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- W2102933766 abstract "Abstract This chapter reviews statistical methods for detecting adaptive molecular evolution by comparing synonymous and non‐synonymous substitution rates in protein‐coding DNA sequences. A Markov process model of codon substitution is introduced first, which forms the basis for all later discussions in this chapter. I then consider the case of comparing two sequences to estimate the numbers of synonymous ( d S ) and non‐synonymous ( d N ) substitutions per site. The maximum likelihood (ML) method and a number of ad hoc counting methods are evaluated. The rest of the chapter deals with joint analyses of multiple sequences on a phylogeny. I review Markov models of codon substitution that allow the non‐synonymous/synonymous rate ratio to vary among branches in a phylogeny or among amino acid sites in a protein. Those models can be used to construct likelihood ratio tests to identify evolutionary lineages under episodic Darwinian selection or to infer critical amino acids in a protein under diversifying selection. I use real data examples to demonstrate the application of the methods. The chapter finishes with a discussion of the limitations of current methods." @default.
- W2102933766 created "2016-06-24" @default.
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- W2102933766 date "2003-07-22" @default.
- W2102933766 modified "2023-10-12" @default.
- W2102933766 title "Adaptive Molecular Evolution" @default.
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- W2102933766 doi "https://doi.org/10.1002/0470022620.bbc10" @default.
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