Assay information for the two TaqMan minor-groove binding dual-probe 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 (RSA493) is listed first, followed by the alternate allele.
dRSA493, TaqMan-MGB probe that is specific to the Nine Mile phase I (RSA493) allele; Alt, TaqMan-MGB probe that is specific to the alternate allele.
eLower case nucleotides in the probe sequences indicates the position and base of the target SNP; probe sequences also show the fluorescent dye label on the 5′ end and the minor groove binder on the 3′ end.