Yes, indigenous South Americans were actively managing the forest.

Scientific American looks at old trees to determine how so-called hunter-gatherers were actually actively “farming” the Brazil nuts and cocoa trees they relied on for food:

[Archaeologist Patrick] Roberts [of the Max Planck Institute] says some of the trees alive in tropical forests are up to a thousand years old. And they’re sort of like time capsules, storing a record of past human activity in their tree rings, chemistry and DNA.

“So we wanted to see how different existing methods might come together to explore past tree populations, tree growth, tree ages by looking at the largest witnesses of the changes in human activity in the tropics—the trees themselves.”

For example, indigenous peoples of the Amazon basin cultivated Brazil nuts for thousands of years. Roberts’s colleague Victor Caetano-Andrade analyzed tree rings to determine the age and growth rates of Brazil nut trees near the city of Manaus. He found that many trees were established in the late 1600s, but there was a steep drop-off in new trees around the middle of the 18th century.

As colonial communities came into Manaus and developed the city, they drove indigenous people out, often killing them. And what Victor found is that, actually, their growth slowed after this period without these traditional management strategies. So these Brazil nut trees that were still standing near Manaus are actually affected by these pre- and postcolonial changes in human settlement and activity.”

Another example is how communities selected for genetic traits in a variety of tropical trees, such as the cocoa tree—used, of course, to make chocolate.

You can read their time-capsule tree research here, in the journal Trends in Plant Science.