The DNA of Asian elephants tells a concerning story. Although all four subspecies are under pressure, there are considerable differences in their genetic health. In the scientific journal Genome Biology and Evolution, researchers show how whole-genome analyses can help identify more precisely which populations are most vulnerable and where conservation measures could have the greatest impact.
The Asian elephant (Elephas maximus) is found across South and Southeast Asia and is classified as Endangered by the IUCN. Habitat loss and fragmentation, human-elephant conflict and poaching are causing populations to become smaller and increasingly isolated. This increases the risk of inbreeding, which can lead to a loss of genetic variation and reduce the resilience of populations.
For the study, the researchers analysed the complete genomes of 81 Asian elephants from all four recognised subspecies. Many of the blood samples came from elephants that now live in European and North American zoos. Thanks to the EAZA Biobank - a kind of international blood bank for zoo animals - and well-documented information on the animals' origins, the researchers were able to reliably assign the DNA profiles to the correct subspecies.
Major differences in genetic health
The analyses show that the genetic health of the four subspecies differs substantially. The Bornean elephant has by far the highest level of inbreeding. In this subspecies, around 65 per cent of the DNA has been inherited identically from both parents, a clear sign of long-term inbreeding. The Sumatran elephant also shows elevated levels of inbreeding, at around 35 per cent. By contrast, populations on the Asian mainland and in Sri Lanka show considerably fewer signs of recent inbreeding, at around 11 and 10 per cent respectively.
"The risk of inbreeding is twofold," says Jeroen Kappelhof, first author and PhD candidate at Wageningen University & Research, who is also affiliated with Rotterdam Zoo. "On the one hand, genetic diversity declines. This makes it more difficult for populations to adapt to changes such as new diseases or climate change. On the other hand, inbreeding increases the likelihood that harmful inherited traits will be expressed, which can, for example, lead to reduced fertility. Both processes make populations more vulnerable and ultimately increase their extinction risk. This is why it is important to identify inbreeding at an early stage."
The researchers assessed this by looking at long stretches of DNA that were inherited identically from both parents. Such patterns arise when related animals reproduce with each other. This happens more often in small, isolated populations, causing inbreeding to increase over generations.
"One surprising finding is that, despite the major differences in inbreeding, the four subspecies still share a large proportion of their original genetic diversity," says Kappelhof. "This is probably because, in evolutionary terms, they have not been separated from each other for very long. The differences we see today have mainly arisen because some populations have lost more genetic variation than others. This offers prospects for conservation, as genetic rescue may be an option for populations with low genetic diversity."
Surprising findings from Sri Lanka
The results for the Sri Lankan elephant were also striking. Island populations often have less genetic variation than mainland populations, but the Sri Lankan elephants actually have relatively high genetic diversity. They also show genetic similarities with several populations on the Asian mainland.
The researchers believe that historical human-mediated movements of elephants may have played a role. For centuries, elephants were transported between Sri Lanka and the mainland for warfare, trade and ceremonial purposes. According to the authors, this history may partly explain the genetic exchange between populations. They emphasise, however, that further research is needed to test this hypothesis.
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Implications for conservation
One possible way to reduce the negative effects of inbreeding is to introduce animals from another population. This brings new genetic variation into the population and can make populations more resilient. This approach is known as genetic rescue. For the Bornean elephant, the researchers consider this a potential management measure. Ecological, practical and ethical considerations all play an important role.
"For the Bornean elephant, this could potentially be used as a management measure in the future to reduce the negative effects of inbreeding," says co-author Benoit Goossens, Director of the Danau Girang Field Centre in Sabah, Malaysian Borneo, and Professor at Cardiff University. "At the same time, such an intervention requires careful consideration. For example, you want to avoid losing local genetic adaptations to the environment. Further research is therefore needed before such measures can be applied responsibly."
About the research
The study is part of an NWO-funded research project led by Mirte Bosse (Wageningen University & Research and Vrije Universiteit Amsterdam) and was carried out in collaboration with international research partners.
