Biogeographic patterns in alpine New Zealand : using nuclear and chloroplast loci to investigate divergence and secondary contact in Notothlaspi (Brassicaceae) : 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

Lineage divergence and hybridisation are integral processes in biological evolution. In New Zealand alpine environments, isolation by distance and isolation by environment are two key processes that drive evolutionary change in plant lineages. The Pleistocene climate fluctuations isolated and re-introduced lineages, and complex geological substrates host several edaphic endemic floras. However, to our knowledge, plant diversification has not been studied at a population genetic scale in New Zealand alpine environments. Here, the three species in the alpine genus Notothlaspi (Brassicaceae) were selected to investigate divergence across heterogeneous landscapes. Three molecular marker types were trialled in Notothlaspi: thirty new nuclear microsatellites, five universal chloroplast loci, and RAPDseq-generated SNPs. Twelve suitable microsatellite markers were selected, and the trnL-F and psbA-trnH loci produced high quality sequences with inter- and intra-specific polymorphisms. The RAPDseq scheme identified 41 promising polymorphic loci with several SNPs. The twelve microsatellite markers, and the trnL-F chloroplast locus, were used to investigate the spatial distribution of genetic variation and to infer historical influences on the evolution of Notothlaspi. Within N. australe, an unexplained biogeographic split within the Kahurangi National park was discovered that deviates from expectations under isolation by distance. This suggests diverged ancestral groupings, such as in glacial refugia, and/or local adaptation to substrate. Within N. rosulatum, the trnL-F chloroplast locus distinguished populations in Marlborough with greater resolution than the nuclear microsatellite data, indicating a prevalence of pollen-mediated geneflow. A potential past or present hybrid zone was also identified in the Richmond Forest Park, an area of range overlap between all three species. Here, we describe the first population genetic investigation in the alpine regions of the northern South Island of New Zealand. The findings make important contributions to future studies on biogeography, and the role of heterogeneous environments on the diversification of the New Zealand flora