Simulated genetic efficacy of metapopulation management and the conservation value of captive reintroductions in a rapidly declining felid

In South Africa, cheetah (<i>Acinonyx jubatus</i>) occur as a relictual, unmanaged population of ‘free-roamers’, a managed metapopulation across fenced reserves, and in various captive facilities. To ensure that the Cheetah Metapopulation Project (CMP) is not at risk of losing overall genetic variation to drift or inbreeding, we propose various interventions, including exchanges between free-roamers and the metapopulation or supplementation with unrelated individuals from captivity. Simulated trajectories of genetic diversity under such intervention strategies over time could directly inform conservation action and policy towards securing the long-term genetic integrity of the CMP. Single Nucleotide Polymorphisms (SNPs) were genotyped for 172 adult cheetah across the free-roamer population, the metapopulation, and three major captive facilities. Management intervention trajectory models were tested including, 1) no intervention, 2) genetic exchange between free-roamers and the metapopulation, 3) translocation from a single captive facility and 4) translocation from several captive facilities into the metapopulation. Discriminant Analysis of Principal Components (DAPC) showed that the two captive populations are highly differentiated from the metapopulation and each other, while the third captive and free-roamer populations are genetically more similar to the metapopulation. Simulated genetic variation over 25 generations indicated that models 1 and 2 show significant losses of heterozygosity due to genetic drift and present a proportional increase in the frequencies of first- and second-degree relatives, while this variation and pairwise relatedness remain relatively constant under models 3 and 4. We emphasise the potential importance of captive facilities as reservoirs of genetic diversity in metapopulation management and threatened species recovery.