For more than a decade, the dark depths of the Knysna forest have been a lonely outpost for the last survivor of South Africa’s once great forest elephant herds.

The eventual death of this elephant, an elderly female called the Matriarch, would mean the country’s last free-roaming elephant would finally join the Knysna buffalo, which once also roamed this forest, on the extinction list.

Or so it was thought – until now.

Recent groundbreaking research, using elephant dung, has revealed that five previously unknown female elephants, possibly the Matriarch’s offspring, are living in the expanse of the lush forest nestled in the Southern Cape.

“Things were so bleak and dismal in the past,” says Gareth Patterson, who, together with US conservation geneticist Lori Eggert, made the discovery, details of which were published recently in the prestigious African Journal of Ecology.

“For years there was just one old female out there,” says Patterson. “That was going to be the end of the Knysna elephants. Shoo, it was too enormously sad. We thought: what have we done [as human beings]? Now there’s real optimism and hope.”

Patterson’s earlier work with lions and with George Adamson of Born Free fame earned him the title of “Father of the Lions” in Botswana. But although the plight of the African lion was his focus, “elephants were always in the background”, he says.

He moved to the outskirts of the Knysna forest seven years ago, determined to learn more about the elusive elephants that lumber like ghosts in the forest.

The San – the first chroniclers of the elephants – depicted them in their rock art, and thought of them as a source of power for shamans. Much later, generations of South Africans were enchanted by their battle with humans for survival in Dalene Matthee’s Circles in a Forest.

It has been estimated that there would have been as many as 100 000 of the creatures today – were it not for the onslaught of ivory hunters during 1790 and 1890, who decimated them in their thousands. By 1994 it was widely believed that only the Matriarch remained.

“When I came here I looked at the size of the forest, which is a vast, unfenced area. I thought to myself: ‘How is it known that there’s only one elephant left in this massive area?’

“The popular perception still exists that they are restricted to the forest – I saw evidence pretty early on that there was more than one elephant. I was finding young adult elephants by their tracks and, on top of that, evidence of elephants beyond the forest and in the mountain fynbos.”

This, he says, shows how incredibly adaptable elephants are in a range of habitats, which is “amazing, considering their size and diet”.

Patterson has traversed thousands of kilometres of the forest, fynbos mountainsides and forestry plantations on foot, interpreting spoor and elephant dung of the world’s southernmost elephants.

“The area is large and the elephants are few. Tracking in these conditions is very difficult. In the forest and even in other areas where the elephants roam, visibility is limited,” he says.

“If an elephant freezes up and stands completely still, it becomes almost invisible, particularly in the dense forest areas.”

Patterson was inspired by the “exciting” work of Eggert, of the University of Missouri-Columbia, with forest elephant populations in West Africa. Eggert had developed a genetic census technique for forest elephants, using DNA extracted from dung samples as a way to manage dangerous and secretive species.

The fibrous vegetation that elephants eat continuously scrapes cells from the intestine, which makes dung a reliable source of DNA. This “genotyping” can reveal the numbers of individuals and sexes, how the animals are related and the level of genetic diversity.

“Lori’s method was well suited to the conditions here,” says Patterson. “It was not disruptive or stressful, as sightings of the elephants were not required.”

Patterson spent nearly a year gathering elephant dung, sending it to Eggert in the US for DNA analysis. Her results were astonishing.

Eggert explains: “The results show there are five different genotypes, or individuals, present in the samples. It also showed that they were all females.

“By looking at the genetic similarity of the genotypes, it revealed that the females were likely to be related. The possible presence of a male is intriguing, but we didn’t detect him. I’d really like to believe that a bull is present, and I believe more study will be needed,” says Eggert.

Patterson is thrilled. “It’s a reason for cautious hope. Theirs [the elephants’] is a most remarkable story of survival against formidable odds.”

But the research on the newfound elephants is seemingly at odds with the findings of SA National Parks, which manages the Knysna forest and says its evidence – based on photographs and sightings – point to only one female elephant, the Matriarch.

“But we do not exclude the possibility that there might be more in the area,” says spokesperson Wanda Mkutshulwa. “All the photographic records we have collected over a number of years seem to derive from only one elephant. The last recent sighting by [elephant researcher] Hylton Herd is considered to be the same animal we usually encounter.”

Herd, who works in the forest, says: “We’re not against Gareth. We know they’ve done their research. But it’s hard for us who are in the forest every day to believe this.

“Five elephants would leave lots of dung and cause lots of havoc, and we’re just not seeing that. Either they’re elephantoms or spook elephants,” he laughs. “But these findings encourage us even more to get out and see the truth … We never realised how accurate dung analysis could be.”

Patterson has encountered the elephants up close, but says it was never his quest to have a sighting.

“A sighting is so limited in what it can tell you. It is no good unless you get a photo, and a photo is no good unless it can tell you something. Photography is not an exact science – the same individual [elephant] can look different. There’s also the danger and disruptive factor,” he says.

“These findings will come as a big shock to some who thought they were doomed. But I think the public is over the moon,” says Patterson, who adds there could be more elephants in the wild.

But there is a concern about their genetic longevity. “The size of this population has been small for a long time – breeding between related individuals reduces the genetic variability of the population and increases the chances that harmful recessive genes will be expressed.

“It reduces the probability that individuals will have the genes needed to adapt to changes in the environment, such as new parasites and diseases, or even changes in climate or available food plants,” says Eggert.

One way to alleviate genetic stasis – and protect the elephants, who now have a range of private, commercial and state land – is through the creation of protected wildlife corridors.

“We need to identify the corridors they are using now,” says Patterson. “Protecting these corridors protects not only the elephants but a myriad other species, and the habitat they all depend on.

“There’s no long-term future for them unless there’s a certain amount of free movement. But obviously it can never be like it was in the past.”

He salutes initiatives that open up wildlife corridors, like the Eden to Addo Corridor Initiative, which aims to create a “living corridor” between the Eden district and the Greater Addo Elephant Park.

Founder Joan Berning says landowners adjoining the Garden of Eden, earmarked to be part of the corridor, seem to be happy that elephants will “march over their land”.

“This will allow a greater range for the five or more Knysna elephants,” she says.

But the future is uncertain for the legendary elephants. “Despite our discovery, there’s no getting away from the fact they’re fragile and endangered,” says Patterson. There are so few in the bigger picture.

“These are iconic elephants. They’re such a potent symbol in our country and mean so many things to different sectors of our population. They’re a romantic link to the past! These are elephants that have somehow come back from the brink. We’ve got to think of the future now,” he says.