SUPPLEMENTARY MATERIAL
Table S1. Estimates of Θ for Euphorbia lomelii. Region abbreviations follow Figure 1 in the main
text. Empirical chloroplast DNA sample sizes (NcpDNA) were used in coalescent simulations. Mean and
standard deviation (Std. Dev.) of Θ-values were calculated from five independent FLUCTUATE runs.
Figure S1. Small-scale survey of 30 published chloroplast DNA substitution rates for coding and noncoding gene regions from diverse taxa. Reported rates were standardized in units of substitutions per
site per year (if a range rather then a point estimate was given, the midpoint value was used), and then
sorted into rate categories. The modal rate category from the histogram (1.1–3.0 x 10-9) contained 12
data points, and the average of these (1.57 x 10-9) was applied to Euphorbia lomelii in the present study
(see Supplementary references for papers used in this literature survey).
Figure S2. Model parameters of alternative vicariance scenarios tested in Euphorbia lomelii. Region
abbreviations follow Fig. 1 in the main text. Effective population sizes (Ne) for extant populations (tips
on the tree) were calculated using theta values given in Table S1 and a mutation rate of 1.57 x 10-9 per
year (see Fig. S1), assuming a generation time of 20 years. Effective population sizes of internal nodes
are the sum of decedent population Ne values. ‘Gens’ represents the number of organismal generations
since a hypothesized splitting event.
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