2022
DOI: 10.3389/fgene.2022.991249
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No evidence for widespread positive selection on double substitutions within codons in primates and yeasts

Abstract: Nucleotide substitutions in protein-coding genes can be divided into synonymous (S) and non-synonymous (N) ones that alter amino acids (including nonsense mutations causing stop codons). The S substitutions are expected to have little effect on function. The N substitutions almost always are affected by strong purifying selection that eliminates them from evolving populations. However, additional mutations of nearby bases can modulate the deleterious effect of single N substitutions and, thus, could be subject… Show more

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“…This discrepancy could indicate that in some branches, the signal of adaptive evolution was cumulative and not strong enough at any particular site. Moreover, the branch-site test is generally considered conservative and sometimes may lack enough statistical power [ 59 , 62 ] (see also [ 98 , 99 ]). Another potential caveat may be the presence of highly variable regions in some AQPs (which could reflect fast evolutionary rates or poor sequence quality), as the employed tests heavily rely on robust alignments [ 58 ].…”
Section: Resultsmentioning
confidence: 99%
“…This discrepancy could indicate that in some branches, the signal of adaptive evolution was cumulative and not strong enough at any particular site. Moreover, the branch-site test is generally considered conservative and sometimes may lack enough statistical power [ 59 , 62 ] (see also [ 98 , 99 ]). Another potential caveat may be the presence of highly variable regions in some AQPs (which could reflect fast evolutionary rates or poor sequence quality), as the employed tests heavily rely on robust alignments [ 58 ].…”
Section: Resultsmentioning
confidence: 99%