What is the scientific explanation for mysterious human ‘ghost DNA’?

It's in our bodies. The proof is there. Scientists just can't point where it comes from, like they can with the Neanderthal DNA and others. There isn't even any fossils found on those ancestors, but we have the DNA inside us. They just completely vanished. A lot of our ancestors obviously died out, but at least proof of their existence have been found. But not of the "Ghost DNA" one. Previously known as "junk DNA".

What is the scientific explanation for mysterious human ‘ghost DNA’?
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