Microsatellite haplotypes
We then genotyped parasite isolates at microsatellite loci to generate multilocus haplotypes for population genetic analyses. Multilocus haplotypes with at least five loci successfully genotyped (out of 9 forP. falciparum and 10 for P. vivax ) were constructed for 860 P. falciparum samples (300 previously published (Jennison et al., 2015; Schultz et al., 2010)), and 755 P. vivax samples (202 previously published (Jennison et al., 2015; Schultz et al., 2010)) (Table S1). Despite having genotyped the samples that were identified as MOI=1 by pfmsp2 , pvmsp1f3 and pvMS2/MS16genotyping, 31% of P. falciparum samples and 49% of P. vivax samples had more than one allele for at least 1 microsatellite locus, suggesting multiple clone infection and the increased resolution of the microsatellite panel. From these we created dominant haplotypes (Schultz et al., 2010). No significant changes in multilocus Linkage Disequilibrium (mLD) were found when comparing single vs. all haplotypes combined within each study (Table S2). Low genetic differentiation was found between single and dominant haplotypes for P. falciparum in MAD2014 (F ST=0.063, p = 0.58), however, this can be explained by small sample size (n=9 dominant haplotypes). ForP. vivax , low differentiation between single and dominant haplotypes in ESP 2012 (F ST = 0.041, p = 0.33), was explained by a cluster of closely related haplotypes, all reconstructed from dominant alleles), which are described in more detail below. The fact that these related haplotypes were independently constructed from dominant haplotypes provides additional confidence in the allele-calling strategy. All other comparisons (within each province for at each time point) showed negligible genetic differentiation between single and dominant haplotypes. Therefore, the haplotypes were combined for further analysis.