were obtained from the Human Genome Diversity Project (HGDP) [Li et al., 2008]. The Native American ancestry proxies from HGDP were the combined samples from the Americas (Surui, Maya, Karitiana, Pima, and Colombian samples). Chen et al. [2013] performed a similar supervised analysis with the ADMIXTURE but with (1) the analysis restricted to chromosome 3 and applied to a subset of unrelated individuals, and (2) proportional ancestries estimated for European, Native American, and African populations. Yorgov et al. [2013] estimated global ancestry proportions for all individuals by averaging supervised local ancestry estimates over chromosome 3 markers. Thornton et al. [2013] also performed an unsupervised individual ancestry estimation analysis with ADMIXTURE for the GAW18 individuals, where reference population samples from HapMap and HGDP were not included in the analysis.
