertebrate evolution, generating novel complement systems in at least three major vertebrate taxa. It is clear from my findings that combining sophisticated phylogenetic models with enriched taxon …