Recently, the observation of a high-frequency private allele, the 9-repeat allele at microsatellite D9S1120, in all sampled Native American and Western Beringian populations has been interpreted as evidence that all modern Native Americans descend primarily from a single founding population. However, this inference assumed that all copies of the 9-repeat allele were identical by descent and that the geographic distribution of this allele had not been influenced by natural selection. To investigate whether these assumptions are satisfied, we genotyped 34 single nucleotide polymorphisms across 500 kilobases (kb) around D9S1120 in 21 Native American and Western Beringian populations and 54 other worldwide populations. All chromosomes with the 9-repeat allele share the same haplotypic background in the vicinity of D9S1120, suggesting that all sampled copies of the 9-repeat allele are identical by descent. Ninety-one percent of these chromosomes share the same 76.26 kb haplotype, which we call the "American Modal Haplotype" (AMH). Three observations lead us to conclude that the high frequency and widespread distribution of the 9-repeat allele are unlikely to be the result of positive selection: 1) aside from its association with the 9-repeat allele, the AMH does not have a high frequency in the Americas, 2) the AMH is not unusually long for its frequency compared with other haplotypes in the Americas, and 3) in Latin American mestizo populations, the proportion of Native American ancestry at D9S1120 is not unusual compared with that observed at other genomewide microsatellites. Using a new method for estimating the time to the most recent common ancestor (MRCA) of all sampled copies of an allele on the basis of an estimate of the length of the genealogy descended from the MRCA, we calculate the mean time to the MRCA of the 9-repeat allele to be between 7,325 and 39,900 years, depending on the demographic model used. The results support the hypothesis that all modern Native Americans and Western Beringians trace a large portion of their ancestry to a single founding population that may have been isolated from other Asian populations prior to expanding into the Americas.
Some elaboration in ScienceDaily of the logic:
In these earlier studies, the researchers concluded that the most straightforward explanation for the distribution of the 9-repeat allele was that all modern Native Americans, Greenlanders and western Beringians descend from a common founding population. Furthermore, the fact that the allele was absent in other Asian populations most likely meant that America's ancestral founders had been isolated from the rest of Asia for thousands of years before they moved into the New World: that is, for a period of time that was long enough to allow the allele to originate in, and spread throughout, the isolated population. As strong as this evidence was, however, it was not foolproof. There were two other plausible explanations for the widespread distribution of the allele in the Americas. If the 9-repeat allele had arisen as a mutation multiple times, its presence throughout the Americas would not indicate shared ancestry. Alternatively, if there had been two or more different ancestral founding groups and only one of them had carried the 9-repeat allele, certain circumstances could have prompted it to cross into the other groups and become widespread. Say that there was a second allele -- one situated very close to the 9-repeat allele on the DNA strand -- that conferred a strong advantage to humans who carried it. Natural selection would carry this allele into new populations and because of the mechanics of inheritance, long stretches of DNA surrounding it, including the functionless 9-repeat allele, would be carried along with the beneficial allele. To rule out these possibilities, the research team, which was headed by Noah Rosenberg at the University of Michigan, scrutinized DNA samples of people from 31 modern-day Asian populations, 19 Native American, one Greenlandic and two western Beringian populations. They found that in each sample that contained the 9-repeat allele, short stretches of DNA on either side of it were characterized by a distinct pattern of base pairs, a pattern they seldom observed in people without the allele. "If natural selection had promoted the spread of a neighboring advantageous allele, we would expect to see longer stretches of DNA than this with a similarly distinct pattern," Schroeder said. "And we would also have expected to see the pattern in a high frequency even among people who do not carry the 9-repeat allele. So we can now consider the positive selection possibility unlikely."
I've addressed the logic of why positive selection would look like this before. These data aren't particular surprising or groundbreaking, but just increase confidence in a particular model of the settlement of the New World.