Investigating the linear and non-linear mechanisms of protein coding innovation across the animal kingdom.
Year: 2017
Type: other
Abstract: In this thesis, evolutionary models and frameworks for studying protein coding\nsequence evolution in the Metazoa are explored. The Metazoa refers to all\nmulticellular animals. The models and frameworks applied are phylogeny and\nnetwork based – we propose that both approaches are necessary to understand the\nvarious mechanisms of protein evolution that can be involved in protein family\nevolution. Firstly, we apply a phylogenetic approach to assess whether the additional\nparameterisation and computational requirements associated with heterogeneous\nmodelling can be justified in terms of model fit and adequacy. The question addressed\nin Chapter 2 is whether we can accurately and adequately model the position of the\nplacental mammal root. We show that model misspecification has resulted in the\nconflicting positions for the root of the placental mammal phylogeny in the recent\nliterature. Therefore, inadequate models can result in wrong inferences about the\nevolutionary history of the sequences. Indeed, phylogenetic models may not be\nappropriate for the evolutionary process at work, for example in the case of\nrecombinatorial processes. Therefore, Chapters 3 and 4 focus on the application of\nnetwork theory, and specifically sequence similarity networks, to model the evolution\nof protein coding sequences by gene fission/fusion and domain shuffling – referred to\nthroughout as gene remodelling events. Little is known about the contribution of these\nremodelling events in protein evolution and in the evolution of the Metazoa in\nparticular. These are innovations in the protein coding sequences that are brought\nabout by shuffling of regions of DNA from different proteins (this is not direct\ndescent with modification and therefore not strictly phylogenetic in nature as it\nrequires multiple roots on the phylogenetic tree). In this thesis, we describe the\napplication of phylogenetic and network based models of protein coding evolution to\nsequence data from all major groups across the Metazoa and we define the basic\ncharacteristics and rules for gene remodelling in the Metazoa.
Author: Ray Moran
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W2768440897