| Summary: | The phenomenon of complexity in living organisms is widely discussed but poorly understood. This thesis attempts to develop our understanding of complexity, particularly the relationship between complexity as manifest in the genome and at the phenotypic level. Firstly, a morphospace encompassing the whole of the animal kingdom is constructed, which demonstrates that the concept of phyla as representing static bodyplans is incorrect, so that organism are diverging rather than converging over time, and that clusters formed by phyla in morphospace are the result of an artefact of extinction of intermediates. This suggests that processes governing the generation of animal form are uniformitarian in nature. There is a clear relationship between an organism's disparity and its histological complexity, as well as its microRNA repertoire, suggestive of a role for GRN expansion in the generation of disparity. However, there is no relationship demonstrated between disparity and domain content within animals, suggesting that the two phenomena are not linked in a straightforward manner. At a larger scale, domains provide an accurate metric of morphological complexity, with domain increases strongly associated with two of the major transitions in evolution, eukaryogenesis and multicellularity. However, there is little evidence of a left wall of complexity guiding the evolutionary process, thus supporting the notion of a driven trend toward increasing complexity over the course of evolutionary history. Finally, domains are also assessed for their value as phylogenetic characters. Domains can overcome some of the limitations of other phylogenetic characters as they can be detected over large evolutionary distance and represent the entire protein-coding region of an organism. Whilst domains resolve many well-established relationships between organisms, they appear to suffer from the same artefacts which affect other phylogenetic character types, but can also reveal interesting domain-sharing relationships between ecologically related species.
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