Assay information for the 12 Melt-MAMA assays used in this study.

aBranch targeted on the phylogenetic tree (see Fig. S2).bAssay name given as the MST locus [7] containing the SNP target of interest followed by the base position of the SNP within the allele alignments for that locus (see also Fig. S1).cBase call in the whole genome sequence of Nine Mile phase I (RSA 493) is listed first, followed by the alternate allele.dRSA493, melt-MAMA primer that is specific to the Nine Mile phase I (RSA 493) allele; Alt, melt-MAMA primer specific to the alternate allele; C, consensus primer.ePrimer tails that do not match the native sequence along with the penultimate or antepenultimate mismatch bases are shown in lower case.fTm can vary based on the instrument used, typically ±1°C.gAssay that had a single incidence of homoplasy for one sample (see text).hAssays designed on the reverse compliment.