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Near Neutral Selectionist Theories (NNST) for SARS-CoV-2 suggested by the substitution-mutation ratio (c/µ) analysis
Fig 5
Summary of the key features of molecular evolution theories.
Two substitution rate models (GSRM and SSRM) and five theories of molecular evolution (ST, KNT, ONNT, NNBST, NNUST) in terms of molecular clock, SSMRSS, DFE and percentage of sites under different selection types. *GSRM (Genomic Substitution Rate Model/Strict neutrality hypothesis); SSRM (Genomic Substitution Rate Model); ST (Selectionist Theory); KNT (Kimura’s Neutral Theory); ONNT (Ohta’s Nearly Neutral Theory); NNBST (Near-Neutral Balanced Selectionist Theory); NNUST (Near-Neutral Unbalanced Selectionist Theory); NNST (Near-Neutral Selectionist Theory): including NNBST and NNUST; 
(Eq. 24a) and
(Eq. 24b) under SSRM: the mean substitution rate 
for a given genomic sequence, segment or collection of sites, can be described as the weighted sum of the substitution rate of the sites under strong negative selection (
), weak negative selection (
), strictly neutral selection (
), weak positive selection (
), and strong positive selection (
) by reducing the discrete c/μ distribution into these five categories; 
: total substitution rate; 
mean substitution rate of strongly deleterious, weakly deleterious, strictly neutral, weakly beneficial and strongly beneficial sites;
: the fraction of strongly deleterious, weakly deleterious, strictly neutral, weakly beneficial and strongly beneficial sites; 
: the fraction of nearly neutral sites; q: time-dependent proportion of deleterious mutations that reach fixation; **Molecular clock presence (Yes/No); SSMRRS: Site Frequency Spectra; DFE: Distribution of Fitness Effects; WNB: weak negative boundary; WPB: weak positive boundary; SN: Strong negative selection (0 ≤ c/µ < WNB) in red color; WN: Weak negative selection (WNB ≤ c/µ < 1) in pink; N: Selectively Neutral selection (c/µ = 1) in dark green; WP: Weak positive selection (1 < c/µ ≤ WPB) in light yellow; SP: Strong positive selection (c/µ > WPB) in dark yellow.
doi: https://doi.org/10.1371/journal.pone.0343410.g005