Understanding the effects of inbreeding, genomic diversity and infectious disease to restore the threatened Mauritius parakeet

Small, isolated populations face elevated risks of extinction due to reduced genetic diversity, increased inbreeding, and vulnerability to emerging infectious diseases. These threats are especially pronounced in island-endemic species, where demographic bottlenecks and limited gene flow can accelerate the loss of evolutionary potential. This thesis investigates how genetic variation, inbreeding, and disease susceptibility interact to influence population dynamics in the Mauritius parakeet (Alexandrinus eques), a species that has undergone dramatic demographic recovery following near-extinction. Combining long-term field monitoring, pedigree data, and whole genome sequencing, this study explores the genetic and ecological drivers of recruitment and resistance to Beak and Feather Disease Virus (BFDV), a key threat to the species. Pedigree-based and genomic measures of inbreeding were used to assess their impact on recruitment success, revealing that inbreeding generally reduces fitness-related outcomes, but that lineage-specific factors can modulate this effect. Genomic analyses identified variation in heterozygosity and runs of homozygosity (ROH), with medium-length ROHs particularly associated with increased disease susceptibility which likely reflecting historical inbreeding occurring around the time of the BFDV outbreak. Regions of the genome showing elevated differentiation between recruited and non-recruited or susceptible and resistant individuals were detected, with several candidate loci overlapping genes involved in immune function and viral response. One such gene, SND1, emerged as a repeated signal across analyses, highlighting the potential for identifying genomic targets of selection even in genetically depauperate populations. This work demonstrates how the integration of genomic data with long-term demographic records can reveal hidden evolutionary processes in conservation-reliant species. It provides critical insight into how historical and contemporary factors shape genetic health and disease resistance, and underscores the importance of maintaining genetic diversity not only for demographic recovery but also for adaptive potential in the face of future challenges.