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On the basis of the assumption that the plants underwent a relatively constant rate of evolution, the oldest common ancestor of the orchid family dated from 76 million to 84 million years ago, in the Late Cretaceous Period.
Early estimates of substitution rates assumed a molecular clock (i.e. a constant rate of evolution) [9], and protein sequence data initially supported this hypothesis [see review by 10].
The priors were taken from the parameters inferred from an analysis of a longitudinal sample of C. jejuni collected over a 3-year period [32] assuming a constant rate of evolution within the genus Campylobacter.
UPGMA is a simple hierarchical clustering method that, by assuming a constant rate of evolution, hence no implicit evolutionary model, outputs a rooted tree where the sum of times down a path to the leaves from any node is the same, regardless of the chosen path.
M0 implies a constant rate of evolution (ω = dN/dS = 0.44) for all branches (Table 2).
These measures were taken to ensure a constant rate of evolution.
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P values for the λ and α parameters were determined from likelihood ratio tests against a model with constant rates of evolution (unconstrained Brownian motion).
Rate smoothing techniques relax the assumption of constant rates of evolution throughout the tree: differences in rates of molecular evolution are smoothed out by assuming that evolutionary rates change gradually throughout the phylogeny.
This method of relative dating does not depend on the assumption of a constant rate of molecular evolution and is thus robust to differences in the rate of evolution in different branches of the tree [ 12].
Deviation from a constant rate of molecular evolution within the PCWDE data sets (ie a "molecular clock") was first assessed using the likelihood ratio test (LRT) implemented in the program HYPHY [33].
This did lead to the concept of a "molecular clock," with a relatively constant rate of DNA evolution in different eukaryote groups.
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