As biodiversity declines globally and here in Aotearoa, many species and populations are now at risk of extinction. Captive insurance populations can safeguard species against extinction and provide individuals for future reintroductions. However, these insurance populations are often established from limited founders, with unknown relatedness and have been established and managed without conservation intent. This can lead to underlying genetic issues associated with small, isolated populations, such as genetic drift, reducing genetic diversity. There is the additional risk of inbreeding and admixture of distinct evolutionarily significant units if founded from multiple distinct populations. All these factors can reduce the suitability of a captive population to act as a long-term insurance population.
The robust skink (Oligosoma alani) is the largest skink species in Aotearoa, with a snout-vent length (SVL) of up to 160 mm. The species is extinct on the mainland due to habitat destruction and predation by introduced mammalian predators, but persists on offshore islands and in captivity. The captive population was established in the 1980s from 20 individuals from two genetically distinct source islands (off the Northland and Coromandel regions, according to the species recovery plan). The population has now grown to over 80 individuals; however, the pedigree is somewhat incomplete. This lack of pedigree information could have led to increased inbreeding and the mixing of genetically distinct offshore island populations in captivity. Additionally, the captive population had mixed husbandry success, and not all founders have contributed to the current captive population’s genetic diversity.
Genomic data can facilitate an understanding of the genetic structure and health of insurance populations. The generation of reference genomes and the use of genome-wide single-nucleotide polymorphism (SNP) data from genotyping by sequencing (GBS) can enable high-resolution population genomics, providing insights into the captive population. However, within Aotearoa’s 151 endemic terrestrial herpetofauna, genomic resources are considerably lacking.
In this thesis, I sequenced both the nuclear and mitochondrial genomes of a captive Whitaker’s skink (O. whitakeri), the first genomic resources for any Aotearoa skink. I assembled a 1.43 Gb nuclear genome and found the genome is highly complete (BUSCO = 96.9%) and has repeat content (45.7%) equivalent to chromosome-level assemblies. The species’ genome-wide heterozygosity is moderate (π = 0.0022), but higher than expected for a highly endangered species. The Whitaker's skink’s historical demography was also reconstructed with a Pairwise Markovian Coalescence model (PSMC), indicating a peak effective population size of 8.8 × 10⁵ individuals ~7.9 million years ago, but has since steadily declined and plateaued to ~ 21,300 individuals. However, sampling of a potentially admixed individual may have inflated these estimates of Ne and π. To gain insights into the captive robust skink population, I used the Whitaker’s skink nuclear genome to align GBS data from 81 captive and 6 wild individuals, which generated 10,460 reference-aligned SNPs, providing insights into population structure, genetic diversity, and inbreeding. Analysis of genome-wide SNPs detected two source populations consistent with the recovery plan records that state the captive population was founded from individuals from Castle Island (Coromandel) and Moturoa Island (Northland). These lineages are highly genetically distinct (FST = 0.7), and my analysis detected admixture between these lineages. Both captive Castle and Moturoa individuals have low diversity and high amounts of inbreeding. However, they show similar diversity to sampled wild individuals. Therefore, low diversity reflects captive individuals being sourced from small, isolated wild populations rather than genetic processes acting during captivity. I additionally reconstructed 91 relationships within the captive population’s pedigree and provided kinship estimates.
For the current captive population to act as an insurance population and maximise diversity while preventing inbreeding, individuals identified with first- or second-degree kinship estimates should not be mated. Admixed individuals should also be excluded from the breeding program to preserve these distinct lineages. We could not provide management recommendations on the Castle individuals due to poor data quality. Overall, I developed the first Aotearoa skink genome and demonstrated its direct benefits for conservation by gaining insights into the genetic structure and health of the captive robust skink population.