The fact that genomic diversity in Native Americans can be recovered from their admixed descendants presents new hope for prehistoric studies, as in many places of the world (e.g., North Africa or Central Asia), admixture events took place that are not as well understood since they did not happen to be well-recorded by historians.
It also showcases the idiocy of statements such as that from the American Indian Program at Cornell...
“In marked contrast to the goals of the Cornell Ancestry Event, which seeks to define ‘diversity’ biologically in terms of universal genetic codes … Indigenous peoples customarily define themselves not biologically, but socio-culturally and politically in terms of varying ideas of nationhood,” the statement says.
... which thus objected to the Genographic Project's sampling of Native Americans.
If researchers can identify Native American DNA in admixed individuals, then there must be something more concrete to being a "Native American" than socio-cultural/political self-definitions.
Moreover, it shows how futile the quest to limit access to Native American DNA for research purposes actually is, because this DNA can be recovered anyway from admixed individuals (such as many Latinos) who don't mind.
Mol Biol Evol (2011) doi: 10.1093/molbev/msr049
Genetic variation in Native Americans, inferred from Latino SNP and resequencing data
Jeffrey D. Wall et al.
Analyses of genetic polymorphism data have the potential to be highly informative about the demographic history of Native American populations, but due to a combination of historical and political factors, there are essentially no autosomal sequence polymorphism data from any Native American group. However, there are many resequencing studies involving Latinos, whose genomes contain segments inherited from their Native American ancestors. In this study, we introduce a new method for estimating local ancestry across the genomes of admixed individuals and show how this method, along with dense genotyping and targeted resequencing, can be used to assay genetic variation in ancestral Native American groups. We analyze roughly 6 Mb of resequencing data from 22 Mexican-Americans to provide the first large-scale view of sequence-level variation in Native Americans. We observe low levels of diversity and high levels of linkage disequilibrium in the Native American-derived sequences, consistent with a recent, severe population bottleneck associated with the initial peopling of the Americas. Using two different computational approaches, one novel, we estimate that this bottleneck occurred roughly 12.5 thousand years ago; when uncertainty in the estimation process is taken into account, our results are consistent with archeological estimates for the colonization of the Americas.