DNA analysis of rare Philippine fruit dove sheds new light on a 70-year mystery

  • The Negros fruit dove is known to science from a single female sample collected in the Philippines in 1953; nothing is known about its habits, song, or even what the male of the species looks like.
  • A recent genetic analysis supports the identification of the dove as a unique species within the genus Ptilinopus.
  • It also identifies habitats where the bird may possibly still be found, based on statistical analysis of its historical range.
  • Whether any Negros fruit doves survive remains a mystery, but researchers say ongoing surveys paired with modern technology like audio loggers and environmental DNA monitoring might help find the species in the wild.

The Negros fruit dove was described from a single specimen collected in the Philippines in 1953 — then never seen again by scientists. Now, thanks to advances in DNA sequencing, researchers and conservationists are closer to unraveling the secrets of one of the world’s most mysterious birds — including identifying habitats where it may still be hanging on.

“As an undergraduate at Yale, the Negros fruit dove was of particular interest because the unique type specimen resides at the Yale Peabody Museum of Natural History [in the U.S.],” says John Nash, who led a team of Yale biologists who conducted a genetic analysis of the dove. The results of their research were published in the journal Ibis on Jan. 29.

Filipino ornithologist Dioscoro S. Rabor obtained the lone specimen in 1953 during an expedition in the forest area of Mount Kanlaon, on the central Philippine island of Negros. He’d shot two of the small green birds, but lost one. That left Rabor and his doctoral adviser, Sidney Dillon Ripley, to base their description of the bird on the sole specimen, a female. Concluding that it was a new species of fruit dove (Ptilinopus), they named it P. arcanus, after the Latin word for “secret” or “hidden.”

Over the years, many have tried — and failed — to find the species. However, save for a handful of unconfirmed reports from hunters within the last 40 years, the Negros fruit dove has remained elusive. Some have also speculated that P. arcanus may not even be its own species, but merely a juvenile or aberrant individual from an already known species.

“We almost know nothing about the ecology of the Negros fruit dove,” says Lisa Paguntalan, executive director of the Philippines Biodiversity Conservation Foundation Incorporated (PhilBio) and an expert on the wildlife of Negros. “Some people have also suggested that this is already extinct.”

The ventral, lateral and dorsal views of the single specimen of Negros fruit dove collected in the Philippines in 1953.
The ventral, lateral and dorsal views of the single specimen of Negros fruit dove collected in the Philippines in 1953. Image courtesy of J.A. Nash, et al. (2024).

An evolutionary enigma

Nash and his co-authors conducted their study to investigate the phylogeny and possible habitat of P. arcanus, a species that, despite not having been sighted by scientists in more than 70 years, is still categorized as critically endangered rather than extinct.

To analyze the lineage of P. arcanus, the researchers compared genetic material taken from the female specimen with that from more than 20 other species of fruit doves. DNA naturally degrades over time, and because they were working with very old samples — some more than 100 years old — they anticipated that they would only be able to work with small DNA fragments, Nash says. Thus, instead of attempting typical methods that require whole-gene sequencing, they focused on ultra-conserved elements (UCEs), which are segments of genetic code that remain almost identical in distantly related species. Based on these, the researchers examined the degree of evolutionary change in the birds they studied. They concluded that P. arcanus came from a “highly distinct, early diverging lineage” that split from the most recent ancestor it shared with other fruit dove species millions of years ago, long before the emergence of the island where it was discovered. This strongly suggests a wider distribution for P. arcanus at some point in its evolutionary history.

Possible habitats of an elusive bird

To identify areas where the bird might be rediscovered, the authors used statistical models to reconstruct the Negros fruit dove’s ancestral range during the Pleistocene. Based on what’s known about how the landscape and sea levels in the region transformed over the course of thousands of years due to the changing climate, the findings point to poorly explored forest regions in Negros and the neighboring island of Panay as places where the Negros fruit dove could still exist.

Paguntalan, who was not a co-author of the study, recalls meeting Nash online in 2022 and providing some information on the species, as well as suggesting places other than Mt. Kanlaon where interested parties can search for the species. Paguntalan says her team conducted general bird surveys on the western side of Mt. Kanlaon, as well as limited surveys in Northern Negros Natural Park and montane regions in central Panay. She notes that her team never encountered the Negros fruit dove in their data-gathering process, though these surveys were not done specifically to search for the species.

Nash was also able to consult Godfrey Jakosalem, PhilBio’s operations manager, while working on the study. “The results of my ancestral range reconstruction confirmed [both Paguntalan’s and Jakosalem’s] intuition that the Negros fruit dove likely represents a montane species, and we all agreed that scientists looking for this species should prioritize surveying the upper elevations of Mt. Mandalagan in Northern Negros Natural Park,” Nash says.

Mount Kanlaon, where ornithologist Dioscoro S. Rabor obtained the lone specimen in 1953 during an expedition in the forest area.
Mount Kanlaon, where ornithologist Dioscoro S. Rabor obtained the lone specimen in 1953 during an expedition in the forest area. Image by Studphil via Wikimedia Commons (Public domain).

Finding the lost fruit dove

The Yale study provides evidence that the Negros fruit dove is a distinct species within the Ptilinopus genus, but the question remains as to whether it has truly gone extinct.

“There is no evidence that it still exists, but no evidence that it certainly doesn’t,” says Desmond Allen, an ecologist and author of the book Birds of the Philippines, who calls the Negros fruit dove “a part of the Negros/West Visayan forest ecosystem functioning.”

Allen mentions two possibly effective ways to find the Negros fruit dove in the region. One would be the use of automatic audio loggers that, if widely distributed year-round in West Visayan forests, may capture unidentified calls that can be attributed to the Negros fruit dove; the other is environmental DNA monitoring, which opens up possibilities of finding not just the Negros fruit dove, but perhaps other unknown or undescribed species as well.

While the new research adds a few pieces to the puzzle, there are still many gaps to fill in the bigger picture. As Nash puts it, “At the moment, we still don’t know what it eats, what it sounds like, or even what the male plumage looks like!”

Both Nash and Paguntalan say the key to demystifying this lost bird is to find it in the wild. Paguntalan and her team are currently conducting surveys in all the mountain ranges of Negros and Panay, and are coordinating with the Philippine government to extend their survey to the islands’ protected areas.

“As a Negrosanon, it is imperative to look [for] and find the remaining population of the species, Paguntalan says. “The loss of an endemic species [like the Negros fruit dove] is not only a loss to Negros and the Philippines, but to the world.”

New map boosts Philippine eagle population estimate, but highlights threats


Nash, J. A., Harrington, R. C., Zyskowski, K., Near, T. J., & Prum, R. O. (2024). Species status and phylogenetic relationships of the enigmatic Negros Fruit Dove (Ptilinopus arcanus). Ibis. doi:10.1111/ibi.13305

FEEDBACK: Use this form to send a message to the author of this post. If you want to post a public comment, you can do that at the bottom of the page.