Applying Population Viability Analysis to Inform Genetic Rescue That Preserves Locally Unique Genetic Variation in a Critically Endangered Mammal

Joseph P Zilko,Paul Sunnucks,Alexandra Pavlova,Dan Harley

doi:10.3390/d13080382

Abstract

Genetic rescue can reduce the extinction risk of inbred populations, but it has the poorly understood risk of ‘genetic swamping’—the replacement of the distinctive variation of the target population. We applied population viability analysis (PVA) to identify translocation rates into the inbred lowland population of Leadbeater’s possum from an outbred highland population that would alleviate inbreeding depression and rapidly reach a target population size (N) while maximising the retention of locally unique neutral genetic variation. Using genomic kinship coefficients to model inbreeding in Vortex, we simulated genetic rescue scenarios that included gene pool mixing with genetically diverse highland possums and increased the N from 35 to 110 within ten years. The PVA predicted that the last remaining population of lowland Leadbeater’s possum will be extinct within 23 years without genetic rescue, and that the carrying capacity at its current range is insufficient to enable recovery, even with genetic rescue. Supplementation rates that rapidly increased population size resulted in higher retention (as opposed to complete loss) of local alleles through alleviation of genetic drift but reduced the frequency of locally unique alleles. Ongoing gene flow and a higher N will facilitate natural selection. Accordingly, we recommend founding a new population of lowland possums in a high-quality habitat, where population growth and natural gene exchange with highland populations are possible. We also recommend ensuring gene flow into the population through natural dispersal and/or frequent translocations of highland individuals. Genetic rescue should be implemented within an adaptive management framework, with post-translocation monitoring data incorporated into the models to make updated predictions.

Highlights

Many threatened species are restricted to small and isolated populations, which places them at elevated risk of inbred matings and loss of beneficial genetic variation by genetic drift [1,2]
Perturbation analysis indicated that no single input parameter had a greatly disproportionate effect on the population growth rate (Table 3)
We estimate that without intervention, all unique lowland Leadbeater’s possum genetic variation will be lost due to extinction of the last population of the lineage within approximately two decades, whereas modest amounts of this unique variation can be preserved with genetic rescue

Summary

Introduction

Many threatened species are restricted to small and isolated populations, which places them at elevated risk of inbred matings and loss of beneficial genetic variation by genetic drift [1,2]. Translocations of individuals from other populations can increase genetic diversity of isolated populations and elevate population fitness by reducing inbreeding depression and alleviating the harmful effects of beneficial variation being lost from the population (i.e., causing genetic rescue), increasing the persistence and adaptive capacity of populations [2,8,9]. Such genetic management is a highly effective conservation tool; when appropriate sources of genetic augmentation are used, outcrossing increases fitness in the vast majority of inbred populations that usually outbreed, and an enhanced ability to adapt can greatly increase population persistence in changing environments [10]

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