The Punan people of the island of Borneo were once rumored to have tails, so elusive did they seem to their neighbors in the 19th century. Unlike the Indigenous farmers, who lived in long houses, the Punan roamed the island’s northern rainforest in family groups, hunting bearded pigs, harvesting starchy plants and gathering forest products for trade.

They were not only misunderstood, but mistreated. Over decades, the Indonesian government stripped the Punan of their ancestral lands and encouraged them, sometimes forcibly, to settle in ready-built villages. By the 1990s, anthropologists believed that the group’s traditional hunter-gatherer lifestyle had vanished. In 2002, a census of the Punan in eastern Borneo focused only on the villages, because so few nomads were thought to exist.

And so in 2018, when Stephen Lansing, an anthropologist at the Santa Fe Institute, and Pradiptajati Kusuma, a geneticist at the Mochtar Riady Institute for Nanotechnology in Tangerang, Indonesia, said they had learned of a clan of about 30 Punan families who sheltered in limestone caves and rarely, if ever, emerged from the forest, many experts were skeptical. But with funding from the National Science Foundation, the scientists made contact with the nomadic group in 2018, and began collecting data with the aim of ensuring their health and welfare.

After that first trip, Dr. Lansing returned to Santa Fe with photographs of a man wearing a loincloth made of bark fiber, along with recordings of a song language he believed resembled no other. His initial description of these people, who call themselves the Cave Punan or Punan Batu, was published last year in the journal Evolutionary Human Sciences. Press reports in the Indonesian media catalyzed the local government to declare the Punan Batu as regular users of their forest, a first step toward obtaining the right to manage it under national laws.

Some experts remain doubtful that this unusual group could really have been secluded for so long. The skeptics have compared the announcement to that of the Tasaday, a “lost tribe” discovered in the Philippines in 1971, whose isolation was eventually determined to be an exaggeration, if not a hoax.

Bernard Sellato, a Punan specialist with the French National Center for Scientific Research, has been particularly fierce in his criticism. In an email, he referred to the Punan Batu and other coastal groups as “‘fake’ Punan.” Based on historical accounts and ethnographies, he remains convinced their ancestors were not native to the island, but rather enslaved people imported from New Guinea and eastern Indonesia several centuries ago.

But a new study focusing on the DNA of the Punan Batu, recently accepted by a scientific journal, is poised to eliminate the doubts of all but the most hardened critics. Based on the limited diversity revealed in the genes of the Punan Batu, they appear to have been isolated for more than 20 generations. Dr. Sellato’s contention that the Punan Batu are the descendants of imported slaves does not fit with these results.

The new findings could also put to rest a century-old debate about when the Punan arrived in Borneo, and how they became hunter-gatherers in the first place. And the research could help make the case that the Punan Batu deserve a hand in managing their forest, which is threatened by encroaching palm oil plantations and commercial forestry operations.

“What they desperately want,” Dr. Lansing said, “is to stop the destruction of their forests.”

Borneo, the third-largest island in the world, is covered by rugged mountains, rainforests and swamps. Its population of 21 million is divided between three countries: Malaysia and the tiny kingdom of Brunei, to the north, and Indonesia, which controls three-quarters of the territory in the south.

The island’s population has been shaped by waves of migration. Caves in the north were used by Stone Age hunter-gatherers at least 50,000 years ago, when a land bridge linked the island to mainland Southeast Asia. Contemporary Indigenous groups, collectively known as the Dayak, are thought to have arrived by sea from Taiwan 4,000 to 6,000 years ago, bringing domesticated rice with them.

Where the Punan came from is unclear. Other parts of Southeast Asia are home to scattered groups of hunter-gatherers who share a suite of physical features including dark skin, a short stature and tight, curly hair. They are the descendants of the first wave of modern humans who departed from Africa more than 60,000 years ago and made their way east, where they encountered and sometimes mixed with now-extinct hominins.

On Borneo, however, the only hunter-gatherers that early European explorers encountered, the Punan, looked similar to the farming Dayaks. And many Punan groups, including the nomadic Punan Batu, had long-established trade relationships with settled communities.

By the mid-1700s, a Muslim kingdom known as Bulungnan controlled part of the northeast coast. According to legend, after the Punan Batu failed to deliver the Sultan a wife, they appeased him with nests of swiftlet birds from the forest, which were exported to China, where they were prized for bird’s nest soup.

