The Orsay and Santeuil populations were found to be genotypically separable based on genomic DNA analysis with microarrays. (A) Principal component analysis (PCA) plot. PC1 on the x-axis separates the main Santeuil group (green) from all other strains, and PC2 on the y-axis separates the Santeuil and out-group strains (purple) from the Orsay strains (yellow). (B) Neighbor-joining (NJ) tree created with the same genetic data as used for the PCA plot. Orsay strains are shown in orange, Santeuil strains in green, and the out-group strains in purple. (C) NJ tree based on the RNA hybridization data. The average log2 ratio per probe (with the mean) per genotype was used. Only probes with a maximum absolute ratio of greater than 0.5 were used. The 192 genes whose expression level was solely influenced by DNA polymorphisms were not included. Orsay strains are shown in orange, Santeuil strains in green, and the out-group strains in purple.