An interesting article came out a few days ago that settled the long-standing debate on whether Native Americans descended from one ancestral population or multiple populations.
Full text can be found here: http://www.sciencedaily.com/releases/2009/04/090428223836.htm
The article details a DNA study that provides very strong evidence for the descending of Native American populations from a single ancestral population. Says Karl Britt Schroeder, a lecturer at UC-Davis and one of the authors of the study:
"Our work provides strong evidence that, in general, Native Americans are more closely related to each other than to any other existing Asian populations, except those that live at the very edge of the Bering Strait"
The results of the study expands upon previous findings of what is termed the "9-repeat allele," which is a genetic marker that occurs in all 41 Native American populations sampled and is absent in all of the Eurasian, African, and Oceanian groups sampled. While the discovery of this allele strongly suggested the 'single ancestral population' theory, there was still a possibility that this allele's prominence could be due to mutations occuring separately in Native American populations or crossing over.
The study found that, in examining the bordering base pairs of the "9-repeat allele," there was a distinct pattern of base pairs not found in individuals without the allele, a pattern that is too short to have been promoted by positive selection and too prevalent to suggest multiple mutations. This is the first study supporting the 'single ancestral population theory' with evidence from DNA carried by both sexes.
In light of the results, it seems that the ancestors of the Native American population were indeed most likely to have been a single population that migrated in one wave to the Americas. This would account for the substantial genetic homogeneity both observed and inferred in Native American populations present and past, bringing to mind the innumerable cases discussed throughout the centuries of Native American populations genetically unequipped to combat foreign illnesses like smallpox.