Continuous and tractable models for the variation of evolutionary rates

DOI10.1016/J.MBS.2005.11.002zbMATH Open1086.92040arXivmath/0506145OpenAlexW2130654651WikidataQ51956099 ScholiaQ51956099MaRDI QIDQ2489580FDOQ2489580

Authors: Thomas Lepage, Stephan Lawi, Paul F. Tupper, David Bryant 

Publication date: 28 April 2006

Published in: Mathematical Biosciences (Search for Journal in Brave)

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.

Full work available at URL: https://arxiv.org/abs/math/0506145

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zbMATH Keywords

phylogeneticsdiffusion processescovariationCox-Ingersoll-Ross processmolecular clocksthree-taxon phylogenies

Mathematics Subject Classification ID

Applications of Brownian motions and diffusion theory (population genetics, absorption problems, etc.) (60J70) Problems related to evolution (92D15)

Cites Work

• A theory of the term structure of interest rates
• Matrix Analysis
• Title not available (Why is that?)
• Title not available (Why is that?)
• Monte Carlo strategies in scientific computing
• Stochastic calculus for finance. II: Continuous-time models.
• Title not available (Why is that?)
• Probability with Martingales
• Stochastic differential equations. An introduction with applications.
• Title not available (Why is that?)
• Title not available (Why is that?)
• Laplace Transforms for Integrals of Markov Processes
• Passage-time generating functions for continuous-time finite Markov chains
• Modeling the covarion hypothesis of nucleotide substitution
• On the dispersion index of a Markovian molecular clock

Cited In (17)

• \(\alpha\)-hypergeometric uncertain volatility models and their connection to 2BSDEs
• Continuous Models for Genetic Evolution in Large Populations
• Convergence rate estimation for the TKF91 model of biological sequence length evolution
• Modeling rate of adaptive trait evolution using Cox-Ingersoll-Ross process: an approximate Bayesian computation approach
• Composite likelihood modeling of neighboring site correlations of DNA sequence substitution rates
• Pricing CIR yield options by conditional moment matching
• A class of fast-slow models for adaptive resistance evolution
• A variational characterization of rate-independent evolution
• Statistical inference for stochastic differential equations
• A consistent estimator of the evolutionary rate
• When can we reconstruct the ancestral state? Beyond Brownian motion
• CVA and vulnerable options pricing by correlation expansions
• Closed form modeling of evolutionary rates by exponential Brownian functionals
• Rate of evolution of a quantitative character.
• Modeling the impact of periodic bottlenecks, unidirectional mutation, and observational error in experimental evolution
• Counting labeled transitions in continuous-time Markov models of evolution
• Mathematical Foundations of Computer Science 2004

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