Continuous and tractable models for the variation of evolutionary rates
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Publication:2489580
Abstract: 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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- \(\alpha\)-hypergeometric uncertain volatility models and their connection to 2BSDEs
- Closed form modeling of evolutionary rates by exponential Brownian functionals
- Convergence rate estimation for the TKF91 model of biological sequence length evolution
- A class of fast-slow models for adaptive resistance evolution
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- Modeling the impact of periodic bottlenecks, unidirectional mutation, and observational error in experimental evolution
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- A variational characterization of rate-independent evolution
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