Abstract
Population declines in endangered species often lead to increased occurrences of inbreeding, resulting in erosion of genetic diversity and the accumulation of homozygosity across the genome. Genetic methods are increasingly being used to monitor endangered populations and inform conservation management strategies, with recent advancements in genomic sequencing promising to revolutionise our understanding of inbreeding and contribute to new strategies for promoting species recovery. However, the advantages of whole-genome sequencing over more cost- effective sequencing approaches in conservation are not always clear, with lower coverage methods carrying the benefit of allowing more individuals in a population to be sequenced.
This thesis employs extensive whole-genome sequencing (WGS) and reduced- representation sequencing (RRS) datasets from the critically endangered kākāpō (Strigops habroptilus) to compare the performance of each approach for inbreeding analysis and to undertake a comprehensive re-evaluation of inbreeding in this species. After a rapid decline in the population during the 1800s, kākāpō were presumed functionally extinct until the discovery of a small surviving island population in the late 1970s. The long-term isolation and small size of the founding population renders the majority of the extant kākāpō population severely inbred. By comparing different inbreeding coefficients and genomic sequencing methods in kākāpō, I demonstrate that variation in inbreeding can be reliably estimated from RRS datasets using coefficients based on runs of homozygosity (ROH), which were highly correlated with estimates produced from WGS data. I then utilise estimates of inbreeding based on ROH to evaluate evidence for inbreeding depression in chick survivorship, female reproductive success, and susceptibility to pathogens. Genome-wide variation in inbreeding strongly predicted egg hatching success but not chick survivorship or pathogen susceptibility. However, additional searches for inbreeding-fitness correlations at the level of individual chromosomes revealed genomic regions associated with significant effects on clutch size and egg volume. By searching for pathogens in discarded WGS reads that do not map to the kākāpō reference genome, I also detected the presence of multiple previously unknown pathogens that pose a potential threat to the long-term health of kākāpō. The research presented in this thesis not only contributes to kākāpō conservation management but also produces significant insights into resource allocation decisions for other species of conservation concern.