Closed form modeling of evolutionary rates by exponential Brownian functionals
In this article, the authors present closed form integral expressions for the probability distribution of the pathwise average of evolutionary rates, assuming a bridged geometric Brownian model with diffusion parameter \(\sigma\) governing the time-dependent fluctuation of the rate itself. The average substitution rate along a branch of a phylogeny whose length corresponds to \(T\) calendar times is then obtained by integrating over the Brownian trajectories conditional on the rates at times \(0\) and \(T\). Using these expressions, the validity of the gamma approximation of the average rate distribution is assessed using a distribution fit based on closed form expression of the first two moments. When \(\sigma^2 T>4\), corresponding to stronger rate fluctuations and/or longer periods, the gamma approximation is no longer accurate. In such situations, the approximating distribution of the average rate along a branch is gamma with a small shape parameter, i.e., with a large proportion of small average rates and few very large values, which is far from the actual density function. As a result, the distribution of the transition probabilities between character states (nucleotide, amino acids or codons) in large time does not match the expected limiting distribution, which is clearly not satisfactory. However, authors' experience with the analysis of real data sets suggests that \(\sigma^2 T\) is generally smaller than 4, so the gamma approximation is likely to perform well in the practice.
- Continuous and tractable models for the variation of evolutionary rates
- Identifiability of a Markovian model of molecular evolution with gamma-distributed rates
- A consistent estimator of the evolutionary rate
- Generating Markov evolutionary matrices for a given branch length
- Modeling a trait-dependent diversification process coupled with molecular evolution on a random species tree
- Continuous and tractable models for the variation of evolutionary rates
- Exponential functionals of Brownian motion. I: Probability laws at fixed time
- scientific article; zbMATH DE number 3736679 (Why is no real title available?)
- scientific article; zbMATH DE number 819734 (Why is no real title available?)
- Laplace Transforms for Integrals of Markov Processes
- Methods for evaluating density functions of exponential functionals represented as integrals of geometric Brownian motion
- Modeling the covarion hypothesis of nucleotide substitution
- Monte Carlo computation of the Laplace transform of exponential Brownian functionals
- On some exponential functionals of Brownian motion
- The coalescent
- The conditioned reconstructed process
This page was built for publication: Closed form modeling of evolutionary rates by exponential Brownian functionals
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q893813)
