Fig. 3

PCA on 241 Manihot esculenta genotypes, using a subset of SNPs in approximate linkage equilibrium. The x-axis and y-axis in this figure represents the first and second eigenvector, respectively. The 241 individuals clustered into roughly three groups. We used cultivated cassava (orange and black) to evaluate BIGRED in simulation experiments. We used 15 individuals (black) to simulate AD data and all 206 (orange and black) individuals to estimate population allele frequencies at sites