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Although the low heritability of most of the aforementioned traits has not made them a primary breeding goal in selection programs, it could be hypothesized that applying sustained but weak negative selection against these traits has increased the frequency of favorable alleles and surrounding haplotypes in the Holstein population.
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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%.
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.
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.
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.
The estimates of negative selection based on divergence are confounded by positive selection (see later); therefore, to infer weak negative selection, we used polymorphism data alone.
In contrast, an excess of polymorphic non-synonymous variants may result from weak negative selection or local, population-specific positive selection.
Alternatively, DoS is negative when the proportion of polymorphisms that are nonsynonymous is higher than the proportion of substitutions that are nonsynonymous, suggestive of weak negative selection [ 9].
Loss of functional constraint or weak negative selection is another explanation for an excess of nonsynonymous polymorphism as measured by the MK test.
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