Since Identifying markers that can be used for ancestry inference among Native American populations can be considered separate from identifying markers to further the quest for history, this article reports on a study that used data on nine Native American populations to compare the results based on a large haplotype-based dataset with relatively small independent sets of SNPs.
Autosomal DNA polymorphisms can provide new information and understanding of both the origins of and relationships among modern Native American populations. Although autosomal markers can be highly informative, they are also susceptible to ascertainment biases in the selection of the markers to use. The current study was interested in determining what types of limited datasets an individual laboratory might be able to collect are best for addressing two different questions of interest. First, how well can analysts differentiate the Native American populations and/or infer ancestry by assigning an individual to her population(s) of origin? Second, how well can analysts infer the historical/evolutionary relationships among Native American populations and their Eurasian origins. This study concluded that only a large comprehensive dataset involving multiple autosomal markers on multiple populations will be able to answer both questions; different small sets of markers are able to answer only one or the other of these questions. Using its largest dataset, this study observed a general increasing distance from Old World populations from North to South in the New World, except for an unexplained close relationship between the Maya and Quechua samples. (publisher abstract modified)