Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture
(A) PCA was done for the full primary core data set before and after masking putative cosmopolitan admixture from sub-Saharan genomes. Reductions in the magnitude of PC1 after filtering are consistent with the admixture identification method being largely successful. (B) PCA was applied to the sub-Saharan genomes only, after admixture filtering. Genomes were found to cluster by geographical region, including southern (SP, TZ, ZI, ZL, ZO, ZS), eastern (CK, RC, RG, UG, UM), and western (CO, GA, GU, NG) African groups.