Abstract
Changes in the physical environment over time has a sustained impact on the physical and genetic features of taxa and populations within a species. New Zealand has had a long and varied history in its 80-million-year existence which has shaped the endemic and native biota that call it home. The recent field of Palaeogenomics has shed light on the complex ways that the changes in the environment have impacted those species. The New Zealand goose Cnemiornis is a genus of recently extinct large and flightless waterfowl which was previously resident on both two main islands in the archipelago: Cnemiornis gracilis on the North Island, and Cnemiornis calcitrans on the South Island. In this thesis, palaeogenetic approaches were used to sample the DNA of Cnemiornis and construct the phylogeographic history and structure of the genus, examining whether the genus has been impacted by geologic events in patterns like those observed in cohabitant avifauna. Recovered partial mitogenomes confirmed the placement of Cnemiornis within the Anatidae family as the sister taxon to the extant Cape Barren goose Cereopsis novaehollandiae. Strong support for the existence of two species of Cnemiornis was shown through phylogenetic analysis, indicating that the two species diverged in the Mid Pleistocene as a result of the closure of the Manawatū strait. Within the South Island species C. calcitrans, phylogenetic analysis found strong support for two genetically distinct clades, called here C. calcitrans “northern” and C. calcitrans “southern”, with divergence attributed to the glacial-interglacial cycles of glacier expansion and contraction in the Southern Alps, and the Mid Pleistocene climate transition (MPCT). Within the North Island species, evidence thought limited was found to support two clades called here C. gracilis “eastern” and C. gracilis “western”, with divergence attributed to the intermittent volcanic events of the Taupō Volcanic Zone in central North Island. This study represents the first in-depth examination of a previously little known extinct New Zealand genus and furthers the evidence for palaeogenomics as a significant tool in the understanding of how a changing world impacts living organisms.