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Thus, the observed frequencies of stop codons in bacterial genomes can be explained only if stop codon are not selectively equivalent, with weak negative selection acting on TAG codon for G-content >16% and weakly positive selection for these two codon when G-content <16%.
Of particular concern is the case of weak negative selection, thus simulations were performed where new alleles were assigned a negative selection coefficient with the strength of selection α = −5.0.
Genes under weak negative selection (suppressing fixation of nonsynonymous changes between species lineages but allowing nonsynonymous polymorphism at low frequency) would have a superficially similar skew in the MK test to that caused by balancing selection [40], but would be associated with low rather than high TjD values [41], [42], as seen here for the genes Pf92/6-cys, and rhop148.
Intron loss partially affects fitness and thus is under weak negative selection.
We show that in bacteria stop codons evolve slower than synonymous sites, suggesting the action of weak negative selection.
However, â F is more robust to hitch-hiking which occurs when weak negative selection is pervasive.
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This is what one would expect if there were weaker negative selection against mutations in the defense response genes, stronger selective pressure and constraints on mutations in protein translation genes.
The crux of the problem is that every site within a virus genome probably evolves at a different rate, with some sites evolving very slowly under strong negative selection (selection that disfavours change) and others evolving more rapidly under either weaker negative selection, neutral genetic drift or positive selection (selection favouring change).
This is consistent with weaker negative selection pressure on the NMD exons.
Both Pa/ Ps ratios and the DFE support weaker negative selection on substitutions in disordered regions.
This is correct for gene families as well: younger families tend to evolve under weaker negative selection.
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