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Philippine fruit bats may be entirely new species of their own, DNA suggests

A white-winged flying fox (Desmalopex leucopterus) getting ready to take off in Palanan, Isabela in the Philippines. Image by Jay Fidelino

  • A recently published genetic study on fruit bats found in the Philippines revealed high genetic difference among island groups and compared to the Southeast Asian region, which could mean they either need to be reclassified as subspecies or be elevated as new species.
  • The study covered 19 of the 27 fruit bat species native to the Philippines, which were assessed using a DNA barcoding technology in a six-year study.
  • Five of the species were revealed to have 6 to 7% genetic distance from specimens elsewhere in Southeast Asia, possibly justifying the need to name them distinct populations of their own, the researchers say.
  • DNA barcoding is part of a growing international effort to create a genetic database to improve wildlife forensics, aid in curbing wildlife trafficking and help implement more efficient species-focused conservation efforts.

MANILA — There might be more fruit bat species in the Philippines than previously thought, according to a genetic study, underlining the possibility that each individual species might be more threatened than initially assumed.

The study on bat genetics, published October 2019 in the peer-reviewed Philippine Journal of Science, highlights two key points: at least four bat species in the country are genetically different from their counterparts elsewhere in Southeast Asia; and one fruit bat found only in the Philippines exhibits significant genetic variation across different island groups within the country.

When analyzing DNA, biologists follow a rule: the greater the degree of variation between species, the higher the possibility that the specimens come from distinct species, lead researcher Adrian Luczon explains. A 2 to 3% difference is the usual benchmark to identify separate species; for bats, the threshold is 2%. “What we saw are a high 6 to 7% difference in genetic distance — it means that it’s already a very different population.”

What’s the implication of this discovery? Luczon says bat species in the Philippines might be more threatened than initially classified and there might be a need for species reassessment, and if necessary, their reclassification.

Bats are notoriously difficult to study primarily because they are hard to find. They are well hidden in caves and forests, which has at times resulted in the species being grouped based on physical similarities rather than more rigorous standards. The advent of DNA barcoding technology more than a decade ago has made it easier to more precisely identify bat species. In 2019 alone, the number of new bat species grew by 35% for one of the biggest families of bats based on records by the American Society for Microbiology (ASM).

The researchers collected samples from 17 sites in the Philippines. Source: DNA Barcodes Reveal High Genetic Diversity in Philippine Fruit Bats (2019)

In the Philippines, there are 79 listed bat species, of which 38 are endemic and at least 12 are threatened, according to the country’s red list. Of the total bat species in the Philippines, 26 are from the Pteropodidae family known as fruit bats or flying foxes; 17 of these are endemic to the country. Eleven of the 12 threatened species are fruit bats.

Habitat loss and massive hunting as prized delicacies in some countries have driven some fruit bat species to critically endangered status. For the recent study, the researchers had since 2013 partnered with the Philippine Department of Environment and Natural Resources’ regional offices to collect tissue samples from 111 bats at 17 sites. But they were only able to get specimens from 19 of the Philippines’ 26 known fruit bat species.

Luczon attributes this to numerous factors: the researchers weren’t trained to handle bats, for one, and getting samples proved difficult for the critically endangered species. “It’s likely that the population is decreasing,” Luczon says. “These bats are either forest- or cave-dwelling so if their habitats are threatened, it’s harder to locate them and get samples.”

The researchers also requested samples from the Field Museum of Natural History in Chicago, where an extensive collection of Philippine bats are well-preserved, all with the goal of documenting and comparing their genetic barcodes.

There are 17 endemic fruit bats in the Philippines including the Philippine dawn bat (Eonycteris robusta), left, and the Greater musky fruit bat (Ptenochirus jagori). Images by Jay Fidelino

Once they’d gathered the samples, they compared them with known genome sequences in the public-access portals Barcode of Life Data System (BOLD) and GenBank.

That allowed them to clearly delineate four bat species in the Philippines from their counterparts elsewhere in Southeast Asia. The Philippine specimens of those species — the long-tongued nectar bat (Macroglossus minimus), Geoffroy’s rousette (Rousettus amplexicaudatus), white-collared fruit bat (Megaerops wetmorei) and the lesser shorter-nosed fruit bat (Cynopterus brachyotis) — were found to have a high 6% genetic difference from specimens of the same species in the region.

“Most of the species collected in the Philippines show barcode sequences that are unique,” the study says, adding that 13 of the species form “distinct lineages” that identify them as separate species. Only the cave nectar bat (Eonycteris spelaea) and the small flying fox (Pteropus hypomelanus) have similar genetics across the same species in the region, the study adds.

The discoveries didn’t end there. The team found out the Philippine pygmy fruit bat (Haplonycteris fischeri), endemic to the country and classified as least concern by the IUCN, actually has different genetics in each island where it occurs in the Philippines. Comparing samples from the main islands of Luzon, Mindanao and Mindoro, researchers found a difference as high as 7% in pygmy fruit bat genetics, which raises the possibility that they might either be subspecies or new species altogether.

This fruit bat species is known for having a longer pregnancy than even humans: an 11-month gestation period considered the longest of any bat in the world. The new findings raise the need to reassess its conservation status and maybe even its taxonomy. “From this study, these species may be flagged for taxonomic reevaluation,” the study says.

Adrian Luczon (pictured) and his team have been doing the DNA barcoding study on fruit bats since 2013. Image courtesy of Luczon/UP Institute of Biology

The group’s study on bats is part of a larger effort by the University of the Philippines’ Institute of Biology and its partners to create a robust database of all species — from wildlife to freshwater fish to plants — in the country. The program started in 2008 with the bigger goal of using the technology to curb wildlife trafficking and poaching and improving wildlife forensics. It’s also seen as addressing the dwindling number of taxonomists studying native species, thanks to its “accurate, rapid, and effective method of species recognition,” the study says.

Luczon says the study is only a stepping stone for further research into fruit bats. While it doesn’t cover the implications of the wide genetic differences in fruit bats, at the very least it opens the portal for reassessing these flying mammals, deepening existing studies on the species, and highlighting their unique genetic lineage.

“There are many endangered and threatened bats in the Philippines,” Luczon says. “If you want to do a conservation program, you might want to create a unique conservation program to implement in each area. Blanket conservations are hard because the needs and threats for each species varies.”


Luczon, A. U., Ampo, S. A. M. M., Roño, J. G. A., Duya, M. R. M., Ong, P. S., & Fontanilla, I. K. C. (2019). DNA barcodes reveal high genetic diversity in Philippine fruit bats. Philippine Journal of Science Special Issue on Genomics148(S1), 133-140.

Banner image of a white-winged flying fox (Desmalopex leucopterus), a fruit bat endemic to the Philippines that is listed in CITES Appendix II. Image by Jay Fidelino

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