Genomic diversity, population structure, and relatedness of critically endangered Philippine eagles under conservation management

The critically endangered Philippine eagle ( Pithecophaga jefferyi ) faces severe threats to its population from habitat loss, naturally slow reproduction cycles, and human encroachment. Thus, 38 years ago, the Philippine Eagle Foundation (PEF) was established for the conservation of the endangered Philippine eagle and its rainforest habitat. To support the PEF’s captive-breeding and rehabilitation efforts, this study investigates the genome-wide single-nucleotide polymorphism (SNP) profiles of 20 wild-captive and 15 captive-bred individuals under the foundation’s care. Sequence reads were quality-filtered and aligned to a previously generated Philippine eagle reference genome. Identified SNPs across the 35 individuals were then further analyzed to assess population structure, isolation by distance (IBD), inbreeding, and relatedness. Population structure analysis revealed that genetic distance tended to increase with geographic distance, suggesting that the wild-captive eagles follow an pattern. Inbreeding analysis meanwhile showed significantly higher levels among wild-captive eagles compared to those bred in captivity, suggesting limited access to genetically diverse mates in the wild, and highlighting the success of the foundation’s breeding strategy in minimizing inbreeding. Finally, kinship analysis confirmed known first-degree relationships among captive-bred eagles and uncovered novel kinships among wild-captive individuals that reinforce the IBD model. These results represent the first comprehensive conservation genomics study on the Philippine eagle, providing insights into the diversity of its captive and wild populations, as well as valuable information that can guide future breeding and conservation efforts.