Scientists have developed a technique that pinpoints key biodiversity hotspots, which they say will lead to more effective conservation strategies.
Researchers used the system to identify vital habitats in Madagascar, which is home to a vast array of unique species.
Writing in Science, they say their methodology identifies exact areas that support a wide variety of organisms.
More than 80% of the known species on the island nation are not found anywhere else in the world.
"Madagascar is an amazing place because of its evolutionary history," explained co-author Claire Kremen, a conservation biologist from the University of California, Berkeley, US.
She said that as a result of it breaking away from the African continent 160-80 million years ago, the flora and fauna had been left in relative isolation from the rest of the world.
"It's really been like an evolutionary laboratory because almost everything you find there is unique.
"Because it is the fourth largest island in the world, it's got a lot of major ecosystems within it - it has desert areas, rainforests, high mountains, lowlands and it also has incredible marine resources as well.
"There has also been a lot of diversification within the island of the plants and animals, so it's not only a place where many species are unique, it is also a place that is very rich in biodiversity.
"The real problem is knowing what areas to protect."
Widening the web
In 2003, the president of Madagascar announced plans to triple the size of the network of protected areas in an attempt to conserve the nation's flora and fauna, many of which were under threat from human developments.
In an effort to help the government decide what areas to protect, the international team of researchers gathered existing data from Malagasy scientists on more than 2,300 species.
"They included many different groups of species: lemurs, geckos, frogs, ants, butterflies and many plant species," Professor Kremen said.
"Once we had accumulated all this data, we put it all into something we called an optimisation analysis. It looks for the best solution to try to protect all of these different species.
"When you have more than 2,300 species you really need a computer to figure it out; what we were looking for was 10% of the country that could include all of those species."
But the analysis went a step further, Professor Kremen added: "It is one thing to include a species in a protected area, it is another thing to think about whether that species would have enough habitat included and a large enough population to survive in the future.
"Our computer software allows us to find a solution that not only includes all of these species, but includes as much as possible of the habitats that they need."
She added that the program was also able to identify what species were at a greater risk of extinction.
"Some species do very well in human-dominated environments, and we do not need to worry too much about them.
"But others may already be severely threatened because they have lost a lot of their habitat, or they may be threatened by future habitat loss because they only exist in a very restricted area.
"In our analysis, we weighted those two types of species much more highly."
In the past, there have been a number of ways to select conservation areas, such as identifying a single "flagship species".
"If you protect enough resources for this important species that demands a lot of territory, you hope that this species will act as an umbrella under which many others will also be protected," explained Professor Kremen.
"It is not that this is a bad methodology, it is just that it may not get all the biodiversity that you want; some species will tend to get lost and will be left out of the protected areas."
Another way is to look at the different habitats or taxonomic groups, and ensure that these are contained within a region's network of protected areas.
"Our results have shown that basing conservation on the needs of single species groups like butterflies just isn't enough," said team member David Lees, a butterfly researcher at London's Natural History Museum.
"It is now feasible to map the complex web of life in the world's richest wildlife areas to help guide tough conservation choices, and increase chances of survival."
The findings surprised the researchers by highlighting habitats that had been overlooked in the past, such as coastal forests and central mountain ranges with small pockets of trees.
The team has given the results to the Malagasy government in order to help it draw up its conservation strategy.
The scientists also said that their approach could be easily transferred to other high-priority regions in the world.