Even animals of the same species don’t always look the same. From birds with different beak shapes to mammals of different sizes and colors, populations in different locations often look very different.
Even more difficult to pinpoint is why this difference occurs. Are they shaped by the local environment? Or is it driven by natural or sexual selection? Or is it simply the result of random loss of genetic variation as populations become isolated and slowly diverge over time?
I was part of a team of leopard conservationists and researchers who set out to answer some of these questions as we surveyed an astonishing population of less than 1,000 leopards in South Africa’s Cape Botanical Gardens region. This region covers parts of the Western Cape, Eastern Cape and Northern Cape provinces of the country.
These leopards are much smaller than leopards in other parts of the continent, in some cases only half their body weight. Researchers and conservationists have debated for decades whether the region’s leopards are truly a separate population from a genetic standpoint, and if so, what accounts for the differences.
Genetic research to date has provided limited answers. Most relied on a small number of genetic markers, specific spots in the DNA that are prone to mutations. While this helps find large-scale patterns, it lacks the detail needed to understand how populations evolve.
To fill this gap in research, we turned to whole-genome data. This means that instead of looking for small regions of DNA where mutations might be expected, they analyzed the complete sequence of paired DNA bases that make up the leopard genome (2.57 billion base pairs, or about 19,000 genes in total). We worked with local leopard experts and evolutionary biologists to collect leopard muscle and skin tissue and compare it to the genomes of leopards from other parts of Africa.
We found that Cape leopards are genetically distinct from other African leopards. This is because they have been isolated from other leopards for a long time and have adapted to one area. This has important implications for conservation.
Cape leopard: a small, solitary, genetically unique leopard
Leopards are the world’s most widespread large carnivores, living in parts of Africa and Asia. Eight subspecies are currently recognized, including the African leopard (pantera panther panther).
Found throughout much of sub-Saharan Africa, African leopards display remarkable variation in fur color, body size, and skull shape. In general, leopards that live in open habitats tend to be larger and lighter in color, while leopards that live in wooded areas tend to be smaller and darker in color.
Leopards in the Cape Floristic Region, a biodiverse region rich in plants found nowhere else in the world, are an exception to this pattern. Its mass is relatively small, but until now no one knew the reason for its distinctive appearance.
Our research shows that the Cape leopard is not only smaller than other African leopards, but also forms its own genetic group, clearly distinguishing it from leopards in other parts of southern and eastern Africa.
A similar pattern appeared in leopards in Ghana, West Africa. In both cases, there was little evidence of recent genetic admixture with neighboring populations.
Leopards live and roam along the Cape Fold Belt, providing refuge for cats. Beyond the northern and eastern ends of this range, leopard movements seem to stop. The very arid semi-desert to the north and high human activity in much of the Eastern Cape pose obvious barriers.
How climate change and human persecution have shaped the Cape leopard over 20,000 years
Looking back helps explain why this population is genetically unique. Our analysis suggests that these leopards began to diverge from populations farther east during the Last Glacial Maximum, the coldest period of the Last Ice Age, about 20,000 to 24,000 years ago.
We estimated this by analyzing whole genome DNA to reconstruct when populations split and how much genes they exchanged in the past. (We effectively read their common evolutionary history written in their genomes.)
During this time, southern Africa became colder and drier, reducing grasslands and food, making it difficult for animals to migrate and survive, and causing populations to separate. More recently, leopard numbers have declined sharply in the 1800s and 1900s, likely due to human hunting, habitat loss, and bounty systems that encouraged farmers to kill leopards. Leopard bounties ended in 1968, and as conservation efforts progressed, leopard populations began to recover.
Because they had been isolated from other leopards and hunted, we expected our study to show that Cape leopards were genetically depleted (small populations inbreeding and losing genetic diversity). Low genetic diversity makes it difficult for populations to adapt to new threats such as climate change, disease, and human pressures. However, their genetic diversity was found to be only slightly lower than other African populations. This is a very positive finding.
Clues in the genome point to adaptation
We also wanted to know why Cape leopards are small in size.
We discovered about 90 genes commonly found in these leopards related to body size, muscle, bone, and energy expenditure. These differences make sense given that the environments they live in have much smaller and more sparsely distributed prey than other leopard habitats. Cape leopards are mainly rock hyraxes (Procavia capensis), Rock Jumper (Oreotragus) and Cape Griesbok (Raficerus melanotis).
Together, these genomic signals suggest that these leopards are small because they have adapted to do so, rather than just due to isolation or genetic drift.
Why is this important for conservation?
Genetically distinct and locally adapted populations are often described as evolutionarily significant units. This means they represent a unique branch in the species’ evolutionary history and require special protection so they can continue to adapt to future changes.
Leopards in the Cape Botanic Gardens region occupy a landscape unlike any other in southern Africa, shaped by low prey availability, unique vegetation, and rapidly expanding populations. Large fenced protected areas are rare, and leopards frequently move through agricultural and urban edge landscapes where conflicts with humans are common.
To protect these leopards, habitats must be connected so that leopards can move unrestricted and safely from persecution. Poaching and road deaths are two further threats that need to be addressed to ensure leopard persistence in the landscape. Working in partnership with landowners and local communities is essential to conserving leopards.
By protecting these leopards, we are not only saving an iconic predator, but also preserving an evolutionary legacy shaped over thousands of years by one of the continent’s most distinctive landscapes.
