Importance of using genetic data to inform conservation captive breeding: A tale of two species of threatened macaws ( Ara spp.)

Captive breeding in private collections is a crucial but often undocumented component of conservation for many threatened species, which can inadvertently pose risks to genetic diversity and species integrity. We used genotyping‐by‐sequencing (GBS) to conduct a genetic audit of one of the largest private collections of two threatened parrot species: the Great Green Macaw ( Ara ambiguus ) and the Military Macaw ( Ara militaris ). Among 45 individuals, our analysis uncovered critical, undocumented historical complexities. We identified seven interspecific hybrids and one morphologically misidentified purebred individual. We also detected pervasive high relatedness, with mean pairwise relatedness values for the Military Macaw ( r = 0.33) and Great Green Macaw ( r = 0.27) approaching the theoretical expectation for half‐siblings, largely driven by the discovery of highly interconnected family networks. Furthermore, we revealed cryptic substructure within the Military Macaws, tracing lineages to distinct Mexican and South American (Bolivian) origins. Together, these findings highlight the unintended consequences of historical breeding without access to genetic data, which can compromise a collection's conservation value if left unresolved. Our results demonstrate that genomic screening is an essential tool for transforming historically undocumented collections from uncharacterized genetic reservoirs into valuable conservation assets. We provide a framework for conservation practitioners to use genomic data to correct pedigrees, guide pairing decisions to minimize inbreeding, and prevent hybridization. We argue that such genomic oversight should be standard policy and practice across all ex situ conservation programs to ensure meaningful contributions to global species recovery efforts.