Genetics link Angola’s ‘ghost elephants’ to populations hundreds of miles away

For more than a decade, conservation biologist Steve Boyes searched for “ghost elephants”—nocturnal giants rumored to roam a remote, high-altitude wetland in eastern Angola. When a motion-sensor camera finally captured their image in 2024, Boyes turned to Stanford scientists for help answering a deeper question: Who are these elephants, and where did they come from?

The answer, drawn from DNA in elephant dung, surprised everyone: The ghost elephants are genetically distinct from any previously sequenced population and most closely resemble elephants in Namibia, hundreds of miles to the south.

The genomic work was led by Dmitri Petrov, the Michelle and Kevin Douglas Professor in the School of Humanities and Sciences. “DNA is the molecule of life, and people have figured out how to read it faster and faster,” Petrov said. “It’s very powerful.”

The quest and the Stanford science behind it are the subjects of a new National Geographic documentary by Werner Herzog. In the film, Herzog follows Boyes, a National Geographic Explorer, as he treks to Lisima Ly Mwono, a high-altitude wetland so remote that the team had to carry motorbikes across rivers to reach it.

The elephants, which are larger than others in the region and nocturnal, have only ever been seen by locals. Boyes theorizes they may be living descendants of the largest living land mammal ever recorded, an elephant named “Henry,” which was killed in Angola in the 1950s and whose remains are located at the Smithsonian National Museum of Natural History.

Boyes brought what he had—dung samples—to Petrov and Katie Solari, a senior scientist in the Petrov Lab and associate director of the Program for Conservation Genomics at Stanford. The Petrov Lab is a group of biologists, physicists, and mathematicians who use genomic tools to study evolutionary adaptation. Former Stanford researcher Jordana Meyer is the senior scientist on the project and the key link that brought this work to the Petrov Lab. Ellie Armstrong, another former Stanford researcher, also contributed to the project.

Hunting for DNA data

In the lab, the team placed the samples in a “bead basher”—a machine that breaks open cells to release DNA. From there, the extracted DNA was sent to a sequencing machine that reads the entire genome.

“This was a really great example of using noninvasive samples because you can’t even see the animal,” Solari said. “The best we can do is get their feces and then throw all our genomic techniques at it to get tissue-level information.”

Petrov and Solari have been testing this process on different mammals, mostly in Africa. They’ve found that if a fecal sample is fresh enough, scientists can obtain the outer mucus layer, which can behave very similarly to a tissue sample.

“Hopefully that sample has more elephant DNA in it than the other things that are in a fecal sample, which is also going to include DNA from their diet, microbiome, and parasites,” Solari explained.

With the ghost elephants’ genome in hand, the team shared the data with Carla Hoge, a postdoctoral fellow at the University of Chicago in the lab of John Novembre, to compare it against sequences from other elephants. But there was a problem: “Surprisingly, when we started this project, there wasn’t a lot of genetic information available for elephants,” Solari said. “There were a few captive individuals that had been sequenced and aren’t helpful for this use case.”

The native ancestry of captive elephants is usually unknown, and Petrov and Solari needed genomic data from wild elephant populations near the ghost elephants to determine whether they were related.

Meyer and Solari spent months collecting blood and tissue samples from other elephants in the area where the filming took place in order to complete the comparison.

“Carla’s analyses have shown that the ghost elephants are actually quite distinct from anything that we have sequencing for,” Solari said. “We’ve been able to tell that they’re most genetically similar to elephants in Namibia, rather than in the Okavango Delta of Botswana, which is surprising.”

Unfortunately, the scientists couldn’t conclusively link the ghost elephants to Henry. So far, the only solid genetic data they have from Henry is mitochondrial—DNA passed down only from the mother—and it shows no link to the ghost elephants. However, more data is coming that could settle the question, Solari said.

Fecal samples from the ghost elephants have yielded more information. They’ve allowed Hoge to identify each individual, determine sex, and see whether any of the elephants were directly related.

“The fact that we can see distinct individuals is really important,” Petrov said. “It’s a very established method, which we’re now using to understand how big the population is. It’s great that we can get all this information without ever disturbing the animals.”

“A lot of these populations we work on are endangered, so the question of conservation becomes central,” he continued. “We try to figure out how we can go into nature and learn about how these ecosystems work so that ultimately we can protect them.” Solari has used the same fecal-DNA approach to count snow leopards in Pakistan—another species too elusive to study solely by observation.

Stanford scientists have conducted similar research using environmental DNA (eDNA) at the Jasper Ridge Biological Preserve (‘Ootchamin ‘Ooyakma), which offers a unique, easy-to-access living laboratory. eDNA is genetic material shed by organisms into water, soil, or air, and it is used as a noninvasive tool for ecological monitoring.

Science and poetic truth

Petrov said he enjoyed the storytelling aspect of the project and the opportunity to collaborate with the Film and Media Studies Department on a campus screening of the movie last October. The event included a panel discussion with Herzog, Petrov, Solari, and Pavle Levi, the Osgood Hooker Professor in Fine Arts.

Petrov said the discussion brought scientists and artists together around how storytelling and data intersect. “It added poetry to the whole process,” he said. “I think there are very few places where you could have that conversation other than here at Stanford.”

The movie captures one moment, but the research goes on. Plenty of questions remain. For example, scientists want to know why the ghost elephants appear to have come from Namibia rather than an area closer to the Angola highlands. “You solve one puzzle, and another puzzle shows up, and then we solve that one,” Petrov said. “It’s fun.”

Who’s behind this story?

Gaby Clark

MA in English, copy editor since 2021 with experience in higher education and health content. Dedicated to trustworthy science news.

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Robert Egan

Bachelor’s in mathematical biology, Master’s in creative writing. Well-traveled with unique perspectives on science and language.

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