Journal of Molecular Evolution

, Volume 64, Issue 6, pp 646–655

How Common Are Intragene Windows with KA > KS Owing to Purifying Selection on Synonymous Mutations?



One method for diagnosing the mode of sequence evolution considers the ratio of nonsynonymous substitutions per nonsynonymous site (KA) to the corresponding figure for synonymous substitutions (KS). A ratio (KA/KS) greater than unity is taken as evidence for positive selection. This, however, need not necessarily be the case. Notably, there is one instance of a high intragenic KA/KS peak, revealed by sliding window analysis and observed in two pairwise comparisons, better accounted for by localised purifying selection on synonymous mutations that affect splicing. Is this example exceptional? To address this we isolate intragenic domains with KA/KS > 1 from more than 1000 long mouse-rat orthologues. Approximately one KA/KS > 1 peak is found per 12–15 kb of coding sequence. Surprisingly, low synonymous substitution rates underpin more incidences than do high nonsynonymous rates. Several reasons, however, prevent us from supposing that the low synonymous rates reflect purifying selection on synonymous mutations. First, for many peaks, the null that the peak is no higher than expected given the underlying rates of evolution, cannot be rejected. Second, of 18 statistically significant incidences with unusually low KS values, only 3 are repeatable across independent comparisons. At least two of these are within alternatively spliced exons. We conclude that repeatable statistically significant intragenic domains of low intragenic KS are rare. As so few KA/KS peaks reflect increased rates of protein evolution and so few hold statistical support, we additionally conclude that sliding window analysis to infer domains of positive selection is highly error-prone.


KA/KS ratio Sliding Window analysis Selection on synonymous mutations Alternative transcripts 

Supplementary material

239_2006_207_Supp.pdf (1.3 mb)
Supplementary material


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Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  1. 1.Department of Biology and BiochemistryUniversity of BathBathUK

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