Depending on which Native Americans we're taking about, some of them drove entire herds of bison over cliffs. Our European ancestors hunted the mastodon to extinction, I think? In Australia and New Zealand a bunch of reptiles and the moa birds were wiped out by humans.
I don't think most humans are ever thinking about genocide exactly (probably some are/were), but that they're focused on feeding and defending their communities and not considering the balance of the ecosystem.
It doesn't matter to me whether there was ever a mystery because that wasn't the interesting part. "What are they working on?" doesn't need to have an amazing answer; it could just be accounting for all I care. What matters is who the characters are, what they have done and will do and why. And more importantly, the way it highlights issues with corporations by drawing interesting parallels within the story. Maybe people in real life will be inclined to question their own conditions and be inspired to protest for better lives.