It now seems clear that modern Humans, being the lascivious monkeys that we are, interbred with Neanderthals 50 or 60 thousand years ago. We know this not because of some ancient cave-painting porn but because most of us actually have Neanderthal genes in our very DNA.
The fact that they could reconstitute 60% of the genome from people dead tens of thousands of years is amazing, They did this by first grinding pieces of bone from 3 separate Neanderthal individuals. You then have to wade through all the modern dna that contaminates it and all the bacterial dna to find just the neanderthal dna. Fortunately ancient dna chemically degrades in a predictable way that allows the software to detect it and correct it.
They then compared this dna to modern european, asian, french, and Popua New Guinean dna. Finally, they compared it to dna from western and southern Africa.
They found that 1 to 4 percent of the Neanderthal dna was part of all the modern dna except the African dna. The most likely interpretation of this data then is that after modern humans left africa but before they could really separate and colonize the world, they interbred with the Neanderthals 60 to 80,000 years ago. The mixing probably occurred in the mid-east somewhere.
1 to 4 percent sounds trivial but that means that our 30 thousand genes contain about 600 neanderthal genes. That’s a lot of genes.
That the interbreeding did occur was not a huge surprise but the amount of dna was. Recent genetic evidence seemed to indicate that any gene mixing was probably minuscule and happened in Europe, not the mid east.
edting: d. d. manias