PhDThe 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-polyploidisationNERC, the Linnean Society, the Systematics Association and
Botanical Research Fun
