Investigating relationships in the New Zealand alpine Ranunculus using RNA sequencing : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Plant Biology at Massey University, Manawatū, New Zealand

Whether the alpine flora of New Zealand is resilient enough to withstand the effects of climate change is an important and unanswered question. Conspicuous amongst the alpine flora are the species of Ranunculus in section Pseudadonis. This monophyletic group of species is hypothesised to have rapidly diversified into distinct mountain habitats, with some species convergently evolving into similar habitats. Investigating how cryptic physiologies have convergently evolved in some Ranunculus species may provide insight into the adaptive potential of this group of plants. It has been argued that hybridisation is an important evolutionary process explaining the morphological and ecological variation of New Zealand alpine Ranunculus species. Hybridisation, and in particular introgression, has also been hypothesised elsewhere as an effective means for closely-related species to share genetic material and undergo rapid adaptation through selection of standing genetic variation. This research aimed to use RNA sequencing technology to address questions of physiology and phylogeny amongst four taxa of the alpine Ranunculus group. Habitat characterisation was carried out before plants were sampled and grown under standardised conditions in a common garden experiment. Bioinformatic approaches were used to analyse high-throughput sequencing data of RNA extracted from these laboratory-grown plants. This research illustrates the potential of RNA sequencing for studying non-model plant species. However, the conservative analytical approaches adopted, and noise within the data, limited inferences of physiological traits and evolutionary relationships. Analyses of heterozygosity and issues with de novo transcriptome assembly suggested greater numbers of gene variants than expected for these small, isolated populations of alpine plants. These gene variants likely occur because of the polyploid genomes of the New Zealand alpine Ranunculus. Further work is needed, however, to confirm this genetic diversity. Overall, this work reinforces the difficulties in studying non-model polyploid systems. Yet, it does hint at a genetic richness within the alpine Ranunculus that might aid survival of this clade during a rapidly changing future