Fig. 2

Effect of CQ selection on mixed progeny populations from the NIH-1993-R × NIH-1993-S cross. a Heat map showing relative prevalences of microsatellite polymorphisms among the mixed progeny populations before and after CQ selection in Aotus or Saimiri monkeys. Colored squares in the heat map represent E values from microsatellite marker analysis of recrudescences in 10 monkeys (blue, E > 1; yellow, E < 1). Among the 14 P. vivax chromosomes, only a region of chromosome 1 shows positive selection in all samples after drug pressure (microsatellites MS334 and In9pvcrt). Columns with both blue and yellow squares indicate no consistent selection of any microsatellites in the other 13 chromosomes and are consistent with different combinations of individual progenies in each monkey. b Linkage group selection analysis of chromosome 1 by targeted genome sequencing. Aggregate smoothed log₂-fold changes of pre-CQ and post-CQ treatment allele frequencies are plotted as dots; 95% CIs for individual points based on bootstrapping with replacement, are indicated by the vertical lines. A bootstrap range that does not overlap with 0 suggests selection of the corresponding region with CQ exposure