I really love this type of paper that focuses on methodological criticism of population genetics work.
Molecular Biology and Evolution, doi:10.1093/molbev/msm225
Native South American Genetic Structure and Prehistory Inferred from Hierarchical Modeling of mtDNA
Cecil M. Lewis, Jr et al.
Genetic diversity in Native South Americans forms a complex pattern at both the continental and local levels. In comparing the West to the East, there is more variation within groups and smaller genetic distances between groups. From this pattern, researchers have proposed that that there is more variation in the West, and that a larger, more genetically diverse, founding population entered the West than the East. Here, we question this characterization of South American genetic variation, and its interpretation. Our concern arises because others have inferred regional variation from the mean variation within local populations without taking into account the variation among local populations within the same region. This failure produces a biased view of the actual variation in the East.