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Background <p>The Philippine eagle (<i>Pithecophaga jefferyi</i>) is one of the rarest raptors in the world and is the national bird of the Philippines. It is listed as Critically Endangered by the International Union for Conservation of Nature and has been the subject of a captive breeding program, which started more than 30&#xa0;years ago to ensure the survival and conservation of the species. To estimate the genetic diversity and infer the demographic history of the Philippine eagle, we sequenced and analyzed genomes of 35 individuals under the care of the Philippine Eagle Foundation.</p> Results <p>Phylogenetic analysis placed <i>P. jefferyi</i> within the subfamily Circaetinae of Accipitridae. Demographic history reconstruction revealed two historical bottlenecks and an ongoing population decline, which was found to predate documented deforestation in the Philippines. This suggests that unobserved natural or anthropogenic factors might have led to declines in the Philippine eagle population long before current habitat degradation. Genome-wide heterozygosity was the lowest measured among raptors. This highlights the precarious genetic state of the Philippine eagle, as low heterozygosity raises risks of inbreeding depression and increased vulnerability to diseases and habitat loss.</p> Conclusions <p>This study demonstrates that genetic diversity of the Philippine eagle is critically low, indicating that breeding and translocation programs must explicitly account for genetic effects to maintain demographic stability and support long-term genetic resilience of this critically endangered species.</p>

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Genomic analysis reveals recent population decline and exceptionally low genome-wide heterozygosity of the critically endangered Philippine eagle, Pithecophaga jefferyi (Aves: Accipitridae)

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年4月20日

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  • Dhan Mikhail Perdon,
  • Franchesca Pascual,
  • Francis Tablizo,
  • Carlo Lapid,
  • John Michael Egana,
  • Renato Jacinto Mantaring,
  • Kris Punayan,
  • Shiela Mae Araiza,
  • Jo-Hannah Llames,
  • Ma. Celeste Abad,
  • Juan Carlos Gonzalez,
  • Jayson Ibañez,
  • Cynthia Palmes Saloma

摘要

Background

The Philippine eagle (Pithecophaga jefferyi) is one of the rarest raptors in the world and is the national bird of the Philippines. It is listed as Critically Endangered by the International Union for Conservation of Nature and has been the subject of a captive breeding program, which started more than 30 years ago to ensure the survival and conservation of the species. To estimate the genetic diversity and infer the demographic history of the Philippine eagle, we sequenced and analyzed genomes of 35 individuals under the care of the Philippine Eagle Foundation.

Results

Phylogenetic analysis placed P. jefferyi within the subfamily Circaetinae of Accipitridae. Demographic history reconstruction revealed two historical bottlenecks and an ongoing population decline, which was found to predate documented deforestation in the Philippines. This suggests that unobserved natural or anthropogenic factors might have led to declines in the Philippine eagle population long before current habitat degradation. Genome-wide heterozygosity was the lowest measured among raptors. This highlights the precarious genetic state of the Philippine eagle, as low heterozygosity raises risks of inbreeding depression and increased vulnerability to diseases and habitat loss.

Conclusions

This study demonstrates that genetic diversity of the Philippine eagle is critically low, indicating that breeding and translocation programs must explicitly account for genetic effects to maintain demographic stability and support long-term genetic resilience of this critically endangered species.