There are many facts that point that we evolved from a primate that isn't around anymore. There are many details of a humanoid skull that are different from a gorilla, as you say.

There is also this newfangled discovery called DNA. They can compare the DNA from the skulls they have found with human DNA from now. We share 98% of our DNA with chimps, but we didn't evolve from them. We share a common ancestor from way, way back, and somewhere along the line our genetic lines split and one branch evolved into us and another evolved into chimps.

The skulls they have found, along with other skeletons are from that common ancestor before the branch separated.

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