I heard from a long-time correspondent this morning concerning introgression of microcephalin from archaic humans. I'm not sharing the whole message, but I thought it would be worth paraphrasing a key point for some thought.
The basic point is this: Why are we talking about "introgression"? Why isn't this just gene flow?
Let me start by saying this: "Introgression" is a useful term because it conveys a genetic reality, regardless of the taxonomic rank we are talking about. The literal meaning is "moving into", and what we are talking about is an allele moving into a new population. But more than that (and what distinguishes the term from gene flow) we are talking about an allele moving onto a new genetic background. The "genetic background" implies that there might be constraints on the movement of such an allele coming from epistasis or negative effects of linked alleles.
I think it is especially useful in the case of MCPH1 because we are interested in the clear positive selection of this allele as a contrast to the clear decline in frequency of most archaic morphologies. The differential fates of different genes seem like a good example of some genes introgressing into a new genetic background.
Now, one may object that "genetic background" isn't really a meaningful term. At the very least, it isn't very specific -- it might be better to have a list of genes that interact with each other and exert epistasis on potential introgressions. But it has the virtue of being empirically quantifiable. The overall genetic differences between archaic humans will eventually be measured, including their differentiation from the later modern population. As I mentioned in the FAQ, we can't narrow these values down right now, but more knowledge of genomics is going to make it quite possible. I think that the idea of archaic genes moving into a modern genetic background is going to describe the some of the evolution of early modern humans -- and I think these are important because they are selected. In other words, it is their dynamics that makes them important, not the other way around.
UPDATE (11/9/2006): Razib gets into the introgression-defining act:
Gene flow is a generic term, and can correctly characterize a whole host of dynamics, while introgression is very specific and precise, a subset of gene flow rather than a synonym.
The description that follows is worthwhile, but it is a little problematic. For instance, there is the introduction of a hybrid zone as a mediator through which introgressive genes move in the process of transfer from one population to another. From some points of view this seems to work. For example, cottonwoods in Utah have well-defined hybrid zones (determined by altitude), through which introgressive alleles are thought to have passed, although now they are distributed widely into the range of the opposite parental population.
But lots of other populations don't have hybrid zones at all. Wolves and coyotes (and dogs) mate fairly extensively wherever they are sympatric. Bison had a time in history when they received lots of genes from cattle, and introgression has continued here and there. There was never any well-defined hybrid zone, unless we consider the entire surviving population of bison to have been the zone. Introgression from mountain hare into European hare in Spain seems to have been structured around ancient Pleistocene contact zones rather than current distributions.
And the whole concept of a "hybrid zone" doesn't really apply well to subspecific interactions.
More in my new post, "What about species?"