Mongabay.com: What does it take to discover a new great ape species?
What does it take to discover a new great ape species?
Geneticists, morphologists and behavioral scientists reveal the inside story of how their research led to the description of the Tapanuli orangutan.
BY LAUREL NEME ON 19 FEBRUARY 2019
Mongabay Series: Great Apes, Southeast Asian infrastructure
- In a paper published November 2017, an international team of scientists described a new species of orangutan.
- The Tapanuli orangutan, the eighth known great ape, is distinct from its Sumatran and Bornean cousins in several key ways.
- The species is also highly threatened, with plans to develop a hydroelectric dam in its only known habitat raising alarm among conservationists.
- This is the first in a two-part series about the discovery of the Tapanuli orangutan. Part Two will be published Feb. 20.
When an international team of scientists published their description of a new ape species, the Tapanuli orangutan (Pongo tapanuliensis), in the journal Current Biology in November 2017, it marked the culmination of years of painstaking research.
It also highlighted the urgent need to protect this rare ape and save its rapidly shrinking upland forest habitat.
The new orangutan species, named for the Tapanuli region in Indonesia’s North Sumatra province, has a population of roughly 800 individuals and is found only in a 1,100-square-kilometer (425-square-mile) patch of the Batang Toru forest ecosystem, an area currently being cleared for a hydroelectric dam and associated infrastructure.
Geneticists, morphologists and behavioral scientists talked to Mongabay about how their research led to the discovery of this new species of great ape.
The Search for Orangutans
In the late 1990s, renowned Dutch primatologist Herman Rijksen wanted to know whether there were any orangutans left in the fast-disappearing forests of central Sumatra. He knew from colonial publications written in the 1920s and 1930s that the apes had been seen as far south as Palembang, in South Sumatra province. He also knew that Indonesian foresters had spotted wild orangutans more recently in North Sumatra: in the Sibual buali forest reserve in South Tapanuli and also near the outlet of Lake Toba a bit further south. So Rijksen commissioned two of his students to check.
In 1997, Rijksen’s then-graduate student Erik Meijaard went to the area south of the Batang Toru River and found that orangutans still lived there, in the forested southern foothills of the Toba caldera.
The existence of orangutans around the Toba caldera was interesting, Rijksen says. Around 75,000 years ago, Toba was the site of the largest volcanic eruption of the last 25 million years. It no doubt blasted all life forms for miles around, creating a boundary for many species. For example, tapirs and bearded pigs are today only found south of the caldera. So Rijksen thought it was unlikely the apes in the area were a dispersion of the North Sumatra populations. Instead, he suspected they were likely genetic relics of the ancestral form of orangutans.
These orangutans also lived at a higher altitude and in a different type of forest than the Sumatran and Bornean populations, who prefer to stick to lower-altitude alluvial forests.
Helicopter overflights and two large field surveys carried out by research teams led by primatologist Serge Wich, then with the University of Utrecht in the Netherlands, confirmed the existence of orangutans in this region.
Over the next few years, teams of Indonesian and international researchers worked to confirm the presence of these apes using flybys and on-the-ground surveys.
In many locations in Sumatra, what they found was depressing: an absence of apes, development pressure from gold mining and other interests, and slash-and-burn cultivation by migrants.
But in a small patch of forest in Batang Toru, they found apes — which in turn prompted work toward protecting that forest and setting up a wildlife monitoring station as a base for additional studies.
The First Clue: Genetics
The first suspicions that the orangutans living in Batang Toru were a new species emerged in 2007, when University of Zürich graduate student Alexander Nater began work on his doctorate.
Under the guidance of professors Carel van Schaik and Michael Krützen, Nater sought to better understand the population structure of Sumatran orangutans. As far back as 1987, Rijksen had hypothesized that Sumatran orangutans might also be divided into different subspecies. At the time, several subspecies of Bornean orangutan had been identified, but Sumatran orangutans still were considered one species.
Perhaps, Nater thought, it was “because nobody had looked closely at their genetics.”
To do that, Nater needed DNA from Sumatran orangutans. He couldn’t rely on samples from zoos, because he needed to know exactly where the samples came from, and zoos couldn’t provide this level of specificity. As a result, in 2008 and 2009 Nater traveled to areas where orangutans lived.
In some places, like the Sumatran Orangutan Conservation Programme (SOCP) field station of Suaq Balimbing, local assistants or volunteers collected samples for Nater. In others, Nater enlisted help from local research teams to help him collect DNA samples.
Finding samples was no easy task. He and his Indonesian team started their daily searches from a village near the forest that could be reached by car or motorbike. Because the density of orangutans was generally low, less than one individual per square kilometer of forest, they had to hike for hours through rugged terrain and dense jungle vegetation.
Actual orangutan sightings were extremely rare. “If we were lucky, we found some fecal samples,” Nater says. “But our main source was hair samples that we found in nests.”
About 90 percent of the time the nests were too old to yield usable samples. And, when they did find a fresh nest, it had to be low enough (below 30 meters, or 98 feet) for someone to climb up and sift through it for tufts of hair.
Even then, Nater says, “typically, we collected five or 10 hairs at a nest. And only in about half of those cases did we manage to obtain sufficient quantities of DNA.”
