Abstract
Anthropogenic impacts are currently causing the sixth mass extinction of life on Earth. Genomics can provide some of the many tools needed to slow this loss of biodiversity. It can improve our understanding of species populations and biology, and genetic factors which exacerbate their declines. These insights should inform management of endangered species.
An endangered species in need of such management is the kākāpō, an endemic flightless parrot of Aotearoa New Zealand. Kākāpō were pushed to the brink of extinction as a result of predation by introduced mammals. Their population is now increasing thanks to an intensive management programme. However, their recovery is slow due to low reproductive success, possibly due to inbreeding, and they have low genetic diversity and adaptive potential. In this thesis, the potential for genomics to aid recovery of the kākāpō, by better understanding their population, and the impacts of the management programme, was explored. A secondary focus was placed on developing resources and methods for future use in kākāpō conservation. Whilst these results primarily help the kākāpō, the methods compared here, or the resources identified as most impactful to conservation, also have potential for broader application to other endangered species.
First, the pedigree of kākāpō was refined based on genomic data, and the most successful methods to do so were identified. Previously unknown parent-offspring relationships were discovered, as well as errors in the originally recorded pedigree. Understanding of the relationships between individuals in a managed endangered population is crucial to mitigate inbreeding between close relatives, so these results have informed genetic management of kākāpō. In addition, trio data from the pedigree was used to improve the variant dataset which has become the foundation for all subsequent genomic work in kākāpō.
Secondly, a phased haplotype dataset was created for kākāpō. This resource can be used to impute variants in low-coverage sequence data, to reduce costs if additional kākāpō are sequenced in future. The haplotype data was also used as input for a forward-in-time population and genome model of kākāpō developed in this work. Using this model, management of kākāpō aiming to preserve genetic diversity was compared to a scenario with no genetic management. Genetic management resulted in loss of fewer founder lineages, and more equal representation of founder genomes, than the scenario without genetic management. However, loss of alleles to genetic drift did not differ between the two scenarios, and instead was influenced by their starting frequency. Therefore, management that focusses on ensuring the representation of individuals which carry rare alleles may result in maintenance of more genetic diversity overall.
Short-read sequencing was then used to produce a dataset for a new cohort of recently-hatched kākāpō. This data will be used to support future work in assessing the genomic consequences of management in real kākāpō, as well as providing continued good understanding of their relatedness.
Finally, a portable nanopore sequencing approach was developed to aid on-the-ground management of kākāpō during the 2022 breeding season, by providing rapid access to sex and parentage results for chicks. Weight, which differs between the sexes, is used as a proxy for chick health. Rapid determination of the sex of chicks after they hatch therefore enables better health monitoring. Parentage results inform translocations of chicks between nests and reveal the results of artificial insemination. The nanopore sequencing which was done informed healthcare of kākāpō chicks, revealed a skewed sex ratio in the 57 hatched chicks, and showed that artificial insemination was successful in producing 8 surviving kākāpō chicks.
Overall, this work produced considerable new resources to further enable genomic support of the Kākāpō Recovery Programme. Whilst demographic management and provision of safe habitat are still critical components of the species recovery, genomics can provide input that can aid even non-genetic aspects of management. This was demonstrated through application of sex results to improve health monitoring of young chicks. Furthermore, the application of genomics to kākāpō conservation provides an example to indicate impactful resources and effective methods from genomics which can aid in the recovery of other endangered species.