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If a commonly used divergence time of five million years (Koch et al., 2000) is assumed, the loss of self-incompatibility is estimated to have occurred more recently than 0·413 million years ago (mya) (Bechsgaard et al., 2006).
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We used divergence times and phylogenies from the literature to produce a composite phylogeny of the vertebrate species used in our analyses (Fig. A1).
We also use divergence time estimates generated using fossil calibrations to qualitatively assess the phylogeographic implications of evolution within the group.
First, we use divergence time estimates and ancestral area reconstruction to estimate the deepest age of an endemic South American clade and thereby infer the minimum time of colonization of South America by plethodontid salamanders.
Rates were calculated as events per unit of time using divergence times of primate species as given in [28], [29] and as events per unit of dS distance.
The approach we took here is to use divergence times from all possible taxa pairs.
The global clock was calibrated using divergence times 96 Myr and 430 Myr for human-mouse and fish-mammal splits, respectively [ 32, 60, 83].
Influenza B virus data sets were also simulated under a strict molecular clock using divergence times, substitution rates and other substitution parameters estimated by Physher.
The interplay between gradual speciation and divergence time estimation would be expected to have a significant impact on those methods using divergence times to test for gene flow and hybridization.
Evolutionary variation is measured using divergence time-corrected Blosum values for the transition between two amino acids at a particular site when comparing sequence ' i' to sequence ' j' at site ' e' and ' k' (θ ek ) ij.
A second calibration used a divergence time between the (Strongylocentrotus, Hemicentrotus) clades and the (Paracentrotus, Mesocentrotus) clades of 13 19 Ma from 12S mitochondrial genes calibrated using a reference point estimated from the fossil record [ 35].
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