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A Beginners Guide to Estimating the Non-synonymous to Synonymous Rate Ratio of all Protein-Coding Genes in a Genome

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Parasite Genomics Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1201))

Abstract

The ratio of non-synonymous to synonymous substitutions (dN/dS) is a useful measure of the strength and mode of natural selection acting on protein-coding genes. It is widely used to study patterns of selection on protein genes on a genomic scale—from the small genomes of viruses, bacteria, and parasitic eukaryotes to the largest eukaryotic genomes. In this chapter we describe all the steps necessary to calculate the dN/dS of all the genes using at least two genomes. We include a brief discussion on assigning orthologs, and of codon-aware alignment of orthologs. We then describe how to use the CODEML program of the PAML package for phylogenetic analysis to calculate the dN/dS and how to perform some statistical tests for positive selection. We then outline some methods for interpreting output and describe how one may use this data to make discoveries about the biology of your species. Finally, as a worked example we show all the steps we used to calculate dN/dS for 3,261 orthologs from six Plasmodium species, including tests for adaptive evolution (see worked_example.pdf).

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Acknowledgements

We thank Ziheng Yang, Caroline Biagosch, and Sanne Nygaard for comments on the manuscript.

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Authors and Affiliations

  1. Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK

    Daniel C. Jeffares, Bartłomiej Tomiczek, Victor Sojo & Mario dos Reis

  2. Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK

    Bartłomiej Tomiczek & Victor Sojo

Authors
  1. Daniel C. Jeffares
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  2. Bartłomiej Tomiczek
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  3. Victor Sojo
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  4. Mario dos Reis
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Correspondence to Daniel C. Jeffares .

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Editors and Affiliations

  1. University of Western Australia, Nedlands, West Australia, Australia

    Christopher Peacock

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A worked example of estimating ω and testing for adaptive evolution in six (PDF 223 kb)

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Jeffares, D.C., Tomiczek, B., Sojo, V., dos Reis, M. (2015). A Beginners Guide to Estimating the Non-synonymous to Synonymous Rate Ratio of all Protein-Coding Genes in a Genome. In: Peacock, C. (eds) Parasite Genomics Protocols. Methods in Molecular Biology, vol 1201. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1438-8_4

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