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By sequencing the selected strains the authors were able to measure the fraction of selection by a reversion mutation versus a compensatory one.
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This parameter is also the expected fraction of the selection differential transmitted from the parental to the offspring generation, and is crucial in artificial selection [ 15].
One possibility is that pervasive epistasis biases the McDonald Kreitman test toward overestimating the true fraction of positive selection in evolution, and, therefore, the test may not be appropriate if epistasis is a common feature of protein evolution.
Together with high response fractions, the possibility of selection bias was restricted.
SFS and the fraction of sites under selection pressure was calculated using original scripts of Moon et al. (see URLs 19.
MAP developed the method of estimating the fraction of positions under selection.
The fraction of positions under selection in intergenic regions of bacterial genomes is roughly similar to that of eukaryotes.
Note that these numbers are not the same as the actual fraction of bases under selection since overlapping windows are used.
We also estimated the fraction of positions under selection in different functional DNA regions of E. coli K12, such as promoters, terminators and TF-binding sites (TFBS) according to RegulonDB.
The fraction of positions under selection for TF-binding sites was higher than in the intergenic regions in general, (~60%) while values for promoters and terminators were approximately the same (45%).
The obtained estimates are shown in Figure 3. Unexpectedly, the highest fraction of positions under selection, approximately 50%, was observed in the synvergon intergenic regions, followed by divergons (slightly more than 44%) and convergons (approximately 11%).
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