Australian study reveals surprising genetics of African leopards

New Australian-led research has unravelled the evolutionary history of the African leopard (Panthera pardus pardus).

Today there are 2 genetically distinct populations of leopards present in Africa – one found across most of the African continent and the other confined mostly to the Western Cape, Eastern Cape, KwaZulu-Natal and Mpumalanga regions of South Africa.

The new study, published in PeerJ, estimates that these leopard populations diverged from each other approximately 960,000 to 440,000 years ago.

In a surprising twist, new genetic data has revealed that they now overlap and interbreed in the Highveld region of South Africa, resulting in the highest level of leopard genetic diversity ever recorded in South Africa.

The new insights increase the need for conservation efforts to protect leopards in the country.

Lead author Declan Morris, who studied leopards in South Africa as part of his PhD at the University of Adelaide, says they compiled the most comprehensive leopard mitochondrial DNA (mtDNA) dataset to date.

“What we found was that there were 2 clear populations present in the eastern and western parts of the Mpumalanga province.”

Mitochondrial DNA is passed down solely from a mother to offspring.

By mapping the distribution of the 2 lineages across modern Africa and modelling known mutation rates of the NADH-5 gene, they showed that the timing of the genetic divergence coincided with the aridification of the Limpopo basin.

A photograph of a young man crouched next to an unconscious leopard lying in the back of a utility vehicle in the field
Declan Morris with a captured, sedated leopard in South Africa. Credit: Courtesy of the University of Adelaide

Between 1 million to 600,000 years ago the Limpopo basin – located at the junction of South Africa, Botswana, Zimbabwe and Mozambique – became an arid desert which separated the 2 populations of leopards.

“The 2 lineages are separated by the Namib and Kalahari deserts, which are still there today and have been for millions of years. But the area that has changed over time is the Limpopo basin,” says Morris.

It is now a subtropical region where the 2 populations have since recombined, and are now co-mingling and interbreeding, resulting in high levels of genetic diversity.

“This information will hopefully help change attitudes towards the management of leopards and be used to inform management decisions – such as choosing translocation instead of issuing destruction permits for problem-causing animals,” he says.

“These sorts of discoveries, they can help leverage more funding, more attention and a place higher importance on the leopards … so there’s a lot more effort going into protecting them.”

As these results are from a single mtDNA gene, next steps will involve further research on whole genome data. Morris, who spent almost 3 years in South Africa capturing leopards to collect biological samples, is eager to return in the future.

A map showing the distribution of the two mitochondrial lineages across the continent of africa
Spatial structure of PAR-I and PAR-II leopard lineages across Africa. PAR-I haplotypes (n = 29) are represented by differing shades of blue and PAR-II haplotypes (n = 18) are represented by differing shades of green. Pie graphs overlaid onto the map represent the number and frequency of haplotypes at that location. (A) The distribution of maternal haplotypes across the African continent. (B) The occurrence and overlap of PAR-I and PAR-II lineages in southern Africa. Grey shaded areas represent regions of intense aridity during the mid-Pleistocene, when gene flow may have been reduced. The red shaded region roughly encompassing the lower Limpopo basin and the Mpumalanga Lowveld suggests the region where PAR-I and PAR-II have come into present day secondary contact. Question marks denote other regions where PAR-I and PAR-II potentially overlap and may be coming into genetic contact. Credit: Morris et al. 2024, PeerJ

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