| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T113 |
0-67 |
Sentence |
denotes |
Most Sites in the SARS-CoV-2 Genome Were under Purifying Selection. |
| T114 |
68-262 |
Sentence |
denotes |
Using phylogenetically informed models (as described above), we identified two sites, residue 614 in S and 13 in N, that were under diversifying selection in a majority of subsampled alignments. |
| T115 |
263-578 |
Sentence |
denotes |
For each protein, subsampled alignments tended to have more sites under purifying selection (median = 7.34 ± 4.06% [±SD]) than under diversifying selection (3.10 ± 1.92%) (Mann−Whitney U test, P = 0.057; SI Appendix, Fig. S4) (purifying selection is indicative of a decrease in genetic diversity in the population). |
| T116 |
579-790 |
Sentence |
denotes |
Likewise, for each codon separately, the proportion of each phylogeny (i.e., the percentage of total branch length) with dN/dS > 1 was small, indicating diversifying selection was episodic and limited (Fig. 3A). |
| T117 |
791-1015 |
Sentence |
denotes |
Global measures of dN/dS varied across genes, ranging from 0.35 ± 0.02 (M) to 1.43 ± 0.24 (ORF10), and were significantly lower for structural genes compared to nonstructural genes (Mann−Whitney U test, P = 0.042) (Fig. 3B). |
| T118 |
1016-1312 |
Sentence |
denotes |
Per-lineage nonsynonymous substitution rates were comparable (Student’s t test, P = 0.218) in structural (0.0011 ± 0.021) and nonstructural (0.0012 ± 0.028) genes, although some subsampled alignments showed rates that could be a hundred times higher than the median over all alignments (Fig. 3C). |
| T119 |
1313-1585 |
Sentence |
denotes |
Across structural proteins, mutations were disproportionately neutral: >70.3% of branch length evolved under neutral (or negative) selection for all sites, and over half of all branch length evolved under neutral (or negative) selection for >82.8% of sites (Fig. 3D) (29). |
| T120 |
1586-1593 |
Sentence |
denotes |
Fig. 3. |
| T121 |
1595-1812 |
Sentence |
denotes |
Evolution across the SARS-CoV-2 genome. (A) Bar plot of the average percentage of branch length under diversifying selection (dN/dS > 1) for each site. (B) Bar plot of dN/dS per gene (dN = dS is shown as dashed line). |
| T122 |
1813-1973 |
Sentence |
denotes |
Error bars indicate SD across subsampled alignments. (C) Box plot of nonsynonymous substitutions per lineage per site across structural and nonstructural genes. |
| T123 |
1974-2188 |
Sentence |
denotes |
Values across subsampled alignments for each gene are plotted. (D) Average percentage (over subsampled alignments) of branch lengths evolving under neutral (or negative) selection per site for each structural gene. |
| T124 |
2189-2229 |
Sentence |
denotes |
Median values are shown by dashed lines. |
