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Fig. S1 Posterior distributions of divergence time estimates for each pairwise comparison for the Machado et al. (9) dataset (no migration in any model). Each line is the posterior distribution for the divergence time parameter for a particular pairwise comparison.

Fig. S2 Posterior distributions of contemporary effective population size parameters for the Machado et al. (9) dataset. Each population size comprises of two estimates each from pairwise model comparisons.

Fig. S3 The maximum clade credibility (MCC) tree produced from Bayesian coalescent analysis in *BEAST. The MCC tree is the combined posterior sample of trees from 6 replicate runs. Node values are divergence times in millions of years and the clade credibility value (in bold) for the Mainland/Mojave group received >70% posterior support. Scale indicates branch lengths.

Table S1 Nucleotide diversity (πS) for each dataset and population.

Table S2 Model selection table for the Mojave vs Baja comparison of the Machado et al. (9) dataset. Models are ordered by AIC with the most likely model at the top.

Table S3 Model selection table for the Mainland vs Baja comparison of the Machado et al. (9) dataset. Models are ordered by AIC with the most likely model at the top.

Table S4 PCR primer details for all 15 X-chromosome loci. Includes forward (F) and reverse (R) primer sequences and annealing temperatures (TA).

Table S5 Model selection results for the Baja vs Mainland comparison of X chromosome data. All models nested within the full IM model are ranked by AIC with the most likely model at the top.

Table S6 Model selection results for the Mojave vs Mainland comparison of the X chromosome data. All models nested within the full IM model are ordered by AIC with the most likely model at the top.

Table S7 Model selection results for the Mojave vs Baja comparison of the X chromosome data. All models nested within the full IM model are ordered by AIC with the most likely model at the top.

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