Back at the lab, Nater and the team analyzed the mitochondrial DNA (mtDNA), which is inherited from the maternal side and is the easiest and most abundant form to extract and amplify.
Right away, the team noticed something strange, Krützen says. “The genetic markers for the Batang Toru orangutans were closer to Bornean orangutans than Sumatran.”
Rather than being closely related to the orangutans on the same island like you’d expect, Nater says, they were more closely related to the orangutans across the sea in Borneo. “It didn’t make any sense.”
A Second Clue: Genome Sequencing
To figure out what was going on, Krützen, Nater and the team knew they needed to know the genetics of not just the maternal line but of the paternal as well. For that, they couldn’t use mitochondrial DNA but instead needed autosomal DNA, which is inherited from both parents and found in the cell’s nucleus. And to get that, old strands of hair wouldn’t do.
Instead, from 2011 to 2016, they sequenced and analyzed the genomes of 37 wild orangutans using blood samples collected at rehabilitation centers across Borneo and Sumatra.
Once again, the scientists were surprised by the results. The DNA showed three distinct genetic lineages: one of Bornean orangutans, another of Sumatran, and a third, which was the oldest: the Batang Toru animals.
This was the moment, Krützen said, “we knew this [Batang Toru] population was special.”
Yet while the geneticists suspected the Tapanuli orangutans could be a new species, they wanted to see if other significant distinctions existed as well.
Enter Indonesian scientist Anton Nurcahyo. He began studying anatomical variations between geographically separate orangutan populations using morphometrics — the quantitative analysis of the size and shape of skulls and bones — for his doctorate at Australian National University.
To detect differences, Nurcahyo needed to analyze orangutan skeletons, and a lot of them. From 2014 to 2015, he traveled to dozens of museums, rescue centers and other institutions across Southeast Asia, Europe and the United States to examine specimens. At each, he spent weeks taking detailed measurements of hundreds of points on a variety of bones. For the skull alone, he made more than 200 separate measurements, including the width, length and position of the eye sockets, the line and height of the mandible, and the size of the brain case.
Information on the origin of the specimens was often vague or incomplete. For instance, Nurcahyo recalls how a Swiss museum listed several of its skulls as coming from the Kapuas River in Borneo. But because there are two such rivers — one in West Kalimantan province and another in Central Kalimantan, called Kapuas Kahayan — Nurcahyo didn’t know which one it referred to. As a result, he had to contact the missionary group that had originally donated the skulls to find out. Indeed, he often had to dig into the diaries of explorers to determine exactly where a specimen had been collected.
Ultimately, Nurcahyo gathered data from about 500 orangutan skeletons. But none were known to be from Batang Toru.
Meanwhile, other researchers were also searching for orangutan skeletons confirmed to be from Batang Toru. Meijaard searched more natural history museums, while another of Rijksen’s former students, Gabriella Fredriksson, now the SOCP’s Tapanuli program coordinator, probed communities living in the Batang Toru area. Yet she had to take care. To make sure nobody mistook her interest as a request to kill an orangutan, Fredriksson and her team hid their objective and only asked indirect questions, like what animals were hunted and what parts were kept. In some villages in Indonesia, hunters kept skulls as trophies. But not these. The local Batak people tended to consume every part of what they hunted.
There was still no orangutan skull from Batang Toru.
But that soon changed.
A Turning Point
In November 2013, the Sumatran Orangutan Conservation Programme received a call about an injured adult male orangutan in the Tapanuli mountains. The ape, named Raya by his rescuers, was near death from multiple cuts, air rifle pellets, and beatings. Rescuers evacuated Raya to the SOCP’s quarantine center for urgent medical treatment, but he died of his injuries eight days later.
Because their earlier attempts to find museum specimens from Batang Toru orangutans had failed, “I wanted Raya to be preserved for study,” says Matt Nowak, director of the SOCP’s biodiversity monitoring unit. He instructed SOCP vet Yenny Saraswati to bury the body. That way, “it could naturally decompose and be studied at a later date in its entirety.”
That date came a few years later, when the SOCP found out about Nurcahyo’s quest and invited him to study the specimen at the SOCP’s facility in Medan, North Sumatra. They dug it up, and in 2016 Nurcahyo, along with Nowak and Colin Groves, an emeritus professor at Australian National University, analyzed it. Armed with these new data points, Nurcahyo then compared them to those of other wild adult males in his data set.
The results were stunning. For the 39 cranial, dental and mandibular (jaw) variables that he measured, two-thirds of them were way outside the typical ranges for both northern Sumatran and Bornean orangutans. Specifically, the Tapanuli orangutan had a significantly smaller skull and significantly larger canines.
“Even though it was only one sample,” Nurcahyo said, “the differences were so big that they became part of the story of describing these orangutans. … This Batang Toru skull fell so outside the range that it made us confident in the difference with the other species.”
While researchers would have preferred a larger sample size, “you make inferences based on what you have,” Krützen says. “And the differences were enough and so big, we could call it a new species.”
Today, Raya’s remains are housed at Indonesia’s Bogor Zoological Museum. While his demise was brutal, in death he was instrumental in identifying the new species — a powerful legacy for any sentient being.