Abstract
Captive insurance populations act as a safeguard against species extinction and can provide a source for future reintroductions into the wild. As more species become threatened globally there is increased pressure on captive insurance populations to support the conservation of their wild counterparts. Consequently, the genetic composition of captive populations becomes increasing important. Captive insurance populations should be both representative of the wild population throughout its range and genetically and demographically viable for long-term management. However, many captive populations have been established with a small number of founders, with unknown source location or relationships. The risks associated with small populations, such as genetic drift, loss of genetic diversity, and increased inbreeding are then exacerbated in captivity if founders are sourced from existing small wild population, where the likelihood that founders are unrelated is low. Therefore, existing captive populations may not be suitable as a future insurance for species.
Kea (Nestor notabilis) are a large species of parrot native to Te Waipounamu o Aotearoa (the South Island of New Zealand), listed as ‘Nationally Endangered’ under the Aotearoa New Zealand Threat Classification System. Despite current conservation strategies, the wild population is thought to still be declining, which has raised interest in the role the captive kea flock might play as a future source for wild reintroductions (i.e., an insurance population). Kea have been held in captivity since at least the early 1960s, with uncontrolled, sporadic breeding and a historical lack of regulations prior to the full protection of the species in 1986. Currently, the 59 kea held in captivity in New Zealand have an incomplete pedigree, skewed sex ratio, skewed founder representation, and unknown genetic structure, which undermines their suitability as a potential insurance population for future management.
In this thesis, genome-wide single nucleotide polymorphism (SNP) data generated through genotyping-by-sequencing (GBS) is used to examine the population genetic structure, genetic diversity, relatedness, and levels of inbreeding in the captive and wild kea populations. Overall, the genetic data presented here will help achieve the long-term goals and sustainable management of kea by i) determining if the current captive population is a viable insurance population for the species, ii) informing genetic management of captive kea to optimise genetic diversity retention, and minimise inbreeding, and iii) investigating the genetic structure and diversity of wild kea at a higher resolution.
Our analyses found greatest support for two genetic clusters in the wild kea population (north and south of the South Island), with a steady gradient of admixture between the two. These data provide support at a higher resolution to previous genetic studies on the wild population. Wild kea to the north of the South Island show lower levels of genetic diversity and higher levels of inbreeding relative to the rest of the wild kea population, and the captive population. Long-term population monitoring and genetic analyses will be essential to accurately examine trends in genetic diversity and inbreeding of wild kea populations, particularly if populations continue to decline.
The pedigree reconstruction using relatedness estimates derived from the GBS data was largely congruent with the studbook pedigree. Notably, however, three putatively unrelated individuals appear to be first-order relatives (parent-offspring or full-sibling). This finding is indicative of a rejection to the typical assumption that founders are unrelated, even for an endangered species with a sizeable wild population. Additionally, an understanding of the relationships among kea in the current captive population has implications for the future genetic management and breeding of the population.
Despite no signs of inbreeding or reduced genetic diversity, the captive kea population is not genetically representative of the wild kea population throughout its range, nor is it viable for long-term management. It is recommended that the captive population be supplemented with additional wild founders sourced from the more genetically diverse, and currently underrepresented, southern end of the South Island. This study highlights the importance of proactive genetic assessments and the integration of genetic information into captive and wild species management, particularly when establishing or supplementing captive insurance populations.