Genetic diversity and inbreeding in an endangered island-dwelling parrot population following repeated population bottlenecks

Genetic diversity and population structure can have important implications for the management of threatened species. This is particularly true for small, isolated populations that have experienced significant declines or population bottlenecks. The Norfolk Island green parrot Cyanoramphus cookii is an endangered species at risk of inbreeding and loss of genetic diversity due to its restricted range and the population bottlenecks experienced in recent decades. To assess the severity of inbreeding and loss of genetic diversity in the population we analyzed single nucleotide polymorphisms (SNPs) for 157 unique genetic samples collected from nestlings and randomly captured adult birds between 2015 and 2022. We also assessed the population for genetic structure, calculated sex ratios, and looked for evidence of past population bottlenecks. Our analysis revealed that 17.83% of individuals sampled were highly inbred (F > 0.125), although expected heterozygosity (HE) did not significantly differ from observed heterozygosity (HO) and the average inbreeding coefficient was low. The estimated effective population size (Ne) was 43.8 and we found no evidence of genetic structure. Demographic simulations provided support for scenarios including multiple population bottlenecks, when compared to those with a single population bottleneck or no past bottlenecks. We discuss the implications of our findings for the future management of the species including any potential attempt to establish an insurance population via translocation. Our study highlights the importance of considering population genetics when determining appropriate management actions for threatened species and the need to assess non-model species on an individual basis.