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Inferring the Dynamics of Diversification: A Coalescent Approach

Figure 3

The coalescent method provides robust estimates of diversification rates from incompletely sampled phylogenies.

The figure shows maximum likelihood parameter estimates for phylogenies simulated under Model 4a (extinction rate is constant over time and speciation rate decays exponentially). The true, simulated parameters of diversification are indicated by dashed lines (expressed in number of events per time unit). Points and error bars indicate the median and 95% quantile range of the maximum likelihood parameter estimates, across 1,000 simulated phylogenies for each parameter set. The right column shows the estimated extinction rate at present, compared to its true, simulated value. Before estimating parameters, species were randomly sampled from the simulated phylogenies. In the left and middle columns the sampling fraction f ranged from 10% of species (poorly sampled) to 100% of species (fully sampled). In the right column, f = 75% of species were sampled. MRCA, time at the most recent common ancestor.

Figure 3

doi: https://doi.org/10.1371/journal.pbio.1000493.g003