Development of Microsatellite Markers for Ex Situ Management of the Harpy Eagle Using Next Generation Sequencing

The Harpy Eagle (Harpia harpyja), one of the largest birds of prey in the world, is threatened with extinction throughout its entire area of occurrence in the Neotropics. While conservation efforts for the wild populations are crucial, it is also important to focus on ex situ conservation actions. To achieve this, understanding the genetic characteristics of the captive population is essential to prevent inbreeding and loss of genetic diversity over time. In this study, we employed a next generation sequencing strategy to develop a new set of primers for microsatellite regions specific to the Harpy Eagle. These markers were validated in Harpy Eagle individuals maintained in captivity at Brazilian zoos and conservation institutions. We characterized these captive individuals using ten highly polymorphic microsatellite loci to estimate relatedness and individual identification at > 95% accuracy. The same effect can be achieved with four loci. Additionally, we developed a statistical test to further refine relationship estimates. Paired with robust sex markers, the new set of microsatellite markers presented here the potential to guide ex situ management strategies, aiming for better reproductive pairings and the maintenance of genetic diversity of the Harpy Eagle.