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Clouded leopards face alarming decline amid ‘genetic crisis,’ study warns

Clouded leopard

Clouded leopards, having experienced a 30% dip in numbers over the past three generations, are deemed vulnerable to extinction by the IUCN. Image by Rhett A. Butler for Mongabay.

  • Supremely adapted to life in the forest canopy, clouded leopards have declined in recent decades due to habitat loss and fragmentation, indiscriminate snaring, and poaching for their patterned coats.
  • New genomic evidence indicates that both species of the big cat have low levels of genetic diversity and high rates of inbreeding and negative genetic mutations — factors that could ultimately compromise their long-term survival in the wild.
  • Conservationists working to maintain genetic diversity among both captive and wild populations may face an uphill struggle. Clouded leopards are notoriously difficult to breed in captivity, and forest loss has fragmented wild populations, limiting genetic mixing in the wild.
  • The new insights could be used by conservationists to focus protected-area design and captive-breeding programs with a view to maximizing genetic diversity.

With their camouflaged coats, impossibly long tails, and extraordinary tree-climbing skills, clouded leopards are evolutionary marvels. They’re beautifully adapted to a feline life in the trees. But what evolution hadn’t reckoned on was us. A new genetic study indicates that the one-two punch of habitat loss and poaching has dealt the genetic diversity of the medium-sized cats a severe blow, compromising their long-term survival in the wild.

The genomic analysis, published in Science Advances, found high levels of inbreeding, limited genetic diversity, and the presence of mutations that could impair reproduction. The authors say the accumulation of these negative genetic features over thousands of years has likely been exacerbated by recent steep population declines triggered by human activity.

“Severe habitat fragmentation has probably accelerated the accumulation of deleterious mutations due to high levels of inbreeding,” the study says. “High levels of inbreeding and deleterious genes are key indicators of the genetic crisis affecting clouded leopard conservation and highlight the need for urgent action for the survival of these imperiled big cat species.”

Sunda clouded leopard
The Sunda clouded leopard (Neofelis diardi) has a slightly darker coat than the mainland clouded leopard (Neofelis nebulosa). Image by Spencer Wright via Creative Commons (CC BY 2.0 DEED)

Smallest big cat 

Clouded leopards were considered a single species up until 2006, when DNA evidence revealed that the populations living on the Asian mainland were sufficiently distinct from those on the Southeast Asian islands for scientists to reclassify them as separate species. The mainland clouded leopard (Neofelis nebulosa) roams from Nepal to southern China and south to Peninsular Malaysia; the Sunda clouded leopard (Neofelis diardi) is found only on the islands of Borneo and Sumatra.

Both species are categorized as vulnerable on the IUCN Red List, with numbers in decline  due to the loss of roughly one-third of their habitat over the past two decades, indiscriminate snaring, and direct killing to supply the illegal wildlife trade driven largely by demand for their plush and cloud-patterned coats that otherwise camouflage the cats in the dappled light of forests. Like all big cats, clouded leopards require vast home ranges and live at low density, and given their arboreal lifestyle, fragmentation of canopy cover severely hinders their dispersal.

Although the smallest of the world’s seven species of big cat, clouded leopards have the longest canines of all cats relative to body size, enabling them to make a swift kill in the canopy by delivering a crushing bite to the back of the neck. Broad paws, rotating ankles, a camouflaged coat, and an extremely long tail are just some of the other adaptations that make clouded leopards forest canopy specialists.

Clouded leopard
Broad paws, rotating ankles, a camouflaged coat, extremely long tails and the ability to make a swift kill are just some of the adaptations that make clouded leopards forest canopy specialists. Image by Tim Ellis via Creative Commons (CC BY-NC 2.0 DEED)

Lions, tigers and clouded leopards

To probe the genetic underpinnings of clouded leopards’ unique adaptations, Jiaqing Yuan from Shaanzi Normal University in China and colleagues from China, the U.K. and the U.S. conducted various genomic analyses using blood samples from captive female clouded leopards representing both the mainland and Sunda species.  

By comparing the clouded leopard DNA with that of several other cat species, including tigers, lions, leopards, snow leopards, African cheetahs and domestic cats, the team also looked into the species’ demographic history and identified the genetic basis for many of the big cats’ unique morphological adaptations, such as their long tails and teeth, and their coat color and pattern.

