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Accordingly, organisms must balance the benefit of accepting advantageous substitutions with the possible cost of deleterious effects on protein folding and stability.
Deleterious (or advantageous) substitutions other than the respiratory droplet transmissible A/H5N1 substitutions can, to a first approximation, be ignored in calculating proportions because such substitutions would on average affect all viruses equally and thus would not specifically affect the accumulation of respiratory droplet transmissible A/H5N1 mutations (6).
These results revealed that the H275Y NA substitution occurred coincidentally with the advantageous substitutions and hitchhiked with a dominant variant during the evolution processes, resulting in the widespread resistant viruses.
Such advantageous substitutions have spread faster in the populations analysed than random substitutions.
As would be expected, the distributions are extremely similar for the neutral and advantageous substitutions.
In this case, the distribution of substitutions would be bimodal, with modes centered around nearly neutral and advantageous substitutions.
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However, the correlation between α and Ne might be misleading because α depends on the rate of effectively neutral and advantageous substitution, variation in either of which could be caused by Ne (Gossmann et al. 2010), that is, α = Dadaptive/(Dadaptive + Dnonadaptive) where Dadaptive and Dnonadaptive are the rates of adaptive and nonadaptive substitutions, respectively.
Also, if selection coefficients are dependent upon conditions determined by genetic backgrounds and environments, even slightly advantageous mutant substitutions may become rapid in small populations as compared with large populations (Ohta 1972).
Although our results on nearly neutral and advantageous mutations and substitutions roughly correspond to previous results obtained with evolution-based methods, we observe a large fraction of highly deleterious mutations (S < −10), better matching the number of experimentally observed lethal mutations.
We also calculated Z ∗ = L o g 10 ((D N + 1 ) (P S + 1 ) (D S + 1 ) (P N + 1 ) ), as in Presgraves (2005), the sign of which is more intuitive; negative values are consistent with an excess of weakly deleterious (negatively selected) polymorphisms and positive values are consistent with an excess of advantageous (positively selected) substitutions.
Even if the positively selected substitutions are advantageous, it could be randomly lost over time due to the bottleneck effect.
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