calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates

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ID: 260503
2017
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Abstract
Site-specific evolutionary rates can be estimated from codon sequences or from amino-acid sequences. For codon sequences, the most popular methods use some variation of the dN∕dS ratio. For amino-acid sequences, one widely-used method is called Rate4Site, and it assigns a relative conservation score to each site in an alignment. How site-wise dN∕dS values relate to Rate4Site scores is not known. Here we elucidate the relationship between these two rate measurements. We simulate sequences with known dN∕dS, using either dN∕dS models or mutation–selection models for simulation. We then infer Rate4Site scores on the simulated alignments, and we compare those scores to either true or inferred dN∕dS values on the same alignments. We find that Rate4Site scores generally correlate well with true dN∕dS, and the correlation strengths increase in alignments with greater sequence divergence and more taxa. Moreover, Rate4Site scores correlate very well with inferred (as opposed to true) dN∕dS values, even for small alignments with little divergence. Finally, we verify this relationship between Rate4Site and dN∕dS in a variety of empirical datasets. We conclude that codon-level and amino-acid-level analysis frameworks are directly comparable and yield very similar inferences.
Reference Key
sydykova2017peerjcalculating Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors ;Dariya K. Sydykova;Claus O. Wilke
Journal pediatrics
Year 2017
DOI
10.7717/peerj.3391
URL
https://peerj.com/articles/3391/
Keywords
rate variationmedicine

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