Mutants first showed up in Marvel comics all the way back in the 1960s, but new canon shows those human speciations branched off from humanity in the Stone Age. This through-line of mutant history is told by a red-haired telepath from prehistory who was the first host to the Phoenix Force. And it turns out humanity’s ancestors feel the same way about their cousins as current humans.
Jason Aaron and Dale Keown’s Avengers #39 introduces humanity's first glimpse at a new type of human distinct from their own species. In canon - a tricky thing to nail down in comics with all the retconning, time travel, and apocalypse(s) - mutants inherited an X-gene that gives them powers and makes them a different species from Homo sapiens sapiens. This X-gene has alternately been described as the result of government experimentation and then bred into the population, or the god-like Celestials introducing the gene into humans to meddle with human history.
But in Avengers #39 it’s a simpler conclusion, mutants were offshoots of humans from the very beginning. An unnamed red-headed telepath explains she was abandoned by her tribe and adopted by another psychic who had built a mutant-only tribe similar to the X-men. Early humans seem to hold the same prejudice toward mutants that current humans do in comics. Some things never change.
But the bigger implication here is that mutants have been living alongside and outcasted among humanity forever. They only stepped out into the light once Professor X built a school. Charles Xavier had tolerance and acceptance in mind for his pupils but was met by humanity outraged that didn’t like being told they were robbed of the much cooler species name Homo sapiens superior. Not a great feeling when you find out the reason you have no superpowers is due to inferior genes. And much like humans’ early ancestors, the first thing they picked up was a torch.
It’s pretty clear from these humble origins why mutants didn’t just overthrow their former kinsmen and become the dominant species. Humans were a nasty, brutish sort that endeavored to have the “different” children left out to die of exposure or to feed the animals. Instead, these mutants are either raised in the wilds by would-be predators or adopted into this progenitor for the X-men. But, humans being the predictably fearful and mean group they are, discovered their abandoned babies were still alive. And once this new tribe of mutants was discovered humans tried to genocide their cousins. Not the best family reunion.
Marvel making mutants date back to 1 million years ago expands the prehistory universe to not just human-only territory. Up to this point, most of the superhumans that come from that far back in time were the earliest Avengers or the Sorcerer Supreme. But having mutants there from the dawn of humanity means this Earth is just as much theirs as it ever was humans’.