Abstract
The ongoing world-wide extinction crisis has spurred major conservation efforts in the last decades. Knowing a species’ evolutionary history and present genetic variability is important to make informed conservation decisions, and for this reason genetic and genomic tools have been increasingly integrated into many aspects of conservation biology and ecology. With an history of long isolation and repeated colonisation events, New Zealand offers unique opportunities for the study of evolution and anthropogenic impacts. Most of its endemic native species have declined since the introduction of invasive non-native pest species and many are now threatened with extinction. The New Zealand kākā (Nestor meridionalis) is an endangered (IUCN) forest parrot endemic to New Zealand. Once common across the country, it is now present only in small patches of its past distribution and thriving only on pest-free offshore islands and mainland island ecosanctuaries. There are two recognised subspecies of kākā, the North Island kākā (N. m. septentrionalis) and the South Island kākā (N. m. meridionalis), which have differences in plumage colour, size and diet. Previous studies have found no evidence of genetic divergence between the two subspecies, using a small subset of nuclear and mitochondrial markers. The aim of this project was to reconstruct the evolutionary history of the New Zealand kākā, using state of the art genomic technologies, and to explore the possible implications of our findings for the conservation management of this species. I produced the first genome assembly for the New Zealand kākā, and used it in a whole genome comparison with kea, kākā’s sister species, to evaluate the drivers of their divergence and evolution to different lifestyles. I then expanded this investigation using genotyping-by-sequencing to produce thousands of genomic markers for 92 kākā individuals from eight populations representative of their current distribution range. I used this data for an assessment of the current population structure of the species and for an exploratory study of local adaptation and selection among the kākā subspecies and populations. Finally, I used ancient DNA methods to produce whole mitochondrial genome sequences for a selection of subfossil and historical specimens from museum collections, and investigate past levels and distribution of genetic diversity in kākā.
The results from this study suggest that kākā genetic variability has been shaped by past and recent demographic events. Kākā and kea diverged about 1.7 mya, during the climatic oscillations of the Pleistocene. As a forest specialist species, kākā populations were affected by reductions in forest habitats and were probably restricted to multiple North Island refugia during glacial periods. Overall, I found high levels of genetic diversity and gene flow in past and present populations and no evidence of population structure distinguishing the two kākā subspecies, suggesting that kākā should be considered as a metapopulation. However, the recent population decline and fragmentation have left indications of lower genetic diversity in a few isolated populations, and I recommend that conservation management increase their efforts to re-establish connectivity throughout the current kākā distribution.