The way some describe it, you’d think the Amazon was a tangle of wilds, virtually untouched by human hand. “The First Eden, a pristine natural kingdom,” is how Stanwyn Shetler, a Smithsonian botanist, described this region of the world in a 1991 book marking the 500th anniversary of Christopher Columbus’ voyage to the New World. “The native people were transparent in the landscape, living as natural elements of the ecosphere. Their world … was a world of barely perceptible human disturbance.”

But was it really? In less-rhapsodical verse, scholars in the past quarter century have shown that this mythical image of untouched nature is just that—a myth. Like humans everywhere, Native Americans shaped their environments to suit them, through burning, pruning, tilling and other practices. And the Amazon is no different: Look closer, and you can see the deep impressions that humans have made on the world's largest tropical rainforest, scientists reported yesterday in the journal Science.

Despite its vastness—the Amazon stretches more than 2 million square miles, and has an estimated 390 billion trees—this rainforest is hardly the untamable, unstoppable force of nature that the Romantics opined about, says José Iriarte, an archaeologist at the University of Exeter. In fact, humans have inhabited the Amazon for roughly 13,000 years, and have been domesticating plants for at least 8,000 years.

"Recent archaeological studies, especially in the last two decades show that indigenous populations in the past were more numerous, more complex and had a greater impact on the largest and most biodiverse tropical forest in the world [than previously thought]," Iriarte says.

In 2013, community ecologist Hans ter Steege and colleagues were taking inventory of the vast diversity of the Amazon's trees. The team sampled 1,170 scattered plots far from modern human inhabitants to identify more than 16,000 different species among those 390 billion individual plants. Then they noticed something odd: Despite that broad diversity, over half of the total trees were made up of just over 1 percent (227) of the species.

About 20 of these "hyperdominant" plants were domesticated species such as the Brazil nut, the Amazon tree grape and the ice cream bean tree. That was five times the amount researchers expected if chance were the only factor. "The hypothesis came up that perhaps people might have domesticated these species a lot [...] which would have helped their abundance in the Amazon," says ter Steege says, who is the lead author of the recent study.

To test this hypothesis, ter Steege teamed up with archaeologists to look more closely at the number of domesticated species in proximity to where there was evidence of pre-Columbian communities. "Indeed, the distance to these archaeological sites has an effect on the abundance and richness of domesticated species in the Amazon," ter Steege says, noting that he and his team were able to plot a decrease in the number of domesticated species as the distance from archaeological sites increased.

The researchers also found that many of these domesticated species were identified far from the areas where they first arose, leading to speculation that humans transported them to cultivate elsewhere. Cocoa, used by some native peoples for beverages and in religious ceremonies, was first domesticated in the northwestern region of the Amazon, where researchers today have identified a larger genetic diversity reflecting more time established there. But today the species is most prevalent in the southern areas of the rainforest.

Iriarte, who was not involved in this research, says ter Steege's study is the largest and most comprehensive analysis of human impact on Amazon flora ever done. He adds that the inclusion of archaeologist and soil scientists helped the study immensely, adding expertise in proving correlations and scrutinizing whether a species would be likely to grow naturally in the soil of a particular area.

"This has made the study really robust by taking into account cultural and natural features of the Amazon in the analysis," says Iriarte, who has does extensive research on the impact of pre-Columbian humans on the Amazon, including plant domestication.

The study may also have exciting implications beyond the ecological origins of this region. In the future, Iriarte hopes this research could be reverse-engineered to help archaeologists locate ancient Amazonian settlements and pinpoint artifacts. By looking for regions that have higher than expected concentrations of domesticated plant species, he says, researchers could better narrow their lens when searching for artifacts in the dense Amazon.

"Perhaps [...] the very biodiversity we want to preserve is not only due to thousands of years of natural evolution but also the result of the human footprint on them," Iriarte says. "The more we learn, the more the evidence point to the latter."

Smithsonian archaeobotanist Dolores Piperno, however, is more skeptical of the authors' conclusions. Piperno, who was not involved in the study, notes that more than five centuries took place between the pre-Columbian era and this study. In other words, a lot has likely influenced the Amazon since then.

Furthermore, researchers today can't always be sure of how plants were used in South America back then. "For some of those species there is little to no evidence for their prehistoric utilization," says Piperno, who has done extensive research on early American plant domestication through the Smithsonian Tropical Research Institute in Panama. "[The study's] interpretations are mainly based on modern-day usages and it's unclear for some species how extensively utilized they are even today."

Piperno also cautions drawing direct conclusions from the tree data. She points to the fact that some scientists once thought that the Mayan civilization in Central America heavily cultivated the breadnut tree based on the larger-than-expected numbers of them often found around Mayan ruins. However, later research found that breadnut tree seeds can actually be spread widely by bats, and that the trees may have started growing around the ruins to take advantage of the limestone they provided to the nearby soil.

For future research, Piperno hopes to see more work done finding and analyzing the remains of plants from prehistoric eras, such as charcoal and mineralized phytoliths and charcoal. "These are the proxies that need to be relied on," Piperno says.