Thornton et al. [2013] also found that the top PCs largely reflected pedigree structure with a standard PCA, and that using the top PCs as surrogates for ancestry was not appropriate. The top PCs from R-PCA, however, reflected ancestry and not pedigree structure. Both Native American and European ancestry estimates from the supervised ADMIXTURE analysis have a correlation of 0.92 with the top PC from R-PCA. The variances explained by the top 10 PCs from R-PCA in a linear regression model for East Asian and African ancestry were reported as 0.74 and 0.69, respectively.
