I read the paper that Afarensis pointed me to, Cranial morphology of early Americans from Lagoa Santa, Brazil: Implications for the settlement of the New World. I found it somewhat persuasive. The authors basically posit two primary waves of humans that settled the New World, a "generalized" form that entered before 10,000 years BP, and a specialized "Mongoloid" form that we know as Native Americans who arrived around 10,000 years ago. As John Hawks notes, this model has been proposed for other regions of the world. In regards to "specialized" human populations, The Real Eve Stephen Oppenheimer spends a lot of time trying to scry the origins of "Mongoloids," and he really comes to no good answers. They seem to simply arrive within the last 10,000 years and explode onto the scene (it could be argued that Mongoloids are the most numerous race of man). We know that there is a particular allele on the MC1R locus which seems to be under strong positive selection in East Asians which results in light skin in these populations (in contrast, Europeans are very polymoprhic and their light skin seems to be predominantly caused from a different loci, though redheads do have associations with some MC1R variants). I wouldn't be surprised of the increase of this allele correlates with the "rise" of the Mongoloids.
I don't know much about morphometrics, though the PC analysis seems pretty clear in this case, the skulls of these ancient Americans are very different than those of modern Native Americans. And the authors make the case that they cluster with extant Melanesians and Australians, and to a lesser extent with sub-Saharan Africans. They point out that the morphological shifts were very quick and abrupt, more remiscient of replacement rather than microevolutionary processes. But a few bones that still have to pick:
1) Where are the physical remains from before 12,000 years ago?
2) Evolution can occur in parallel if the same forces are at work. Populations the world over have grown smaller and more gracile over the last 10,000 years due to a variety of factors.
3) Evolution can be very fast, note that English faces have changed significantly in 650 years. Are the paleoanthropologists willing to say that their dating techniques are precise enough not to mistake a snap microevolutionary change as a population replacement (they note that skull morphology does not respond to fast selection, I'm skeptical, but those in the know can correct me).
4) The skulls match extant Australians and Melanesians, and to a lesser extant sub-Africans. The authors suggest that such morphologies were common in Asia >10,000 years BP. Does that imply that stabilizing selection has constrained Australian Aboriginals, Melanesians and sub-Saharan Africans to an "ancestral state." I'm not concerned about issues of political correctness, but I would like people to speak plainly!
5) What spurred the "specialization" that has occurred over the last 10,000 years of some groups? I'll point the finger at demographic expansions and lifestyle changes associated with agriculture, but the settlement of the New World by Mongoloids predates this.