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Table S1 Correlation among independent variables used in general linear models to test the role of past niche suitability and stability on present genetic diversity.

Table S2 Mean log likelihood (lnP(K)), its standard deviation (SD), and ΔK calculated from 10 replicates for each of 1–10 clusters (K) using a Bayesian clustering analysis implemented in structure.

Table S3 Analyses of molecular variance based on Φ-statistics for nuclear microsatellite (nSSR) sample sites within structure clusters, chloroplast microsatellite (cpSSR) sites, and cpSSR baps clusters.

Table S4 Percent contribution and permutation importance of each variable used to construct valley oak (Quercus lobata) ecological niche models in maxent.

Table S5 Nuclear microsatellite (nSSR) allelic richness and heterozygosity, niche suitabilities, and niche stabilities by site for samples used in genetic analyses (additional sites were used to construct niche models).

Fig. S1 Maps of genetic variation in valley oak showing haplotype distributions for (a) glyceraldehyde 3-phosphate dehydrogenase (g3pdh) and (b) elongation factor 1-α (ef1α).

Fig. S2 Posterior distributions for per-locus mutation rate-scaled parameter estimates from the IMa2 run with the highest effective sample size.

Fig. S3 Biplots of partial redundancy analyses of (a) nuclear microsatellite and (b) chloroplast microsatellite variation on Last Glacial Maximum (~21 ka) climate after controlling for present climate and geographic position.

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