Figure S1. Marginal posterior probability distributions for model parameters obtained in the IMa analysis (see text for details).

Figure S2. Comparisons of nucleotide diversity at silent sites in S. parvifolia with those observed in herbaceous and woody plants.

Figure S3. Locations and clustering assignments of S. parvifolia populations investigated in this study and in Cao et al. 2006 on the modeled vegetation map for LGM.

Table S1. Geographic location and sample size for the investigated Shorea species.

Table S2. Sequences of primers for PCR, nested PCR and sequencing.

Table S3. Summary statistics for the levels of polymorphism and recombination.

Table S4. Summary of Tajima's D statistics.

Table S5. Pairwise Fst statistics between populations for individual loci.

Table S6. Estimates of demographic parameters obtained by the IMa program for the five and the four loci datasets.

Table S7. Tests of nested models for Sumatra-Malay group versus Borneo group for the five loci dataset.

Table S8. Lower and upper limits of Tajima's D statistic distributions under the inferred demographic model.

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