The smaller a genepool is, the more genes look the same.
Consider this part.>Take any two unrelated humans today, Pääbo noted, and they'll differ in millions of places in their genetic code.
Fact is, most people today ARE related.
Compare say, a Japanese guy and a French-Canadian, and you'll discover very soon that they have genetics in common.
Why? Quite simply, the human genepool is fucking shallow.
Most of the human genepool went extinct somewhere a few ten thousands years ago.
For example, if you compare two chimansees that live maybe 2km apart, you'll see taht those two guys have more genetic variance than the French-Canadian and the Japanese guy.
Because chimpansees never experienced a genetic bottleneck, a near-extinction.
Now we can look back at the neanderthal genepool. Neanderthals are extinct. But they left a genepool in mankind.
The majority of the neanderthal genes have probably already been bred out of the human genepool.
Only a few remain, and that's that 4%, those hundred thousand positions.
It's like a tiny half-starved pool, inside a pool that technically also is tiny and half-starved.