In the Footsteps of the Kenyan Cheetah: A Genetic Odyssey

Surprising challenges, missing answers, and what science looks like behind the scenes

Research rarely follows a straight path. More often, it feels like following footprints that suddenly vanish, only to re-emerge in surprising or unexpected places. My work on Kenyan cheetah genetics has embodied such a journey.

My work on Kenyan cheetah genetics began during my MSc study, which looked at the subspecies of cheetahs occurring in Kenya to understand how connected the Kenyan cheetah population really is. This study was made possible by the infrastructure and expertise of the Cheetah Conservation Fund (CCF) genetics laboratory and the field monitoring efforts of our collaborators Action for Cheetahs in Kenya (ACK), the Mara Cheetah Project, and the Kenya Wildlife Service (KWS), who have been studying cheetahs in Kenya for over 15 years. They provided our laboratory with DNA samples, which allowed us to perform genetic analyses on this East African cheetah population at our genetics laboratory in Namibia, thousands of miles away from their natural range.

At first the results were as expected. Most Kenyan cheetahs carried the expected genetic signature (i.e. their mitochondrial haplotype) of Acinonyx jubatus raineyi, the East African cheetah. However, we then came across a couple of samples that gave different results and matched the A. j. soemmeringii subspecies (also known as the Northeast African cheetah) instead. This was surprising, as cheetah distribution maps indicate A. j. soemmeringii should not occur in Kenya. We also knew from our other research performed at the CCF laboratory, that cheetahs in the illegal wildlife trade confiscated in Somaliland are of the A. j. soemmeringii subspecies. This important research (Schmidt-Küntzel et al., 2024) contributed to the uplisting of the subspecies from Vulnerable to Endangered which will encourage more focus on the conservation of this subspecies. So the Kenyan individuals with A. j. sommeringii genetic signature (in the mitochondria) found in Kenya piqued our interest. As geneticists, we know that the mitochondrial DNA does not tell the entire story so we had to take a closer look. We were truly thankful to the Rufford Foundation for supporting the extension of my genetic analysis on Kenyan cheetahs. It allowed us to look at other genetic signatures. We found that the rest of the cheetah genetic signature (nuclear genome vs mitochondria) of those individuals did in fact match other Kenyan samples, so they were not simply individuals that moved across the border (whether through natural migration or illegally by people). So the story was consistent with what we expected.

Our work however suggested that there are some very interesting population dynamics occurring in Kenya involving both subspecies.

Thus, we requested additional support from Rufford to further question the occurrences of North-eastern cheetah DNA material within Kenyan cheetahs. Could it be because of a natural recent hybridization happening between the Eastern African cheetah and the North-eastern cheetah? Or was it simply a remnant of past connectivity? Which meant we needed to dive deeper into the Kenyan cheetah DNA!

With the financial support from The Rufford Foundation, I and my CCF colleagues were ready to set out to determine whether hybridization occurs between the two subspecies. However, sometimes it is not the difficulty of a research question that gives us sleepless nights, sometimes the challenges come from an entirely different direction.
Our collaborators at ACK doubled efforts to collect samples from the region of interest. But those areas are not easy to reach and the project started facing delays. Luckily we had some interesting samples remaining at CCF, so we processed those until… we ran out of DNA for most of those samples, leaving the dataset frustratingly incomplete. We were eagerly awaiting the new shipment, which was to include additional DNA of those samples as well as the long-awaited samples from the region closer to the borders where we suspected to find more individuals with the interesting genetic signature. Those samples held the potential to shed some light on the Kenyan cheetah genetics and the possibility of naturally occurring subspecies hybridization. Sadly, a restructuring within KWS prevented our Kenyan government collaborator from obtaining permission to send the additional samples as planned, leading to further delays. Then, last year, we found out that those samples could not be sent to Namibia at all for this project. As a result, we had to wrap up the project for the grant using only the data we had generated so far, without being able to investigate those mixed individuals. We were all extremely disappointed.

Still, this is not the end of the story. We remain deeply committed, working hand in hand with our Kenyan partners to find solutions, overcome these challenges, and bring the project to completion. Because in research, setbacks don’t erase the goal — they sharpen the determination to reach it.