It is a unique evolutionary hotspot home to thousands of plants found nowhere else on Earth. However, Madagascar’s special trees, palms and orchids – which provide habitats and food for dozens of species of rare lemur and other animals – are now facing catastrophic destruction caused by land clearances, climate change and spreading agriculture, scientists will warn this week.

Thousands of plant species could be lost to humanity in the near future according to a report, The State of the World’s Plants, by scientists at the Royal Botanic Gardens, Kew, and due to be published on Thursday.

Forests and plants across the world are suffering from the effects of climate change, spreading agriculture and uncontrolled land use, but in Madagascar – which is a focus of particular attention in the report – the danger is particularly intense. “Habitat degradation is substantial and continuing,” it says.

Madagascar is the world’s fourth-largest island, having become detached from other land masses in the Indian Ocean about 88 million years ago, and this long isolation has made it a unique evolution laboratory, unmatched anywhere on Earth.

Today it is home to 11,138 native plant species, and of these 83% are found nowhere else on the planet. Yet almost half of these unique species are now at risk of extinction. In fact, these extinctions have already been going on for some time, said Stuart Cable, leader of Kew’s research team in Madagascar. “Dozens of species are known from old collections but have not been seen since. Extinction is happening all the time here. It is very scary.”

One of the most seriously affected plant groups are palms, a species whose position is particularly precarious. There are 204 species of palm found in Madagascar, and 200 are unique to the island. More than half of these palm species are known from a single site or have fewer than 100 individuals in the wild.

“The Madagascar government is trying, and has increased its protected areas for plants from 3% to around 10% of its total land in recent years,” added Cable. “But we are finding many very rare species of plants in single tiny fragments of forest. We cannot protect these. They are disappearing all over the place, all the time.”

Another especially threatened set of Madagascar plants is its orchids. The island has almost 1,000 species of orchid, of which 90% are unique to the island, and 70% are threatened with extinction. On a wider scale, the island’s western dry forest, with its strangely shaped baobab trees and grasslands that consist of dozens of grass species unique to Madagascar, have both lost more than half their land cover since the 1970s.

“The problem is that this is a desperately poor country and most people live as subsistence farmers,” said Cable. “They slash down forests and burn the trees to make charcoal and to free land to grow crops or graze cattle. Unless we can stop that, there is no hope.”

A lot of land in Madagascar is being left barren by ‘slash and burn’ cultivation. Photograph: Stuart Cable

A further problem was highlighted by David Goyder, an expert – based at Kew – on plants in Africa and Madagascar. “A lot of invasive plant species are arriving from Australia and these are much more flammable than native plants. When the temperatures go up, they are much more likely to catch fire and cause even more damage.”

In addition, climate change is beginning to take its toll on the island’s land use. “The south is becoming much drier, and people are moving north into areas that were previously not affected by slash-and-burn farming,” added Goyder. “The result has been even more habitat loss.”

One solution has been the establishment of seed banks, and Kew has helped to store seeds from around 2,400 plant species as insurance against extinction. “However, we can only focus on drier areas this way,” added Cable. “Plants from humid zones, from rainforests, have bigger fruit and seeds with higher water content – so we cannot freeze them in seed banks. The only option is to try to preserve the forest – and that is not proving easy.”

Not every story is one of gloom, however. The orchid Angraecum longicalcar was found a few years ago in a small patch of Madagascar’s central highlands, though researchers could find only 12 individual plants.

Yet Angraecum longicalcar has the biggest flower of any of Earth’s 25,000 species of orchid and also possesses a huge spur, a 40cm hollow tube with nectar at its furthest end. This sugary inducement is designed to tempt hungry hawkmoths, who will then pick up pollen from the orchid that they will pass to fertilise other plants. Only hawkmoths that have 40cm tongues can reach that nectar, however.

“We have set up camera traps near flowers to observe a moth visiting but have never seen one,” said Cable. “We think they may have gone extinct.”

Geographically isolated and unable to be pollinated, the orchid looked doomed until a project led by Kew researchers, and involving local schoolchildren, arranged for specimens of Angraecum longicalcar to be hand pollinated, and seedlings grown in greenhouses. Today there are around 150 specimens growing at several locations in Madagascar, with another 500 ready to be introduced.

“It is a heartening story but it is just one plant among thousands that are threatened in Madagascar,” said Cable. “How we save the others is a much bigger challenge.”