They know from testing of found remains of Neanderthals that we didn't evolve from them. They also know we didn't evolve they found the genetic modifications made in our DNA which they know are impossible to have due to natural selection or other theories of evolution. Darwin stated he had a theory which would probably be overturned some day as knowledge progressed.
There are also some cases of evident cannabalism and that the Neanderthals were not exactly a friendly species. The rabbit hole might go deeper than we think, especially as modern history is mostly a coverup. The original 'proto-human' was sasquatch, then they were succeeded by others that followed. But those sasquatch/bigfoot races are still around. The 'Missing 411 Series' has some good info on this and is worth a read.
Anyway, I've been meaning to make an article about this, but to put it succinctly, the theory is that not only were some of the Neanderthals hostile but possibly even at war with ancient civilizations. I think it's possible that the original neanderthals were created by the enemy E.Ts when they began their genetic engineering experiments to create what will become known as the 'jewish race'. Initially, what ended up at first was a hybrid ape-reptillianoid monstrosity; maybe what some could refer to as an Orc, or literall description of a 'troll'.
Perhaps it was part of the enemy E.Ts concieved idea of planting their own agents, they needed it to be done on a massive and efficient scale. So they unleash these monstrosities from the underground who would then begin to terrorize and conquer civilization. Beginning a campaign of rape and interbreeding, the start of an apocalypse. Those that escaped fled to the caves, some civilizations would even resort to residing underground. Giving explanation to underground cities like in the ones in Turkey.
Eventually, humans drove them off after learning how to use the bow and arrow, and perhaps direct intervention from the gods, wiping out the most dangerous variants but some of the offspring survived. This is why jews and neanderthals look so out of place, it's NOT natural.