THE Philippine Eagle Foundation (PEF) and scientists from the University of the Philippines Mindanao-Philippine Genome Center (PGC) have completed the first mitochondrial genome study of Philippine Eagles from the Greater Mindanao Faunal Region (GMFR).
Michael G. Bacuse, lead author and researcher at the Philippine Genome Center Mindanao and the Department of Biological Sciences and Environmental Studies at UP Mindanao, explained that the results will directly support conservation breeding. He said their findings show that while the species’ overall genetic diversity is low, the eagles surprisingly possess a variety of maternal lineages.
“By mapping these lineages, the PEF can now secure new genetic stocks from the wild and pair more birds in a smarter way — aiming to retain as much genetic diversity as possible in every chick that hatches,” he said.
Dr. Lyre Anni E. Murao, UP Mindanao Chancellor, co-author of the study, and lead for wildlife and genomics research at the university, said the study exemplifies how UP Mindanao’s close collaboration with a conservation NGO can generate globally relevant science.
“We are proud that the students and young researchers of UP Mindanao–PGC are helping decode the genome of our national bird and turning that knowledge into concrete tools for saving it,” she added.
Meanwhile, Dennis I. Salvador, executive director of PEF, said that for years, they have carefully bred Philippine Eagles through pedigree records and field experience. He noted that the study shows that after nearly four decades of meticulous pairing and breeding, the PEF has managed to maintain a healthy mix and preserve precious haplotypes (bloodlines) ex situ.
“These insights also show where new genetic stocks can be secured from the wild and can guide us in choosing pairs and release candidates more wisely, so we can keep the gene pool as healthy as possible in the long term as a safety net against extinction,” he said.
Moving forward, PEF plans to integrate the new genetic insights into its breeding plans at the NBBS. This includes securing — pending government permission — new genetic stocks from Samar, the Pantaron Range, Mt. Busa – Kiamba, and Kampalili – Puting Bato, which harbor unique eagle maternal lineages. These lineages will help guide future reintroduction efforts in Luzon and Leyte, where suitable eagle habitats still exist.
High diversity despite captivity
The study provides new genetic information that will guide captive breeding and future releases to the wild. Published in the open-access journal Ecology and Evolution, it analyzed mitochondrial genomes from 32 eagles housed at the Philippine Eagle Center (PEC) and the National Bird Breeding Sanctuary (NBBS).
The team discovered that eagles across the GMFR share very little genetic variation, confirming how close the species is to extinction.
Despite the low overall nucleotide diversity, results show that the PEF’s captive collection — which includes rescued and captive-born eagles — still retains a high diversity of maternal lineages (haplotypes). Some of these are rare bloodlines found among eagles bred and hatched on-site.
The study reported that captive-bred birds carry all 17 haplotypes detected, indicating that the breeding stock holds the remaining known genetic variation of the species.
Researchers also discovered two main genetic clusters of Philippine Eagles and identified three distinct haplotypes, including one from Samal Island Natural Park. Genetic distinctiveness was also observed in Samar and biodiversity-rich areas such as Mt. Busa–Kiamba, Mt. Kampalili–Puting Bato, and Mt. Pantaron—highlighting geographically important lineages that should be better represented in the current breeding stock.
The study confirmed that the Philippine Eagle belongs to the subfamily Circaetinae within the raptor family Accipitridae, alongside species such as the crested serpent eagle (Spilornis cheela) and Circaetus pectoralis.
This highlights how mitochondrial genomes can serve as practical genetic tools for threatened species with limited full-genome data.
Mariglo Rosaida I. Laririt, assistant director of the Biodiversity Management Bureau (BMB) of the Department of Environment and Natural Resources (DENR), congratulated UP Mindanao–PGC and PEF for the study, which will strengthen national efforts to save the Philippine Eagle.
Dr. Cynthia P. Saloma, Dean of the UP Diliman College of Science, former PGC Executive Director, and one of the country’s leading molecular biology and genomics experts, emphasized that the Philippine Eagle symbolizes the nation’s forests and that this project demonstrates how the PGC network can support frontline conservation groups.
“Moving forward, the Biodiversity, Ethnicity and Forensics Program of the Philippine Genome Center in UP Diliman will also contribute to the growing use of genomic research to understand and save our national bird through detailed studies of the nuclear genomes of Philippine Eagles,” she said.
What is mitochondrial DNA, and why does it matter?
Mitochondria are tiny energy-producing parts of a cell—often called the powerhouse. Unlike DNA found in the nucleus, mitochondria have their own separate DNA that is passed almost entirely from mother to offspring. Mitochondrial DNA (mtDNA) changes slowly over time and is inherited through the maternal line.
Studying mtDNA helps scientists determine how many maternal lineages remain in the endangered Philippine Eagle. Identifying these lineages is crucial for breeding the critically endangered species, improving the genetic health and survival of captive populations, and guiding their eventual release into the wild. RGP