Population Problems For Sumatran Rhinos Have Very Ancient Origins

From the sequencing of just a single individual, the history of an entire species has been told, with confirmation from geographic evidence. 

If you're ever told that you should be over something that happened in your distant past, you now have the perfect comeback. Sumatran rhinoceroses suffered a population slump almost a million years ago, and it's a big part of the reason the species is endangered today. In other words, take all the time you need.

There are just 200 Sumatran rhinoceroses (Dicerorhinus sumatrensis) left in the wild, making them one of the most threatened mammals on the planet. It's easy to assume their problems, as with so many other species, are humanity's fault, and that's certainly partly true. However, new research in Current Biology indicates that the Sumatran rhino's resilience against the damage we are doing to their ecosystem was greatly reduced by events in the middle Pleistocene.

Dr Herman Mays of Marshall University, West Virginia, sequenced the genome of a male Sumatran rhino named Ipuh, who died in Cincinnati Zoo four years ago. "Our genome sequence data revealed that the Pleistocene was a roller-coaster ride for Sumatran rhinoceros populations," Mays said in a statement.

Around 900,000 years ago, low sea levels meant many Indonesian islands were joined to the Malay Peninsula in an area known as Sundaland. Numerous species flooded south from Asia, displacing locals that were unready for the competition.

Relatives of the now-extinct wooly rhino were one of the arriving species, achieving a population peak of more than 50,000 as they spread across the available range. Fluctuating sea levels fragmented habitat like roads or farms do today, leaving isolated pockets with too few members to maintain genetic diversity. By 9,000 years ago, there were probably only 700 Sumatran rhinos surviving.

"Their population bottomed out and never showed signs of recovery," Mays said. No doubt the presence of humans in this era was not helpful to the rhinos, but they managed to maintain a toehold of survival until the recent combination of poaching and forest destruction, which looks likely to extinguish the weakened species, at least outside zoos.

Mays described this history using a combination of what we know about sea levels over the last few million years and genetic data using a pariwise sequential Markovian coalescent (PSMC), which estimates the breeding population of a species over time based on a single individual's genome. PSMC identifies periods when population numbers were low, reducing the genetic diversity within a population so that the genes from each parent have a recent common ancestor. However, Mays acknowledges in the paper that it does a poor job of identifying recent changes in population numbers.

While the future of rhinos in the wild looks bleak, Ipuh contributed to the species' survival, having two sons and, so far, two grandchildren.

Ipuh is now gone, but fathered two sons, one of whom has already helped keep the species alive in captivity. Tom Uhlman



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