Defining Minimum Founder Population Sizes to Improve Genetic Diversity Retention in Captive-Bred Stocks of Otago Skink, Oligosoma otagense

Abstract

Captive breeding programmes are becoming an increasingly used management method for conserving species where extinction is otherwise likely due to significant in situ threats and marginal translocation possibilities. Retaining high levels of representative genetic diversity in captive populations may help improve the success of captive-bred individuals upon release to the wild. However, this requires careful planning prior to population establishment to successfully mitigate some of the significant genetic bottlenecks encountered when founding a new captive population. Here I used population viability analyses to define the minimum number of founders necessary to maintain a predefined level of representative genetic diversity within a captive population of eastern provenance Otago skink, Oligosoma otagense, over time. As inbreeding depression can reduce the accuracy of population viability analyses, I also explored the potential effect of inbreeding occurrence on individual survival probability within the existing captive eastern provenance Otago skink population.

Inferences of individual inbreeding occurrence were generated based on existing or newly genotyped microsatellite data, and pedigree data from the eastern provenance Otago skink studbook. Genetic and pedigree-based inferences of inbreeding occurrence were compared to determine the effectiveness of using either technique. Heterozygosity-heterozygosity correlations showed a poor relationship between genetic inferences of inbreeding occurrence and likely inbreeding occurrence (heterozygosity by locus R2 = 0.18 ± 0.0004 SE, internal relatedness R2 = 0.15 ± 0.0004 SE), with poor correlation also found between genetic and pedigree based inferences of inbreeding occurrence (P = 0.048, R2 = 0.029 and P = 0.006, R2 = 0.064 for internal relatedness and heterozygosity by locus respectively). The use of genetic based inferences of inbreeding occurrence was afterwards discontinued in this study. Survival analysis of lifespan data from the eastern provenance Otago skink studbook (n = 206) showed that increasing individual pedigree-based inbreeding coefficients (ƒi) were not significantly affecting individual survival probability (hazard ratio = 1.004, P = 0.712). This result is similar to those of other studies of inbreeding depression in captive populations, where the effect of inbreeding on fitness traits such as survival has been found to be weak. Given this result, inbreeding depression was not included in the population viability analysis models used to define minimum founder population numbers.

Population viability analyses were undertaken using demographic data from the existing captive eastern provenance Otago skink studbook, previous studies of Otago skink demographic rates, and unpublished rates of translocation survival. This study found that at least 60 founder individuals would be required to retain rare alleles from the source population (those alleles originally occurring at a frequency of 5% in the gene pool) in a new captive population of eastern provenance Otago skink with a >95% probability to the end of a 20 year period in captivity. Given this outcome, a minimum founder population size of 60 individuals is recommended in the establishment of captive populations of threatened lizard species with similar life histories in future. However, differences in the demographic rates experienced by other threatened species populations in captivity may alter the number of founders necessary to maintain this level of genetic diversity retention. It is therefore recommended that managers of threatened species intending to create new captive populations undertake prior planning to define the number of founders necessary to retain representative genetic diversity within the captive stock, using the methods detailed in this study.