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.