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Title: Unravelling the origins and evolution of the Animal Kingdom using genomics
Author: Guijarro, Cristina
ISNI:       0000 0004 9348 7881
Awarding Body: University of Essex
Current Institution: University of Essex
Date of Award: 2020
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There are ~35 classified phyla/sub-phyla within the Animal Kingdom; some of which have unresolved relationships. The advent of genomics has made it possible to study new aspects of animal evolution, including comparative genomics (e.g., gene loss/gain, non-coding regions, synteny, etc), gene family evolution, and their evolutionary relationships using genome-wide data. No study to date has compared all the wealth of genomic data available to understand the evolution of the Animal Kingdom. Using a core bioinformatics pipeline and dataset to infer Homology Groups (HGs), the losses and novelties of these HGs were proven integral to the diversification of the animal kingdom. The same core pipeline was used to extract homeobox gene HGs, a key family used to understand origin and diversification in animals. Gene trees were inferred from the core dataset HGs to determine the evolution of a gene family iconic in the study of animal body plans. Conserved animal genes were also mined using the same pipeline and dataset. Animal phylogenomics is one of the most controversial areas in modern evolutionary science. Whilst many new methods have been developed, no study to date has tried to assess the impact of gene age in the reconstruction of evolutionary trees. The phyla with the largest count of HG losses also had the highest counts of HG novelties. Not all of these were strictly de novo, but the numbers suggest a re-manufacturing of the genetic material from the genes reduced to those that were more recently diverged. A comprehensive classification of all the diversity of animal homeobox genes is lacking. The gene trees showed complex patterns, with similar homeobox expansions between more distant species,and interlapping homeobox families. The highly conserved HGs recovered, for the animal phylogenies, well-established relationships between some phyla using maximum likelihood and Bayesian inference methods. Ctenophora was consistently recovered as sister to all other animals, and interesting relationships between ecdysozoans and lophotrochozoans. However, it was proven that it takes more than a highly conserved set of genes to infer a stable and correct phylogeny. Each of the additional methods used to extend the core bioinformatics pipeline revealed a pattern of correlation, particularly among the fast evolving species, such as platyhelminthes, nematodes and tardigrades. These HG losers, and gainers also had lineage specific homeobox clades, and caused artefactual problems in the phylogenies.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: Q Science (General) ; QH426 Genetics ; QL Zoology