TARAPOTO, Peru—For tropical ecologist Gregory Asner, flying over the Peruvian Amazon from the town of Tarapoto is like traveling back in time. Modern houses, rice paddies and oil palm plantations give way to steep, forested mountains and then to green, unbroken forest that curves toward the horizon.

Suddenly the tree canopy below the twin-engine plane turns a mottled gray-brown, a sign of drought damage that he estimates may affect as many as half the trees.

In this remote corner of Peru’s Ucayali region, Asner, a tropical ecologist at the Carnegie Institution for Science at Stanford University, is afraid he is seeing the future. In the last few years this patch of forest has been hit by two “once-in-a-century droughts”—one in 2005 and another in 2010. These dry spells may become more frequent as temperatures in the tropical North Atlantic Ocean rise and as humans burn thousands of square kilometers of forest for farming. Although it has seen warmer temperatures in the past, the western Amazon is under siege now from a combination of a warming climate and human population growth that it has never faced before, and scientists are scrambling to determine whether existing protected areas will be enough to buffer against the changes to come.

Behind the plane Asner glimpses smoke rising from fires set to clear land for farming. Migration from the Andean highlands has boosted Peru’s Amazonian states to the top of the population growth chart, and the influx of people is taking a toll on the forest.

Peru’s Ministry of Environment—using satellite images and Carnegie-provided software—calculates that the country lost about 6,475 square kilometers of forest, an area the size of Delaware, between 2005 and 2009, up from some 4,550 square kilometers in the five previous years. Losing forest reduces precipitation, further stressing the remaining trees. “About 50 percent of the rain that falls in the Amazon is generated by the forest itself, through transpiration and evaporation,” Asner says. “Deforestation exacerbates the drought problem, because it removes that internal engine.”

Clearing fields and pastures also leaves more exposed forest edges, drying out the interior and making it more likely to burn if an agricultural fire escapes. Fires during the 2005 and 2010 droughts added 3.8 gigatons of carbon to the atmosphere, according to Simon Lewis, a forest ecologist at University College London. In recent genetic studies Lewis found that Amazonian trees have weathered past climatic warming, but the changes were slower then and were not exacerbated by humans, he says.

Faced with warmer, drier conditions, trees have three options:

“Individuals can acclimate, species can adapt or migrate, or they go extinct,” says Kenneth Feeley, a biologist at Florida International University. A floral species can expand its range into a cooler region, but only as fast as seed dispersal allows. Feeley, who studies trees on the eastern slope of the Peruvian Andes, was surprised to see range changes there in just a few years. “Species are moving upslope about three vertical meters a year—that’s really fast,” he says, although perhaps not fast enough. “Based on the climate change that’s already happening, they need to move nine or 10 vertical meters a years.”

In the lowlands, deforestation reduces the areas to which species can move, and fields, pastures and roads create barriers to dispersal. Peru has some large protected areas, such as Manú National Park, where Feeley does his work, but scientists don’t know if they are big enough—or in the right places—to allow species to migrate in a rapidly changing climate.

So the scientists, like the trees, are racing against time. Because rainfall, geology and topography in the western Amazon have given rise to a mosaic of ecosystems so diverse that they are virtually unknown, scientists have little data on which to base conservation plans, Asner says.

Whereas Feeley tracks changes on the ground, Asner flies over the forest in a plane equipped with a laser-imaging system and a supercooled spectrometer that can detect 21 chemicals in the leaves of canopy trees. After a decade of comparing spectrometry data with the chemistry of leaves lopped from treetops, Asner says he can identify chemical “fingerprints” of species with 80 percent accuracy—enough to create a diversity map of canopy species in the western Amazon, from Colombia to Bolivia, that will give scientists a base line against which to compare future changes. He is also measuring forest carbon, which will aid in calculating greenhouse gases released by deforestation.

As some species thrive and others fail to adapt, climate change will produce “winners and losers,” says Asner, who presented his preliminary findings on the drought damage on December 7 at the American Geophysical Union meeting in San Francisco.

He foresees “major shifts in the basic configuration of the Amazon” in a fairly short time. “I’m 44,” he says. “If I am lucky enough to live to be 80, I will see all of it.”