Afarensis has a post on Brazilian evidence relating to the origins of Native Americans (via Gene Expression). It's a good summary of recent work by Neves and colleagues, including the background to this:
In essence, Neves et al, is saying that Paleoindians were part of the expansion of H. sapiens out of Africa, whereas Native Americans represent a later expansion of specialized populations. I find this suggestion intriguing. There are skeptics, as you can see from the above quote from The National Geographic article. Powell is arguing that because America was populated by small populations, genetic drift would kick in and you would see a lot of variation between populations and that the Lagoa Santo populations fit within the pattern af variation seen in Native American populations. If that is the case, I would expect one or two populations to display morphology similar to Australians and Melanesians. Instead, what we have is a series running from southern Chile to Florida - and now Kennewick in Washington (which was not included in either study)- all of which display morphology similar to Australians, Melanesians and Polynesians.
The idea of a "generalized" form for early modern humans has been around for awhile now, applied not only to Paleoindians, but also the Upper Cave crania from Zhoukoudian, and -- by some -- early modern Europeans.