Razib Khan has started writing up his notes on this week's conference of the American Society of Human Genetics: "Reflections on the evolution at ASHG 2012". He includes some reactions on the presentations in human population history, which will be well worth following. There's an exciting agenda of discovery underlying many of the current projects.
Khan mentions the work on Neandertal genetics at the meeting:
Sriram Sankararaman had a poster on Neandertal admixture in modern human lineages. In the broad outlines the Reich lab and the Wall lab seem to agree (along with others, like Melinda Yang in the Slatkin lab). Were seeing the convergence of a new orthodoxy/paradigm.
I agree that a new paradigm is being written, but I don't expect it to rise to an orthodoxy. At the moment, there is an obvious path forward with extensions of standard tools and new data, and that is what constitutes the active research paradigm. I think of this as a path of least parameters. But so far nobody writing outside our group has published any serious effort to match genetic results with archaeological evidence.
Thus far, some of the reactions by established players in archaeology can be described as falling in Pauli's "not even wrong" category. Paleogenomes just shocked the systems of some people who should really have hedged their bets on modern human origins. But modern human origins are no longer the interesting issue. Genetics has moved the ratchet forward, and there is no going back to the simple paradigm.
Now we have to grapple with a complex population history. That history was multilayered, with many more than one or two waves of significant admixture leading to the samples at hand. The great promise is that genetics will at last allow us to test a lot of anthropological assumptions about human hunter-gatherer population dynamics. But the theoretical challenge is that admixture estimates from genetics are conditioned on extremely simple population models that are really far from the ways we know humans have interacted in the past.
On that note, I will point to my current paper, which has just gone online in the Journal of Anthropological Sciences: "Dynamics of genetic and morphological variability within Neandertals". As I put the paper together, I began to appreciate the difficulty of describing each of these different sources of data -- genetic, morphological and archaeological -- for specialists in the other areas. I will post on some of my favorite parts of the paper later in the week.