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Table S1 List of the populations sampled in this study.

Table S2 Summary of the genes sequenced and the primer sequences used in this study.

Table S3 Neutrality tests for each population of the two species.

Table S4 Summary of the Shimodaira–Hasegawa (SH) tests comparing relaxed trees with constraint trees.

Table S5 Maximum-Likelihood Estimates (MLE) and the 90% Highest Posterior Density (HPD) intervals of demographic parameters from IMa analyses except for Waxy

Fig. S1 Schematic diagrams of five nuclear loci and locations of the regions sequenced. Exons are shown as open boxes, and exon numbers are labelled with capital roman numbers. Thin lines between open boxes refer to introns. Locations of primers for each fragment are sketched above the diagrams.

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