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Codon EvolutionMechanisms and Models$
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Gina M. Cannarozzi and Adrian Schneider

Print publication date: 2012

Print ISBN-13: 9780199601165

Published to Oxford Scholarship Online: May 2015

DOI: 10.1093/acprof:osobl/9780199601165.001.0001

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Parametric models of codon evolution

Parametric models of codon evolution

Chapter:
(p.12) Chapter 2 Parametric models of codon evolution
Source:
Codon Evolution
Author(s):

Maria Anisimova

Publisher:
Oxford University Press
DOI:10.1093/acprof:osobl/9780199601165.003.0002

This chapter focuses on parametric models of codon evolution. Parametric models describe the evolution of the system using a finite set of parameters such as the nonsynonymous/synonymous rate ratio, transition/transversion rate ratio, and codon frequencies at equilibrium. The chapter first explains the basic Markov models of codon substitution and the computation of equilibrium codon frequencies. It then describes models and tests used in evaluating selective pressures at the protein level. It also examines measurement of selection on physico-chemical properties of amino acids, as well as modelling of site-dependence in coding sequences. The chapter concludes with a discussion of the latest advances in parametric models.

Keywords:   parametric models, codon evolution, Markov models, codon substitution, codon frequencies

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