The largest genomic study of African elephants to date shows that elephants once moved great distances and exchanged genes across the continent, but today habitat fragmentation is pushing entire populations into dangerous genetic isolation.
In the largest genomic study of African elephants to date, an international team of researchers shows that the history of elephants on the continent was shaped by their ability to move great distances and exchange genes across Africa. But now, as elephant habitats become increasingly fragmented, the study documents the clear genetic consequences of isolation, and suggests ways to incorporate genomic information into elephant conservation programs today and in the future.
In the study, published in Nature Communications, the researchers analyzed 232 complete genomes of elephants from both African species—savannah elephants and forest elephants—collected in 17 African countries. This is the first large-scale continental genetic study since African elephants were recognized as two separate species. To accomplish this task, the researchers used samples that had been preserved in biological sample repositories for more than 30 years, and extracted high-quality genomes from them as part of the iConserve program of the biotechnology company Illumina.
The results show genetic signs of isolation in some populations, where elephant herds have been cut off from each other by a history of hunting, alongside human population growth and the expansion of agriculture and infrastructure. According to the lead researcher, Prof. Patricia Pechenerova of the University of Copenhagen and Lund University, until recently elephants were linked to each other over vast distances. This freedom of movement created genetic resilience, as populations interbred. Today, she says, the picture is different: elephants live in a world where space is increasingly limited, and some populations are becoming isolated.
Two remote areas in northeastern Africa, Eritrea and Ethiopia, are among the areas most affected. They are home to small, isolated populations of elephants, more than 400 kilometers from other populations and surrounded by human settlements and farmland. In these populations, researchers have found a high degree of inbreeding, low genetic diversity, and the accumulation of mildly deleterious mutations—traits that increase the vulnerability of populations to environmental changes and disease.
A similar, but more complex, pattern has been found in West Africa, where high human population density and a long history of ivory trade have also led to the isolation and decline of elephant populations. Contrary to expectations, savanna elephants in West-Central Africa do not show the same decline in genetic diversity found in isolated populations in Eritrea and Ethiopia. Although there is also high levels of inbreeding there, caused by past bottlenecks and isolation, the loss of genetic diversity is partly masked by the influx of forest elephant genes into these populations through interspecific hybridization.
It has long been known that savannah and forest elephants interbreed in a small number of areas where their habitats meet. To the researchers' surprise, the study found that even savannah elephants far from the meeting areas carry small traces of genetic ancestry from forest elephants. It is not yet clear whether this reflects a different location of the meeting areas in the past, or whether forest elephant genes were transported long distances across the continent by elephant movement. Either way, the finding highlights that gene exchange was important not only within each species, but also occurred between the two species of African elephants.
However, when it comes to practical implications for conservation, the researchers urge caution. Professor Alfred Rocca of the University of Illinois at Urbana-Champaign, one of the senior authors of the paper, said that reconstructing the genomic history shows that savannah and forest elephants have followed very different evolutionary paths over the past four million years, and that more than 85% of the total genetic variation between elephants stems from their differences. Therefore, he said, gene flow between the species is unlikely to be beneficial, and the transfer of hybrid elephants as part of reintroduction or translocation operations should be avoided. Even within savannah elephant populations themselves, although high historical connectivity has reduced regional differences, the differences that exist between southern Africa, eastern Africa, and west-central Africa suggest that transfers between these regions are also undesirable.
The patterns of gene flow revealed in the study were ultimately shaped by one central factor: the elephants’ ability to move across the landscape. The positive impact of preserving this movement can now be clearly seen in South Africa, in the Kwankwo-Zambezi Transboundary Conservation Area, also known as KAZA. This area spans five southern African states and covers some 520 square kilometers, one of the world’s largest nature reserves. There, elephants have maintained a high level of genetic diversity because populations have remained interconnected and able to exchange genes.
According to Pechenerova, who is also a National Geographic researcher and a colleague of Branco Weiss, elephants are highly intelligent animals that can live in close proximity to humans and adapt. But one of the most important forces in their evolution is the ability of genes to move from population to population. In South Africa, she explains, the landscape still allows movement between protected areas, and there you can see that the genetic health of the elephants remains largely intact.
The researchers warn that without ecological corridors and international coordination between countries and nature management authorities, even protected populations could be weakened by genetic isolation. The “highways” of the animal world are disappearing: landscapes that were once open and allowed elephants to move, connect, and exchange genes are becoming increasingly fragmented. To ensure the long-term survival of elephants, the researchers conclude, it is not enough to protect the animals themselves—the landscapes and the connections between them must also be protected.
The study also carries a partially optimistic message. Forest elephants display higher genetic diversity and fewer potentially harmful mutations than savanna elephants, a figure that gives hope for their short-term survival, despite the continuing sharp decline in their numbers. At the same time, the new genomic atlas is not only a source of knowledge about the elephants’ past and movements, but also a practical tool for conservation authorities. The researchers and their partners from Save the Elephants and the San Diego Zoo Wildlife Alliance are now developing DNA tools that can be used in the field to monitor wild elephant populations, and all the data has been made available for future research and conservation purposes.
According to researchers Charles Masamba and Vincent Mwanika of Makerere University in Uganda, the findings provide important insights into the genetic health and connectivity of African elephant populations. Identifying distinct population units and the levels of gene flow between them could guide more effective conservation strategies, including habitat management, protection of ecological corridors and decisions about animal relocation. In addition, the genomic tools and data developed in the study could also help identify the origin of confiscated ivory, thereby strengthening the fight against illegal wildlife trade.
Among the key findings of the study: 232 complete genomes of elephants from 17 countries were analyzed; forest elephants and savannah elephants have undergone different evolutionary paths over millions of years; evidence of both old and new hybridization between the two species was found; isolated peripheral populations, such as in Eritrea and Ethiopia, show clear signs of inbreeding and a decline in genetic diversity; large, contiguous natural areas in South Africa demonstrate how high connectivity helps maintain good genetic health of populations.
Image caption: Elephants in Rwanda. In the largest genomic study of African elephants to date, an international team analyzed 232 complete genomes of savannah and forest elephants collected in 17 African countries. Credit: Laura Bertola
For the scientific article DOI 10.1038/s41467-026-71262-w.
