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Title: Characterising the impact of directional forces on genomic variation
Author: Barton, Henry Juho
ISNI:       0000 0004 8501 4515
Awarding Body: University of Sheffield
Current Institution: University of Sheffield
Date of Award: 2019
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Mutation generates new genetic material on which evolutionary processes, such as selection and genetic drift, can act. Consequently, understanding mutations, and the forces that determine their fate, is vital for understanding how the variety of life seen today evolved. Technological and methodological advances over the past decade have lead to a growing availability of whole genome sequencing and re-sequencing datasets, allowing existing questions in genome evolution to be addressed more broadly, and previously understudied topics to be addressed. Two such areas are the selective landscape of insertions and deletions (INDELs), and the impact of GC biased gene conversion (gBGC) on non-coding base composition. To date, INDELs have remained understudied relative to point mutations, despite being the second most common form of variation. In part, this is due to the challenges of calling and correctly orientating INDELs, and in part due to a lack of methods available to quantify the selective pressures acting on them. Work on gBGC has largely concentrated on its action in coding regions, often with a view of how it confounds inferences of selection in these regions. In this thesis I make use of a number of publicly available datasets to extend the present state of knowledge in these two areas. Chapter 2 introduces a new method for inferring the distribution of fitness effects for INDELs, demonstrating its accuracy through simulations and using it to characterise the selective pressures on INDELs in coding sequences in Drosophila melanogaster. Chapter 3 applies the method to a dataset of great tit (Parus major ) genomes and extends it to the non-coding regions in this species. Finally, Chapter 4 addresses the role and strength of gBGC across the non-coding genome of the great tit and the zebra finch (Taeniopygia guttata), and how gBGC and INDELs have contributed to base composition in these species.
Supervisor: Zeng, Kai ; Slate, Jon Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available