Genomics to the Rescue for Sumatran Rhinos

Sumatran rhinoceroses are solitary creatures that browse the dense rainforests of Borneo and Sumatra, living in small, scattered, shrinking groups. Taking a census is challenging, although they “sing.” It isn’t known how many of them exist, exactly, but the number is small.

A multinational research team has unearthed clues in the genomes of 21 of the animals, five “historical” from the Malay Peninsula where they are extinct, and 16 modern genomes from the remaining populations on Sumatra and Borneo. “Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations” appears in Nature Communications.

A Sumatran rhino is the smallest rhino, weighing just under a ton and standing nearly five feet. It’s more closely related to the woolly rhinos of the ice age than the other four species (Indian, Javan, and white and black in Africa).

The Sumatran rhino is critically endangered, a result of periodic isolation of populations as sea levels rose and fell during the Pleistocene epoch from 2.6 million to 11,700 years ago. Stranded animals mated with relatives, leading over the generations to diminishing genetic diversity as recessive alleles (gene variants) doubled up and caused disease. The tiny populations have been shrinking, as the animals die faster than they can replace themselves. (Females do not like mating in zoos.)

Clues to the evolutionary history of the animals lie in their DNA sequences. An ancestral species split into three about 360,000 years ago. The rhinos diverged further within those groups as they became separated into small geographic areas called refugia, dramatically so after a giant volcano, Mount Toba, erupted about 71,000 years ago and killed many animals. Ash spewed across the Indian Ocean, Indian Peninsula, and South China Sea.

The small and separated Sumatran rhinoceros populations plunged at the end of the Pleistocene, but the animals remained from the Himalayan foothills to Borneo and Sumatra. The numbers began to fall again in the 1930s, and then precipitously so, by about 70 percent, during the past two decades due to poaching and habitat destruction. Today conservationists think that fewer than 100 animals exist. The Malayan contingent is already gone, and the Borneo population consists of one female and fewer than 10 males.

Shrinking populations trigger a vicious cycle. The few individuals maintain only part of the long-ago genetic diversity, as effects of mutations that make it through are amplified. The mating of close relatives matches up those deleterious recessive alleles (gene variants), upping the odds of genetic disease.

One way to save the Sumatran rhino may be to transport males, or their sperm, from one natural population to another, in an attempt to promote genetic diversity that might in turn improve health. But at the same time, interfering with natural mating by moving males may disrupt the adaptations that have come to persist that enable small groups to survive in their particular environments. Move an animal from where it is perfectly happy to an area with a different temperature or humidity, and it might not fare as well.

And so the researchers, led by a group from the Centre for Palaeogenetics in Stockholm, with team members from the US, UK, Malaysia, Denmark, Norway, Ireland, Germany, and South Africa, sought clues in genomes to guide the “translocation” of male Sumatran rhinos from their home turf to help populate other groups.

Signatures of inbreeding are evident in sequenced genomes at sites where the two copies of a gene match. This happens when the alleles are inherited from a common ancestor, such as a shared great-great-great grandparent.

“To our surprise, we found relatively low inbreeding levels and high genetic diversity in the present-day populations on Borneo and Sumatra,” said Johanna von Seth, a PhD student at the Centre for Palaeogenetics and co-lead author on the paper.

Considering the genetic findings along with the natural history of the recent drop in population size suggests, according to the researchers, that there’s time to intervene to up the numbers and possibly save the species. That is, the inbreeding isn’t yet dire enough to be as threatening as has been assumed. Still, a few harmful recessive mutations could get in the way of replenishing the numbers.

More rhino sex is clearly needed – the genomes of the Malay Peninsula animals revealed a rapid rise in inbreeding coupled with an increase in frequency of harmful mutations, just preceding their extinction.

“Unless the populations start increasing in size, there is a high risk that inbreeding levels will start rising, and consequently that genetic diseases will become more common,” said Nicolas Dussex, a postdoctoral researcher at the Centre for Palaeogenetics who also co-led the study. Added Love Dalén, professor of evolutionary genetics, “The Sumatran rhino is by no means out of the woods. But at least our findings provide a path forward, where we might still be able to rescue a large part of the species’ genetic diversity.”

That path might include genome sequencing to choose the best animals to pair up – Bumble for rhinos?