The Punan Batu performed risky work for the Sultan, collecting nests from the caves and honey from treetops, along with rattan and fragrant agar wood. In exchange, the Sultan gave them tobacco, rice and metal tools. Though they were no longer exclusively reliant on wild food staples, they remained isolated. In 1903, a Dutch resident described them as being “at the lowest level of development.” Thirty years later, another Dutchman, a geologist, referred to them as “a backward group, which almost does not mix with other Punan.”

Even after the Sultanate dissolved in 1959 and its territory became an Indonesian regency, the family maintained control of its forest resources. Abdul Karim, a voluble man in his late 60s and a descendant of the Sultanate, said that as recently as the 1980s one of his older relatives, Prince Har, treated the Punan Batu almost as his slaves. Har was “really strict to the Punan,” Karim said, telling them: “You stay in the forest, you cannot go to the city.”

Scientists, in the meantime, have long questioned the notion of a Punan identity. In 1945, Fay-Cooper Cole — an anthropologist who had defended natural selection during the Scopes Monkey Trial — argued that the Punan were not full-time hunter-gatherers. He suggested that they were villagers out “camping.”

Later researchers noted that Punan groups in different regions spoke different languages, which were more closely related to those of neighboring Dayak communities than to other Punan. The Punan, they suggested, were actually Dayak who had abandoned agriculture to focus their activities on the forest.

Dr. Lansing came to Borneo after spending 40 years studying rice farmers on a far more developed Indonesian island, Bali. There, he found that a thousand-year-old system of coordinating irrigation and planting through regular gatherings at local temples provided greater yields than did the application of fertilizer and pesticides. His work led, in 2012, to the designation of the water temple landscape as a UNESCO World Heritage Site.

Over the last decade, he began collaborating with researchers at one of Indonesia’s pre-eminent genetics laboratories, in an attempt to understand human migration across the archipelago. During a trip to Borneo in 2017, he and Dr. Kusuma first heard a report about the Punan Batu from a self-appointed Punan leader from another area, Thomas Mita. Mr. Mita offered to guide the researchers there — for a steep price.

In his grant proposal with the National Science Foundation, Dr. Lansing described how he would be making “first contact” with the Punan Batu, a bold claim that contributed to early concerns about his credibility. Experts did not believe there were any uncontacted Indigenous groups in Borneo. It was only after Dr. Lansing paid Mr. Mita to take him there in 2018 that he learned Mr. Mita had previously brought in other foreigners. “I guess he was running little tours to discover the ‘exotic primitives,’” Dr. Lansing said.

Far from being discouraged by such stage management, the incident piqued his curiosity, for the people he met were practicing a nomadic, subsistence lifestyle that no longer existed in other parts of Borneo. When Dr. Lansing was planning to return in 2019 with three other scientists, he invited me and a photographer to accompany him. The group planned to spend five days camping with the nomads, conducting interviews and handing out GPS ankle bracelets to record their movements.

A dozen or so Punan Batu met us on our first morning at Abdul Karim’s trading post, where the Indonesian Ministry of Health held a monthly medical clinic for them. In the afternoon, we all climbed into a small fleet of motorized canoes for the journey up the Sajau River. The longtail engines snarled and popped as the boats seesawed over fallen logs and jolted up small rapids.

Three hours up the meandering river, we arrived at our first campsite. Dr. Lansing and his entourage disembarked from the canoes and, the following day, climbed the lower flanks of a small mountain, guided by the Punan Batu and their pint-size, brown hunting dogs. The men cleared a trail through the muddy forest while the women carried their infants and possessions in baskets on their backs.

One man held a blow gun and wore a loin cloth with blue gym shorts underneath. A young boy whose family no longer lived full-time in the forest had a machete-like knife slung across his shoulders. His eyes were glued to a cellphone in his hands, though there was no reception. He was playing a video game.

Halfway up the mountain was a cavern as large as an amphitheater. The cave, which contained a dense concentration of swiftlet nests, is a sacred site for the Punan, who consider it the source of all things. Once inside, a man named Ma’ruf took a seat on the dirt floor. He was in his early forties but appeared to be half that age, with swooped-over bangs and the youthful skin that comes from a life lived in the shade.

When Ma’ruf was a boy, he told Dr. Lansing, his father and two other Punan men tried to collect and sell birds’ nests from the highest reaches of this cave, but without the permission of Prince Har. They were caught and spent months in prison; it was a desperate time, when Ma’ruf and his mother struggled to survive.

