The Sumatran rhinoceros (Dicerorhinus sumatrensis) is one of the most threatened mammals on earth. By 2011, only about 200 of the rhinos were thought to remain living in the wild. Now, an international team of researchers has sequenced and analyzed the first Sumatran rhino genome from a sample belonging to a male made famous at the Cincinnati Zoo. This study reported in Current Biology shows that the trouble for Sumatran rhinoceros populations began a long time ago, around the middle of the Pleistocene, about one million years ago.
Photograph of Ipuh, the Sumatran rhinoceros (Dicerorhinus sumatrensis) at the Cincinnati Zoo [Credit: Tom Uhlman] |
"Our genome sequence data revealed that the Pleistocene was a roller-coaster ride for Sumatran rhinoceros populations," says Herman Mays, Jr., of Marshall University.
"This species has been well on its way to extinction for a very long time," adds Terri Roth at the Center for Conservation and Research of Endangered Wildlife at the Cincinnati Zoo and Botanical Garden.
The Sumatran rhinoceros population peaked at a time when fossil evidence shows an invasion of continental mammals into Sundaland (a biogeographical region of Southeastern Asia), around 900,000 years ago, according to the researchers. By about 12,000 years ago -- the end of the Pleistocene -- many large mammals had suffered, and Sumatran rhinos were no exception.
Photograph of Ipuh, the Sumatran rhinoceros (Dicerorhinus sumatrensis) at the Cincinnati Zoo [Credit: Tom Uhlman] |
"Their population bottomed out and never showed signs of recovery," Mays says.
The researchers came to these conclusions by using an approach called pairwise sequential Markovian coalescent (PSMC). PSMC makes it possible to elucidate the population history of a species from the genome sequence of a single individual, which is especially important for studying rare or extinct species. The team combined PSMC with ecological niche modeling to understand how changes in population size were related to climate change in the past.
The researchers estimate that the Sumatran rhinoceros population peaked at an estimated effective population size of approximately 57,800 individuals about 950,000 years ago. (Effective population size is the size of a population consistent with the genetic diversity in that population. It gives an estimate of the number of reproducing individuals contributing to a population.)
Photograph of Ipuh, the Sumatran rhinoceros (Dicerorhinus sumatrensis) at the Cincinnati Zoo [Credit: Tom Uhlman] |
The DNA sample that Mays and his team sequenced belonged to a rhino named Ipuh, after the locality on the island of Sumatra where he was originally collected. Ipuh lived at the Cincinnati Zoo for 22 years until his death in 2013, and his remains are still on display at the Cincinnati Museum Center. Roth reports that two of Ipuh's sons continue to live at the Sumatran Rhino Sanctuary in Sumatra. One of them has already sired two calves.
"The Sumatran rhinoceros species is hanging on by a thread," Roth says. "We need to do more to save it."
Source: Cell Press [December 14, 2017]