Mailbag: Neandertal ancestry and founder effects

I am writing a paper regarding the hybridization of Neanderthals into AMH population and there are a few things I just cannot understand, I know you must be incredibly busy, and there is little chance you are going to answer this email, or even receive it at all, but I shall take my chances. I love Anthropology although my major is Philosophy, I am nowhere near a scientist and genetics is rather obscure within the realms of my mind, so my question might sound basic. In your research to find the lets call it statistical number or amount of sexual encounters between these two species, it is mentioned that if these encounters were in fact "occasional" or "sporadic" all non-African humans would show the same small percentage of DNA in their genome... how can--genetically speaking--you tell from the percentage of Neanderthal DNA in each person if the encounters between these species were a few or significantly larger? in other words, why if the encounters were few all humans now would show the same small amount of neanderthal DNA? and viceversa if the encounters were frequent and Neanderthals were absorbed into our population why would some regions of the world show more of their DNA present?

Small groups inevitably carry genes that are not a perfect representation of the larger population from which they came. This is called the “founder effect” in biology – when you have a very small group, they really substantially overrepresent some rare genes, and lose many common genes entirely, giving rise to a rapid genetic differentiation.

If there had been a very small number of Neandertal-modern contacts (like a dozen or so) then everybody who carries Neandertal genes today should have the same small set of them, all inherited from the founder effect of those few Neandertal ancestors. So your Neandertal genes and my Neandertal genes should all be pretty much the same. And most of the genome should have no Neandertal genes today at all.

Now, we don’t have a definitive answer yet about this, but so far the data don’t look like that pattern. Your Neandertal genes and mine are mostly different, and we have a large fraction of the Neandertal genome represented today in one person or another. There haven’t been a tremendous number of Neandertal genes lost entirely from humans. That suggests that the number of contacts was not very small – more like the low thousands or high hundreds than dozens. Remember that the entire human population from that time era acted like a breeding population of fewer than 100,000 people, so 3000 Neandertal ancestors are quite a large fraction of that.