What’s much harder to pin down is why these differences arise. Are they shaped by local environments? Or driven by natural or sexual selection? Or are they simply the result of the random loss of gene variants as populations become isolated and slowly diverge over time?

I’m part of a team of leopard conservationists and researchers who set out to answer some of these questions when we investigated a remarkable population of fewer than 1,000 leopards in South Africa’s Cape Floristic Region, an area that covers the country’s Western Cape, and parts of the Eastern Cape and Northern Cape.

These leopards are much smaller than leopards elsewhere on the continent – in some cases only half the body mass. For decades, researchers and conservationists have debated whether the leopards of this region are truly a separate population in terms of their genes, and if so, what might be driving that difference.

Previous genetic studies offered only limited answers. Most relied on a small number of genetic markers – specific spots in the DNA where mutations tend to happen more. This is useful in finding out large-scale patterns, but misses the finer details needed to understand how populations evolve.

To fill this gap in the research, we turned to whole-genome data. This means that instead of looking for small regions of the DNA where we expect variation, we analyzed the full sequence of paired DNA bases that make up the leopard’s genome (2.57 billion base pairs or roughly 19,000 genes in total). Together with local leopard experts and evolutionary biologists, we collected muscle or skin tissue of the leopards and compared them with genomes of leopards from other parts of Africa.

We found that leopards of the Cape are genetically different from other African leopards. This is because they’ve been isolated from other leopards for a long time and have adapted to one region. This has important implications for conservation.

Leopards in the Cape: smaller, isolated, and genetically unique

Leopards are among the most widespread large carnivores in the world, found across Africa and parts of Asia. Eight subspecies are currently recognized, including the African leopard (Panthera pardus pardus).

The African leopard found across most of sub-Saharan Africa shows extraordinary variation in coat colour, body size and skull shape. In general, leopards living in open habitats tend to be larger and paler, while those in forested areas are often smaller and darker.

The leopards of the Cape Floristic Region (a biodiverse area rich in plants found nowhere else in the world) are an exception to the pattern. They’re relatively small in mass, but until now, no one knew the reason for their distinctive appearance.

Our research found that the leopards of the Cape are not just smaller than other African leopards, they’ve also formed their own genetic group, clearly separated from leopards elsewhere in southern and eastern Africa.

A similar pattern emerged for leopards from Ghana in west Africa. In both cases, there was little evidence of recent genetic mixing with neighboring populations.

Leopards occur and move all along the length of the Cape Fold Belt mountain chain, which serves as a refuge for the cats. Beyond the northern and eastern edge of this mountain chain, it appears that leopard movement stops – the apparent barriers being very dry semi-desert in the north and high human activity in much of the Eastern Cape.

How climate change and human persecution shaped leopards in the Cape over 20,000 years

Looking back in time helped explain why this population is genetically unique. Our analyses suggest that these leopards began diverging from populations further east around 20,000-24,000 years ago, during the Last Glacial Maximum (the coldest phase of the last ice age).

We estimated this by analysing whole-genome DNA to reconstruct when populations split and how much they exchanged genes in the past. (We effectively read their shared evolutionary history, written in the genome.)

During this time, southern Africa became cooler and drier, with fewer grasslands and less food, making it harder for animals to move and survive and causing populations to become separated. More recently, leopard numbers fell sharply in the 1800s and 1900s, likely due to human hunting, habitat loss, and bounty systems that encouraged farmers to kill leopards. In 1968 the leopard bounty ended and the leopard population began to recover as conservation efforts grew.

Because they’d been isolated from other leopards and hunted, we expected our research to show that the leopards of the Cape were genetically depleted (when small populations inbreed and lose genetic diversity). Low genetic diversity makes it harder for populations to adapt to new threats like climate change, disease and human pressure. However, we found they have only slightly lower genetic diversity than other African populations – a really positive finding.

Clues in the genome point to adaptation

We also wanted to find out why the leopards of the Cape are smaller in size.

We found about 90 genes that were more common in these leopards, linked to body size, muscles, bones and energy use. These differences made sense given that the environment they live in has much smaller, more sparsely distributed prey than other leopard habitats. Leopards in the Cape feed mostly on species like rock hyrax (Procavia capensis), klipspringer (Oreotragus oreotragus) and Cape grysbok (Raphicerus melanotis).

Together, these genomic signals suggest that these leopards are small because they’ve adapted that way, and not only because of isolation or genetic drift.

Why this matters for conservation

Populations that are genetically distinct and locally adapted are often described as evolutionarily significant units. This means they represent a unique branch of a species’ evolutionary history and need specific protection so that they can continue to adapt to future change.

Leopards in the Cape Floristic Region occupy a landscape unlike any other in southern Africa, shaped by low prey availability, unique vegetation, and rapidly expanding human populations. Large fenced reserves are rare, and leopards frequently move through agricultural and urban-edge landscapes, where conflict with people is common.

To conserve these leopards, their habitats need to be connected so that they can move around unrestricted and safe from persecution. Poaching and road mortalities are two further threats that need to be addressed to ensure the persistance of leopards in the landscapes. Working in partnership with landowners and communities is essential to protect leopards.

By conserving 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 most distinctive landscapes on the African continent.