Mitochondrial Genome Analysis of Philippine Eagles ( <i>Pithecophaga jefferyi</i> Ogilvie‐Grant 1896) From the Greater Mindanao Faunal Region

The population of the endemic and critically endangered Philippine eagle (<i>Pithecophaga jefferyi</i> Ogilvie-Grant 1896) has dramatically declined, which may lead to reduced genetic diversity and increased inbreeding and extinction risk. To address the concern, there is an urgent need for genetic data to guide conservation breeding, preserve the genetic diversity of the species, and improve reintroduction outcomes. In this study, we performed mitochondrial genome sequencing and assessed the genetic diversity of Philippine eagles. Analysis of partial mitogenomes (12 protein-coding genes, 17 tRNAs, and 16S rRNA) revealed a very low overall nucleotide diversity (<i>π</i> = 0.00054 ± 0.00030) among 32 eagles from the Greater Mindanao Faunal Region. A higher number of haplotypes were observed in the eagles bred in captivity at the Philippine Eagle Center (<i>h</i> = 17) compared to the wild captives (<i>h</i> = 13), but both population subsets had comparable nucleotide and haplotype diversity. At least two distinct Philippine eagle subpopulations based on maternal ancestry were identified, although there is generally low genetic differentiation based on <i>F</i> _<i>ST</i> analysis. Furthermore, isolation by distance analysis (geographic isolation) showed a weak positive correlation between the genetic distance and the geographic distance of the eagle population. This suggests possible historical connectivity or limited influence of geographic separation on the genetic differentiation in Philippine eagles. Nevertheless, three genetically distant haplotypes and several eagles from KBA dyads with moderate levels of genetic differentiation were identified, representing the existence of genetically useful breeding stocks that can be prioritized in the current conservation program. Finally, phylogenetic analysis of Philippine eagles and other members of the family Accipitridae corroborates previous findings on the inclusion of the species in the subfamily Circaetinae and its monophyletic status. Altogether, we demonstrate the utility of mitogenomes in assessing genetic diversity and evolutionary relationships for species conservation.