Ma’ruf began to hum, a deep and powerful vocalization that rose from his chest and echoed through the cave. Words took shape in a language only the elders understood. “I am like a porcupine who comes to the cave to rest,” he chanted, according to a translation of a recording of the chant made by Dr. Lansing.

The next singer up was a shirtless man in his sixties named Bo’odon. “I am a true friend of yours,” he sang to Dr. Lansing. “When might this bear fruit, I ask myself. May our relationship bring the return of our lands to us.”

Such song languages represent a fluid form of creative expression. Unlike a typical spoken language, where different speakers will identify common objects and concepts using the same words more than 95 percent of the time, there was only a 70 percent overlap in the vocabulary used by different Punan Batu singers, according to word lists Dr. Lansing has gathered.

Dr. Lansing has wondered if any unknown words in the songs may have been passed down from Borneo’s Stone Age hunter-gatherers, who we know from bones and cave paintings. Determining whether the Punan Batu are descendants of those cave dwellers, or if they may have coexisted with them, would require a genetic analysis.

Dr. Kusuma has collected blood from 12 individuals, with approval of his institution’s ethics board. Because most of the Punan Batu cannot read or write, he explained to them how their blood would be analyzed, and obtained their consent.

He has now analyzed those DNA samples, along with samples of other Punan and Dayak in Borneo and those of Indigenous groups from Sumatra and West Papua. The Punan Batu, the study found, are most closely related to the Punan Tubu and Punan Aput found on other rivers.

By comparing the Punan’s genes with the ancient remains of a female hunter-gatherer from an island in the Taiwan Strait, Dr. Kusuma has concluded that the Punan broke away from mainland populations more than 7,000 years ago. The findings rule out the possibility that they were Dayak farmers who had recently reverted to a hunting and gathering lifestyle.

The study has been accepted for publication in the journal Cell Reports, Dr. Kusuma said.

Hoh Boon-Peng, a geneticist at the International Medical University in Kuala Lumpur, Malaysia, said that the results align with a growing view that the settlement of Southeast Asia was achieved through multiple waves of migration. He noted, however, that more fossil DNA is needed to precisely date the split between the ancestors of the Punan and the Dayak.

Dr. Sellato of the French National Center for Scientific Research has long maintained that the Punan were not “farmers gone bush,” as he put it, yet he remained skeptical of the significance of the Punan Batu to that century-old debate. He admitted that he did not have the expertise to evaluate the new genetic data, but argued that “any sensible, self-respecting Punan would quickly disappear into the far hinterland” rather than become a “slave.”

From the beginning, Dr. Lansing hoped to follow the model that had succeeded within Bali, where scientific research became the pillar that supported cultural preservation.

Borneo has lost more than one-third of its forests since 1980. Although the Bulugnan regency recently recognized the Punan Batu as traditional users of the forest, their land has not received formal protection. Three companies have rights to harvest trees there, though none have yet acted on them.

More troubling to Dr. Lansing are the ever-expanding palm oil plantations, one of which has been intruding from the north, according to satellite maps.

Judging from the GPS ankle bracelets the researchers left with the Punan, family groups typically spend eight or nine days at one of their camps before moving several miles to the next one. Their traditional territory is about three times the size of Manhattan.

The Nature Conservancy and the Leakey Foundation are working to have the craggy landscape declared a park, to prevent the mining of the limestone mountains for cement. The material is in demand as Indonesia builds its new capital, Nusantra, 250 miles to the south.

It’s unclear how much longer the Punan Batu lifestyle will last. One morning, Edi, a compact, muscular man in his twenties who has become skilled with a chain saw, gave us a tour of his one-room home in the middle of the forest. It was elevated on stilts, with fresh sawdust still on the floor. The surrounding vegetation had recently been burned, in preparation for planting sweet potatoes and sugar cane.

Dr. Lansing and Dr. Kusuma both expressed surprise at this development, which had occurred more abruptly than they had imagined. They knew of Punan who had left the forest for the city, but the only other houses this far upriver had been built by Abdul Karim, as temporary shelters to facilitate trade.

Though Edi’s framed house and farm marked a shift from the caves and bamboo lean-tos he had grown up sleeping in, he barely acknowledged its significance. “It’s nice,” he shrugged.

It has been said that a life lived on foot can make the Punan unceremonious when it comes to rites of passage. Edi said he would keep hunting, and collecting honey, but he needed to think about his children and their future. A permanent home was a start.



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