Beginner's Guide on the Use of PAML to Detect Positive Selection. (25th April 2023)

• Record Type: Journal Article
• Authors: Álvarez-Carretero, Sandra; Kapli, Paschalia; Yang, Ziheng
• Editors: Crandall, Keith
• Is Part Of: Molecular biology and evolution. Volume 40:Number 4(2023)
• Publication Date: 2023-04-25
• Subjects: adaptive evolution -- dN/dS -- nonsynonymous substitutions -- PAML -- positive selection -- synonymous substitutions; Molecular biology -- Periodicals; Molecular evolution -- Periodicals; Evolution, Molecular -- Periodicals; Molecular Biology -- Periodicals; 572.8
• DOI: 10.1093/molbev/msad041
• Languages: English
• ISSNs: 0737-4038

Abstract

Abstract: The CODEML program in the PAML package has been widely used to analyze protein-coding gene sequences to estimate the synonymous and nonsynonymous rates ( d S and d N ) and to detect positive Darwinian selection driving protein evolution. For users not familiar with molecular evolutionary analysis, the program is known to have a steep learning curve. Here, we provide a step-by-step protocol to illustrate the commonly used tests available in the program, including the branch models, the site models, and the branch-site models, which can be used to detect positive selection driving adaptive protein evolution affecting particular lineages of the species phylogeny, affecting a subset of amino acid residues in the protein, and affecting a subset of sites along prespecified lineages, respectively. A data set of the myxovirus ( Mx ) genes from ten mammal and two bird species is used as an example. We discuss a new feature in CODEML that allows users to perform positive selection tests for multiple genes for the same set of taxa, as is common in modern genome-sequencing projects. The PAML package is distributed at https://github.com/abacus-gene/paml under the GNU license, with support provided at its discussion site (https://groups.google.com/g/pamlsoftware ). Data files used in this protocol are available at https://github.com/abacus-gene/paml-tutorial .