PMC:7519301 / 17918-19435 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7519301","sourcedb":"PMC","sourceid":"7519301","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7519301","text":"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. 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). Likewise, for each codon separately, the proportion of each phylogeny (i.e., the percentage of total branch length) with dN/dS \u003e 1 was small, indicating diversifying selection was episodic and limited (Fig. 3A). 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). 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). Across structural proteins, mutations were disproportionately neutral: \u003e70.3% 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 \u003e82.8% of sites (Fig. 3D) 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