An investigation into the contribution of gene remodeling to protein coding gene family evolution across the Metazoa

This thesis explores gene evolution throughout the history of Metazoa. This group of multicellular organisms represents a wide range of diversity, embodied by the number of species, the multitude of morphological and developmental traits, and the complexity within the genetic elements dictating these traits. Although a significant amount of research has been carried out on gene family emergence and expansion in animal genomes, comparatively little research has been published on how these genes are formed. Of specific interest here is the role of complex, reticulated mechanisms of gene evolution in forming new genes, these include processes such as gene fusion and fission - hereafter referred to as gene remodeling. Current methods of gene family prediction are not sensitive to these mechanisms of gene evolution. We apply both network and phylogenetic models to characterise the traits and role of gene remodeling across Metazoa and take a data focused approach to attempt to resolve remaining issues within the animal tree of life (AToL). ​In Chapter 2 we took a novel network approach to quantify the contribution of gene remodeling events to novel protein coding gene family evolution in the animal tree of life. Using graph theory we analysed the partial homology shared between a set of animal proteomes spanning most major clades, and we placed these gene remodeling events onto the species tree. In addition to this, in Chapter 3 we sought to assess the phylogenetic properties of these events and their ability to reconstruct AToL, ultimately our aim was to determine if gene fusions could be deployed to resolve contentious regions within AToL. As a consilient approach is most desirable in phylogeny reconstruction, in Chapter 4 we examine the potential for resolving AToL using a combination of data types, i.e. gene fusions and previously published phylogenomic datasets. Specifically, we examined potential issues in annotation of homology and orthology within previously published animal phylogenomic datasets and focussed on determining what impact inaccurate definitions of orthology have had on resolving difficult or contentious parts of AToL.