Microsatellite Analysis of Plasmodium Parasites

We conducted microsatellite analysis as described elsewhere (10 (link)). In brief, for each sample originating from Sudan, South Sudan, or Nigeria, we analyzed 7 neutral microsatellite markers (TA1, PolyA, PfPK2, TA109, 2490, 313, and 383). We amplified markers per PCR conditions and primers listed (Appendix Table). We sized amplicons using an ABI 3100 Genetic Analyzer (Applied Biosystems, https://www.thermofisher.com). We scored alleles manually using Peak Scanner Software version 1.0 (Applied Biosystems), including a minimum peak height of 300 relative fluorescence units (Appendix Figure 1). To exclude artifactual stutter peaks (likely polymerase slippage on extended tandem repeats, which are frequent in Plasmodium genomes), we disregarded peaks less than one third of the predominant peak (24 (link)).