We propose a continuous model for evolutionary rate variation across sites and over the tree and derive exact transition probabilities under this model. Changes in rate are modelled using the CIR process, a diffusion widely used in financial applications. The model directly extends the standard gamma distributed rates across site model, with one additional parameter governing changes in rate down the tree. The parameters of the model can be estimated directly from two well-known statistics: the index of dispersion and the gamma shape parameter of the rates across sites model. The CIR model can be readily incorporated into probabilistic models for sequence evolution. We provide here an exact formula for the likelihood of a three taxa tree. Larger trees can be evaluated using Monte-Carlo methods.

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ABSTRACT. We extend to quantum mechanics the technique of stochastic subordination, by means of which one can express any semi-martingale as a time-changed Brownian motion. As examples, we considered two versions of the q-deformed Harmonic oscillator in both ordinary and imaginary time and show how these various cases can be understood as different patterns of time quantization rules.