FIG 2.

Two-dimensional plot of the principal-component analysis using 50,469 SNPs. (A) PCA performed using all samples. (B) To account for the possibility that covariation among parasites that share recent ancestry has a disproportionate impact on PC weightings, the PCA was repeated keeping only a single representative of the two dominant Haitian lineages. (C) PCA performed using a subset of 149 sequences created by removing samples resulting from apparent clonal (epidemic) expansion identified in Fig. S2 or having complexity of infection.