Their analyses indicate the genus Neofelis diverged from the genus Panthera (which includes tigers and lions) during the last Ice Age, roughly 6.19 million years ago. Climatic shifts associated with glacial peaks and troughs during this period created myriad new habitats, such as grasslands and tropical forests, the researchers say. These new habitats nourished a diversity of herbivore prey species, which in turn triggered specialization among predators, such as the arboreal niche of clouded leopards.

The team also found the genetic signatures of mainland clouded leopards place them into one of two groups according to geography: clouded leopards from China and Southeast Asia are genetically distinct from those from northern Myanmar and India. While this finding corroborates prior accounts of two separate mainland subspecies, the authors note that the two groups cannot technically be classified as subspecies due to a lack of evidence of morphological differences.

But most significantly, their analyses revealed concerningly high levels of inbreeding, low genetic diversity, and genetic mutations linked to negative traits, such as heart defects and abnormal sperm development. Levels of heterozygosity, a measure of genetic diversity, were typically two to five times lower in clouded leopards compared to members of the Panthera genus of big cats.

Oil palm and forest
The proliferation of oil palm, like this plantation in Sabah, Malaysia, is a major driver of forest loss across the clouded leopards’ range. Image by Carolyn Cowan for Mongabay.

‘Genetic crisis’

Nobuyuki Yamaguchi, a wildlife biologist at University Malaysia Terengganu who was not involved in the study, said the researchers made good use of genetic samples that are often difficult to obtain and analyze at the scale of this study. Yamaguchi added that the findings suggest that recovery of struggling wild populations of clouded leopards will present an uphill struggle for conservationists.

“In principle, it is safe to assume that high level of inbreeding and low level of genetic diversity are not good news for species conservation,” Yamaguchi told Mongabay. “The conservation community had better assume that some reproductive difficulties and inbreeding depressions may be occurring in the wild (e.g. low reproductive success), which may slow down population recovery and genetic health of the wild clouded leopards.”

Yamaguchi added that focusing conservation efforts and limited financial resources on identified strongholds with known wild populations will be crucial. “As the only country where both species of clouded leopards occur, I hope that Malaysia will play a key role to contribute to clouded leopards conservation,” he said.

The new insights into the evolutionary history and genetic diversity of clouded leopards should “promote more effective conservation efforts by providing information about the selective pressures important to their evolution and adaptation,” says the study.

Ultimately, the concerning findings underscore the scale of what the authors call the “genetic crisis” facing clouded leopard conservation and the challenges of managing both wild and captive populations. Clouded leopards are notoriously difficult to breed in captivity, sometimes with pairs selected for mating killing each other. Meanwhile, forest loss has fragmented wild populations throughout both species’ ranges, limiting genetic mixing in the wild.

The authors advocate action to maintain and enhance genetic diversity of wild and captive populations as a matter of urgency, through careful protected-area planning and captive-breeding programs.

Clouded leopard
Clouded leopards have the longest canines of all cat species relative to their body size. Image by Sam Whitfield via Creative Commons (CC BY-NC-ND 2.0 DEED)

Carolyn Cowan is a staff writer for Mongabay. Follow her on 𝕏 @CarolynCowan11.

Banner image: Clouded leopards, having experienced a 30% dip in numbers over the past three generations, are deemed vulnerable to extinction by the IUCN. Image by Rhett A. Butler for Mongabay.


Yuan, J., Wang, G., Zhao, L., Kitchener, A. C., Sun, T., Chen, W., … Li, G. (2023). How genomic insights into the evolutionary history of clouded leopards inform their conservation. Science Advances, 9(40). doi:10.1126/sciadv.adh9143

Hearn, A. J., Ross, J., Bernard, H., Bakar, S. A., Goossens, B., Hunter, L. T. B., & Macdonald, D. W. (2017). Responses of Sunda clouded Leopard Neofelis diardi population density to anthropogenic disturbance: Refining estimates of its conservation status in Sabah. Oryx, 53(4), 643-653. doi:10.1017/s0030605317001065

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Nepal’s clouded leopard research needs more attention: Q&A with Yadav Ghimirey

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