Supplementary Material
Figure S1. The (relative) error in estimating the parameters as a function of clade size A) Speciation-initiation rate,
B) Extinction rate, C) Incipient diversification rate (speciation-initiation rate minus extinction rate), D) Speciation-
completion rate, E) Duration of speciation in species that complete the speciation process (a composite of the
speciation-initiation rate, the speciation-completion rate and the extinction rate, Eq. (4)). The scatterplots represent
the absolute errors (A-C) or relative errors (D-E) in the estimates for 1000 replicate simulations, and the blue
arrow indicates their mean clade size, while the green arrow indicates their median value. The various plots are
for different simulation parameter sets: speciation initiation rate is 0:5 (all panels), the extinction rate  takes the
values 0, 0:1, and 0:2 (rows) and the speciation completion rate  takes the values 0:1, 0:3 and 1 (columns). The
simulated trees all had a crown age of 15 My.
Figure S1A.
IFigure S1B.
Figure S1C.
IIFigure S1D.
Figure S1E.
IIIFigure S2. Speciation rates estimated with a constant rate birth-death model from phylogenies simulated with the
protracted speciation model. The various plots are for different simulation parameter sets: speciation initiation rate
is 0:5 (all panels), the extinction rate  takes the values 0, 0:1, and 0:2 (rows) and the speciation completion rate  
takes the values 0:1, 0:3 and 1 (columns). The simulated trees all had a crown age of 15 My.
Figure S2.
IVFigure S3. Speciation rate, estimated using the constant-rate birth-death model, versus the speciation-completion
rate, estimated using the protracted speciation model, for 80 avian clades. To obtain these 80 clades we downloaded
all stage-1 trees (i.e., including only genetic species) based on the Hackett backbone typology from the posterior
distribution of trees available from http://birdtree.org/. We selected 1 tree at random from the posterior distribution
for analysis and identified those genera that were monophyletic (we also included clades where together two genera
formed a monophyletic group).
Figure S3.
V