Demographic history modeling
We used the Generalized Phylogenetic Coalescent Sampler (G-PhoCS)
version 1.2.3 (Gronau et al. 2011) to estimate divergence times,
effective population sizes and gene flow. Because of the computationally
intensive nature of this analysis, we restricted our data set to a
maximum of 10 individuals per subspecies, selecting one sample per
location. We ran G-PhoCS using the standard MCMC settings described in
Gronau et al. (2011) and default parameters with 75,000 burn-in
generations and 750,000 additional sampling generations. We assessed
adequate mixing and convergence using Tracer. Divergence times and
effective population sizes were converted from mutation scale to
generations (T) and individuals (Ne) respectively, by assuming an
average mutation rate of 10-9 mutations per bp per
generation (Kumar and Subramanian 2002). The model implemented in
G-PhoCS is conditioned upon a given phylogenetic topology. Thus, we ran
G-PhoCS using the topology of the nuclear genomic tree (which is
concordant with the Bayesian and MP mitochondrial trees, see the Results
section below).