Genomics-informed management of ex situ populations

The European Association of Zoos and Aquariums (EAZA) manages insurance populations for hundreds of species through its EAZA ex situ programs (EEPs). EEPs help safeguard against extinction in the wild and provide source populations for genetic rescue programs. However, like wild populations, populations in EEPs are at risk of genomic erosion, undermining population viability. Current population management is based on studbook and pedigree records, and this information is used to maintain genetic diversity and prevent inbreeding. We examined how genomics-informed conservation management can improve current practices. Using computer simulations, we identified EEP species' characteristics that make them more prone to genomic erosion. EEP species with large ancestral population sizes and low fecundity (i.e., K-strategists) were most at risk of a genetic load of harmful mutations and inbreeding depression. Founder population size is critical for EEP species with large ancestral population sizes and high fecundity (r-strategists), especially if the initial population growth rate is slow. Large breeding population size and effective population size were beneficial for viability for all EEP species. We showed that inbreeding depression peaked at approximately 10 generations after founding and that fitness never completely recovered in EEP species compared with in wild ancestors. Due to a time lag (drift debt), genomic erosion did not become apparent until after ∼3 generations, which implied that biobanking (the long-term storage of biological samples) would be best conducted within this initial period. Thus, genomics data can be used to better maintain genetic diversity, reduce genetic load, and minimize inbreeding depression in EEPs. Genomics data can also identify inadvertent hybridization, which threatens ex situ programs managing closely related species or evolutionary significant units together. Genomics-informed management can improve the viability, fitness, health, and genetic rescue potential of ex situ populations.