Conservation Genomics Provides Essential Insights for the Management of Endangered Populations and the Utility of Ex Situ Collections for Species Recovery: A Case Study in Encephalartos latifrons

ABSTRACT Background and Aims Ex situ collections can be reservoirs for endangered species to be used in reintroductions but critical data on the provenance and genetic diversity of these collections is often lacking. For example, while more than 70% of Cycad species are threatened with extinction, many individuals are held in private collections and botanical gardens. However, their utility is hampered by our limited understanding of genetic diversity among wild populations and unknown provenance of many ex situ plants. Conservation genomics can meet both challenges by providing estimates of allelic diversity among both wild and ex situ plants, and by identifying source populations of ex situ collections. We demonstrate this approach with Encephalartos latifrons, a Critically Endangered species occurring at the edge of a close relative, E. longifolius. Recently documented populations could potentially double the number of E. latifrons plants in the wild but are of unknown identity due to complex morphological trait distributions. Methods We assessed genetic structure, genetic diversity, and gene flow among populations. Coancestry was used to assign ex situ individuals to species/population of origin. We also assessed the allelic diversity of in situ populations captured in ex situ collections. Key Results Newly documented populations of Encephalartos do not belong to E. latifrons. Populations are not inbred and genetic diversity is relatively high. Ex situ collections harbor a substantial amount of allelic diversity, but this is not evenly distributed nor redundant across sites. Multiple individuals in ex situ collections were not assigned to their species of record. Conclusions This work highlights the promise and pitfalls of using ex situ collections in the restoration of endangered species and the effective role that conservation genomics can play in determining their actual conservation value. Comprehensive genomic analyses are essential to maintain the genetic structure and diversity of wild populations.