John Hawks probably has the answers you need in this long, thorough post.
Now that this has finally been confirmed, i’m waiting for the news through the coming years of other extinct humans making contributions to the modern human genome… say, like the newly discovered Desinova hominin or Homo floresiensis. Hawks has this tidbit:
If Eurasians got less than 4 percent from Neandertals, doesn’t that mean that they got more than 96 percent from Africa?
I look at the 1-4 percent estimate as a minimum, for several reasons. As I’ll note below, this estimate mainly refers to the excess Neandertal ancestry outside Africa, which means there may be some additional amount that both recent African and non-African populations share.
But more important, Neandertals weren’t the only people living in Eurasia 100,000 years ago. China didn’t have Neandertals, nor did Southeast Asia and Java. India was full of hominins, which might or might not have shared substantial genetic similarity with Neandertals. They’re close enough to the known Neandertal range to speculate that they may have been close, but the only available fossil, the Middle Pleistocene Narmada skull, is not very informative. Any of these populations might have been genetically different from Neandertals, and might have also contributed genes to present-day human populations — genes that wouldn’t show up by scanning the Neandertal genome.
The recent genetic sequencing of the Denisova pinky (a.k.a. the X-woman) from the Altai Mountains reminds us that these populations outside of Africa may have been quite a bit closer to us, genetically, than we might have expected from the 1.8-million-year record of humans outside Africa. These populations were dynamic in ways that many paleoanthropologists haven’t yet appreciated.
This is getting to be very, very fun. It’s hard to explain why this entertains me, but it does.