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Title: Sequence capture for phylogenomics in salmonid fishes : reconstructing evolution after genome duplication
Author: Robertson, Fiona M.
ISNI:       0000 0004 6498 1338
Awarding Body: University of Aberdeen
Current Institution: University of Aberdeen
Date of Award: 2017
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Whole genome duplication (WGD) is thought to promote evolutionary diversification via the divergence of retained duplicate genes (ohnologues), which occurs during the post WGD rediploidization process. The long-term evolutionary consequences of the rediploidization process for ohnologue evolution remains poorly characterized. In salmonid fishes, the rediploidization process is yet to be fully resolved since an ancestral WGD event (Ss4R) ~95 Mya. This group of fishes provides an ideal system for investigating the link between WGD, rediploidization and evolutionary diversification. However, the sequence resources available for salmonids remains restricted to a few lineages. The overarching goal of my thesis was to generate new genomic resources for salmonids to study the evolutionary consequences of Ss4R in the broadest possible phylogenetic framework. Using targeted sequence capture, large amounts of high-quality data was obtained across the salmonid phylogeny, allowing high-resolution phylogenomic investigations. This approach was successful in recovering thousands of protein-coding sequences, including a rich representation of ohnologues. The resultant dataset was thoroughly validated and used to test a newly proposed model - 'lineage-specific ohnologue resolution' (LORe) – to address the evolutionary consequences of delayed rediploidization. Under LORe, speciation precedes rediploidization, allowing independent ohnologue divergence in sister lineages sharing an ancestral WGD. LORe was characterized by reconstructing the rediploidization histories of Hox gene clusters retained from Ss4R and using a phylogenomic approach exploiting the Atlantic salmon genome as reference. This study provided strong empirical support for LORe and revealed its role as a significant source of lineage-specific sequence variation after Ss4R, The broader implications of LORe for our understanding of eukaryotic genome evolution were also considered on multiple levels. The sequence capture data was also utilized to characterize the post-Ss4R evolution of the insulin-like growth factor system at unprecedented phylogenetic resolution. This work demonstrated that it was possible to build complete protein-coding genes from sequence capture data that can correctly distinguish and identify new Ss4R ohnologues. As a result, I was able to characterize the historic selection regimes driving sequence divergence in IGF system ohnologues, which will be a useful approach in future investigations. Overall, my thesis demonstrates that targeted sequence capture offers a viable alternative to whole genome sequencing to investigate genome evolution in salmonids. While genome sequencing projects are underway or nearing completion for many salmonids, it is concluded that sequence capture still has a place in the ongoing research of these societally important fishes.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: Salmonidae