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Computational Molecular Evolution$
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Ziheng Yang

Print publication date: 2006

Print ISBN-13: 9780198567028

Published to Oxford Scholarship Online: April 2010

DOI: 10.1093/acprof:oso/9780198567028.001.0001

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Neutral and adaptive protein evolution

Neutral and adaptive protein evolution

(p.259) 8 Neutral and adaptive protein evolution
Computational Molecular Evolution


Oxford University Press

This chapter introduces the basic concepts of negative and positive selection and the major theories of molecular evolution, and reviews tests of neutrality developed in population genetics. It discusses the use of codon models in phylogenetic analysis to detect positive selection driving the fixation of advantageous replacement mutations. The rest of the chapter proceeds as follows. Sections 8.3 and 8.4 consider methods to detect positive selection affecting particular lineages on the phylogeny or individual sites in the protein. Section 8.5 discusses methods aimed at detecting positive selection affecting only a few sites along particular lineages. Section 8.6 discusses assumptions and limitations of methods based on the ω ratio, in comparison with the tests of neutrality. Section 8.7 reviews examples of genes detected to be undergoing adaptive evolution.

Keywords:   negative selection, positive selection, adaptive evolution, neutrality

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