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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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The future of codon models in studies of molecular function: ancestral reconstruction and clade models of functional divergence

The future of codon models in studies of molecular function: ancestral reconstruction and clade models of functional divergence

Chapter:
(p.145) Chapter 11 The future of codon models in studies of molecular function: ancestral reconstruction and clade models of functional divergence
Source:
Codon Evolution
Author(s):

Belinda S. W. Chang

Jingjing Du

Cameron J. Weadick

Johannes Müller

Constanze Bickelmann

D. David Yu

James M. Morrow

Publisher:
Oxford University Press
DOI:10.1093/acprof:osobl/9780199601165.003.0011

This chapter focuses on the use of codon models for ancestral sequence reconstruction, and for use in clade models of functional divergence. It first reviews codon-based ancestral reconstruction methods, followed by an example of their use in inferring synonymous evolution in mammalian rhodopsins. It then discusses clade models of molecular evolution, followed by a description of a recently proposed clade model likelihood test of divergence and its application to teleost short-wavelength visual pigments. The promise of both approaches lies in the possibility of generating specific hypotheses of molecular function, which can be then interpreted in the context of data on molecular structure and function, particularly for genes for which a variety of biochemical assays and other functional data exist.

Keywords:   codon models, molecular function, ancestral reconstruction, clade models, functional divergence, molecular evolution, rhodopsins, visual pigments

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