Africa’s two elephant species have been secretly interbreeding

New genome data show that Africa’s forest and savannah elephants have exchanged genes for millions of years. The finding does not blur the line between the two species; it reveals how complicated that line can be.

Researchers analysed hundreds of elephant genomes and found evidence of a surprising love affair – Africa’s two elephant species, the iconic savannah elephant and its smaller and reclusive cousin, the forest elephant, have been interbreeding for a long time.

Using decades-old DNA samples taken by dart gun, the scientists identified modern hotspots of hybridisation and traces of ancient gene flow – evidence that forest and savannah elephants occasionally exchanged DNA even after they began evolving into separate species nearly 4 million years ago, according to results published in Nature Communications.

But if forest and savannah elephants have been exchanging genes for millions of years, how does that affect the idea that they are distinct species – and the conservation of elephants today?

“Rather than questioning whether we are talking about two sister species or one, this shows how complicated the relationship between two sister species can be,” explains co-author Rasmus Heller, an evolutionary biologist at the University of Copenhagen in Denmark.

When does one species become two?

Since the 1930s, naturalists have suspected that Africa was home to not one but two species of elephant. Remote mountain forests of western Africa and rainforests of the Congo basin are home to elusive herds of smaller pachyderms. “Fully grown forest elephant males are probably half the size of a fully grown savannah elephant,” Heller says. “Their ears are more rounded, and their tusks are thinner and straighter. Unfortunately, the ivory trade prefers forest elephant ivory because it is harder and easier to carve.”

But the fact that two populations look different is not enough to deem them two species.

Are two creatures of different species if they cannot produce healthy offspring? What if their offspring are infertile? Or is it enough that they rarely interbreed in nature? Biologists have debated these questions for decades, and different definitions can lead to different answers.

The distinction is crucial for conservation managers. For elephants, a cornerstone species beset by poachers, habitat loss and conflict with humans, knowing which populations can be combined without a loss of precious genetic diversity is vital.

Genetic studies in 2001 confirmed that forest and savannah elephants are distinct, but not until 2021 were they formally recognised as separate species – a change that dramatically altered how conservationists assess their risk of extinction. Previously, the combined species African elephants was considered vulnerable by the International Union for Conservation of Nature Red List of Threatened Species. Today, savannah elephants are classified as endangered and forest elephants as critically endangered.

Old dart-gun DNA revealed a hidden history

The early genetic analysis found evidence of limited interbreeding between the two species. But since these studies analysed only a handful of elephant genomes, the researchers suspected that there might be more interspecies fraternisation that had not been captured.

To find out, Heller and co-authors looked to banks of elephant tissue samples collected primarily in the 1990s, before a surge in poaching in the 2000s and 2010s wiped out tens of thousands of individuals. Researchers, including co-author Nicholas Geordiadis, had used rifles outfitted with biopsy darts to nick tiny pieces of skin from the elephants’ thick hides.

“It would just be like a bug bite to them,” Heller says. Although darts do not seem to break elephants’ stride, the proximity of researchers trying to recover samples can be enough to irk some elephants.

“The main thing was finding the dart afterwards,” Heller adds.

These days, conservation teams often collect DNA from elephant dung instead of tissue samples.

In total, Heller and his team analysed samples from 232 elephants collected in 17 African countries. They assessed the population structure within each species – how related forest elephants in one place are to forest elephants elsewhere, and the same for savannah elephants – and searched for evidence of shared genes. Such shared genes can reveal whether animals from different populations, or even different species, have exchanged DNA in the recent past.

The elephant family tree stretches across a continent

The researchers say that they were surprised to find that savannah elephants across Africa are quite closely related. Savannah elephants share genes “across the whole species range, to a much higher extent than pretty much any other mammal we can think of and that we have investigated,” Heller says. “Elephants are obviously very connected to each other, historically speaking.”

This likely reflects both long-distance migration and a social structure that helps genes travel across vast distances.

“Herds are headed by matriarchs, older females,” who act as the anchor of all-female social groups composed of “related females across generations,” Heller explains. “The males leave the herd when they hit reproductive age, so gene flow is really mediated by males.”

Meanwhile, the researchers found that the pockets of forest elephants are smaller in size but more genetically distinct from each other. “That is a little bit surprising, because there are fewer forest elephants and their range is smaller,” Heller says.

The researchers expected isolated forest elephant populations to show more signs of inbreeding. Instead, the opposite was true: savannah elephants carried the larger inbreeding burden.

The scientists suspect that this could result from increased competition among male savannah elephants – when males enter musth, they compete intensely for access to females.

The result is that a relatively small number of dominant males father a disproportionate share of the next generation. “I think what may be happening is that a larger proportion of forest males may be mating,” Heller says.

Separate species, shared genes

Hybridisation was rare but most common where forests meet savannahs. Yet despite millions of years of occasional interbreeding, the two species remain genetically distinct. This suggests that hybrids must have some competitive disadvantage, Heller says.

“There is something that is preventing the two species from completely homogenising.”

Some of this interbreeding stretches back to the split between the two species roughly 4 million years ago. “The rampant hybridisation we have seen at Queen Elizabeth National Park in Uganda could be at least partly influenced by human activities,” Heller notes.

“In Uganda in particular, we see these very high levels of hybrid elephants,” says co-author Al Roca, a population geneticist at the University of Illinois Urbana-Champaign, United States. “There was civil strife in Uganda in the 1980s and 1990s, and I would say that more than 90% of the elephants were hunted by ivory poachers.”

When researchers examined the genetic makeup of elephant herds in Uganda in 2001, they found that females within a given herd were often unrelated. “So many of the elephants had been killed that unrelated females joined together to form new herds, disrupting the social structure that normally shapes who mates with whom,” Roca says. “It is quite possible that something like that may also have contributed to hybridisation.”

Why does this matter for conservation?

How does the finding that forest and savannah elephants sometimes interbreed affect conservation management? First and foremost, just because they can interbreed does not mean they should, Heller and Roca agree. This should not be interpreted as an excuse to translocate elephants willy-nilly and purposefully introduce populations of the two species.

Instead, the findings highlight how important long-range migration corridors are for maintaining healthy elephant populations. Without them, populations can become genetically isolated, making it harder to maintain genetic diversity over time.

“Probably more than any other species, they really need these large areas,” Heller says. “This does not need to be national parks, necessarily – just maintaining these migration corridors between the core areas where they need to find food and do their stuff.” But since these corridors can span many countries, this is a tall order that requires extensive international collaboration.

Heller says further study will be necessary to understand why pairings between forest and savannah elephants remain so uncommon – perhaps because of differences in courtship behaviour or something as simple as incompatible anatomy. “If we want to understand what contributes to keeping them discrete and separate over longer time scales, we need to home in on those hybrid zones and figure out what is going on,” he explains.