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The M8 model indicates that 24% of codons are subject to moderate positive selection (ω = 1.16).
The examination of site-specific selection pressures by REL analysis identified only one site under moderate positive selection (BF ≥ 50) for UCP2 and UCP3 and our further analyses using more strict criteria (BF ≥ 100) did not support strong evidence for positive selection at these sites.
M1a and M2a explicitly model a class of purely neutral sites (ω = 1) although it might not exist in a given data set; in which case sites having ω = 1 could reflect an artefact of averaging over sites subject to moderate positive selection and other sites subject to purifying selection.
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Therefore, the genomic region containing HIF1A can be considered to have a moderate signature of positive selection.
We demonstrate by simulation that the method can accurately estimate selection intensity for moderate and strong positive selection.
The moderate-high performance jacks and mackerels exhibited moderate-high conservation, with limited positive selection.
Those results show that, even with moderate positive correlation (rg = +0.18 in line W1), selection based on group selection or on information from relatives kept in family groups enables substantially greater response to selection than individual selection alone.
The LRT of positive selection is robust to moderate levels of recombination according to the simulation of Anisimova et al. (2003) but can generate excessive false positives if recombination is frequent.
Moderate changes (categories 1 and 2) characterize most of the positive selection detected.
The Meiotic Recombination pathway is another candidate for being affected by positive selection, with a relatively high DN/DS ratio and a moderate PN/PS ratio (fig. 1 F).
When the nucleotide sequences of the coding regions of all the proteins in this study are used, a positive selection from the ancestor to Pi6C was 1.6216 with a moderate negative selection (Ka/Ks = 0.6399) for the tomato ARPI (See Node 6 in Table S1 and Figure S2).
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