Jun 7, 2017

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

PeerJ
Dariya K Sydykova, Claus O Wilke

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 thedN∕dSratio. 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-wisedN∕dSvalues relate to Rate4Site scores is not known. Here we elucidate the relationship between these two rate measurements. We simulate sequences with knowndN∕dS, using eitherdN∕dSmodels or mutation-selection models for simulation. We then infer Rate4Site scores on the simulated alignments, and we compare those scores to either true or inferreddN∕dSvalues on the same alignments. We find that Rate4Site scores generally correlate well with truedN∕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∕dSvalues, even for small alignments with little divergence. Finally, we verify this relationship between Rate4Site anddN∕dSin a variety of empirical datasets. We conclude that codon-level and amino-acid-level analysis frameworks are directly comparable and yield ver...Continue Reading

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Mentioned in this Paper

Significance Level
Animal Cancer Model
4,4'-dinitro-2,2'-stilbenedisulfonic acid
Site
Codon Genus
Codon (Nucleotide Sequence)
Simulation
Mutation Abnormality

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