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Although a 95% HPD upper bound could not be computed for the coalescent-based estimates of divergence time (Table 2; Additional file 1: Figure S1D), the values obtained are very close to the interval of divergence time based on sequence divergence (0.20 to 0.30 Myrs) (Table 1).
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The 95% confidence intervals of divergence times and the Spearman's rank correlation between our dating and those of recent publications.
Mean ages and 95% HPD intervals of divergence times are in millions of years before the present.
Node numbers refer to Figure 3. Posterior mean ages and 95% HPD intervals of divergence times are in millions of years before the present.
Credible intervals of divergence time for every species tree node over the final chronogram are shown in supplementary figure S3, Supplementary Material online.
The phylogeny, and 95% credible intervals of divergence times, are provided in Fig. 3. Overall support for the phylogeny is very high with 13 clades strongly (i.e., statistically) supported.
The earliest margin of the 95% credible interval of this divergence time estimate overlaps with the presence of a large lake that formed in the Bonneville Basin approximately 650,000 years ago [ 83], although it remains unclear whether the catastrophic flooding event proposed by Ore [ 82] occurred at that time.
While the reliability intervals of these divergence time estimates are large, they are consistent with major geophysical changes on the African continent.
In the full data set (Table 2), the width of the 95% highest probability density (HPD) intervals of the divergence time inferences were considerably smaller than those previously described (Fig. 4, Full boxplots).
The 95% confidence intervals of older divergence events are large compared to most of the more recent events, as we allowed for a wide calibration range for the root node.
After removing the first 2,000 trees as burn-in, the remaining 10,000 sampled trees were analyzed with TreeAnnotator v1.7.1 [ 53] to estimate the 95% highest posterior intervals of the divergence times.
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