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dc.contributor.authorDodsworth, Steven Andrew
dc.date.accessioned2016-06-13T10:39:39Z
dc.date.available2016-06-13T10:39:39Z
dc.date.issued2015-12-24
dc.date.submitted2016-06-10T14:03:20.483Z
dc.identifier.citationDodsworth, S.A.2015, Genome skimming for phylogenomics, Queen Mary University of London.en_US
dc.identifier.urihttp://qmro.qmul.ac.uk/xmlui/handle/123456789/12815
dc.descriptionPhDen_US
dc.description.abstractThe advent of next-generation (or high-throughput) sequencing (NGS/HTS) has revolutionised biology, with much impact on the field of molecular phylogenetics. Traditional debates of taxa versus characters are now somewhat defunct in the phylogenomics era. In this thesis I focus on one particular HTS approach, ‘genome skimming’ as a phylogenomics and genomics method. I extend the scope of genome skimming to encompass more of the data present from low-coverage genome sequencing, using a novel method to analyse genomic repeat abundances as phylogenetic characters in addition to the assembly of high-copy organellar and nuclear DNA (plastomes and the nuclear ribosomal DNA cistron). The methodology for using nuclear repeats is initially developed, and then genome skimming is used to explore the phylogenetic relationships within a recent radiation – Nicotiana section Suaveolentes (Solanaceae). These data provide a significant improvement in our phylogenetic understanding of the group, despite low levels of genetic divergence between the core Australian species of Nicotiana section Suaveolentes and significant incomplete lineage sorting. Support is garnered for the whole genome duplication (WGD) radiation lag-time model in section Suaveolentes, with a significant increase in diversification in the last 2 million years following a lag of approximately 4 million years after the origin of the section at ~6.8 mya (allopolyploidisation event). Associated with this diversification are various processes of diploidisation including chromosome number reduction and genome downsizing. In addition to genomic patterns, there are ecological ones associated with diversification, including a general switch from perennial to annual life history strategy (with some notable reversals). These results paint Nicotiana section Suaveolentes as a recent and ongoing radiation, and are placed in the broad context of angiosperm diversification post-polyploidisation
dc.description.sponsorshipNERC, the Linnean Society, the Systematics Association and Botanical Research Funden_US
dc.language.isoenen_US
dc.publisherQueen Mary University of Londonen_US
dc.subjectBiological and Chemical Sciencesen_US
dc.subjectnext-generation sequencingen_US
dc.subjectmolecular phylogeneticsen_US
dc.titleGenome skimming for phylogenomicsen_US
dc.typeThesisen_US


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    Theses Awarded by Queen Mary University of London

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