Genomic Analysis Reveals Recent Population Decline and Exceptionally Low Genome-Wide Heterozygosity of the Critically Endangered Philippine Eagle, Pithecophaga jefferyi (Aves: Accipitridae)

The Philippine Eagle ( Pithecophaga jefferyi ), is one of the rarest eagles in the world and is the national bird of the Philippines. It is listed by the International Union for Conservation of Nature (IUCN) as a critically endangered raptor and has been the subject of an intensive captive breeding program which started more than 30 years ago to ensure the survival and conservation of the species. To infer the genetic diversity and demographic history of the Philippine Eagle, we sequenced and analyzed the genomes of 35 individuals under the captive breeding program of the Philippine Eagle Foundation. Phylogenetic analysis of the draft reference sequence generated in this study placed P. jefferyi within the subfamily Circaetinae of Accipitridae. Demographic history reconstruction from genome-wide variants revealed two historical bottlenecks, as well as an ongoing population decline which was found to predate documented deforestation in the Philippines. This observation suggests that unobserved natural or anthropogenic factors might have severely affected the Philippine Eagle population long before habitat fragmentation. Genome-wide heterozygosity estimates placed the Philippine Eagle as having one of the lowest genome-wide heterozygosity levels measured among raptors. This highlights the precarious genetic state of the Philippine Eagle, as critically low heterozygosity raises risks of inbreeding depression, reduced reproductive success, and increased vulnerability to diseases, climate change, and habitat loss. The genomic resources generated in this study can therefore guide conservation strategies such as breeding program design, genetic monitoring, and other efforts to diversify existing populations to ensure both demographic stability and genetic resilience of the Philippine Eagle.