L-Shaped Distributions of the Relative Substitution Rates (c/micro) in SARS-COV-2 with or without Molecular Clocks, Challenging Mainstream Evolutionary Theories

A definitive test to quantify fitness changes of mutations is required to end a continuing 50-year "neutralist-selectionist" debate in evolutionary biology. Our previous work introduced a substitution-mutation rate ratio c/{micro} test (c: substitution rate in Translated Region/TR or UnTranslated Region/UTR; {micro}: mutation rate) to quantify the selection pressure and thus the proportions of strictly neutral, nearly neutral, beneficial, and deleterious mutations in a genome. Intriguingly, both a L-shaped probability distribution of c/{micro} and molecular clock were observed for SARS-COV-2s genome. We found that the proportion of the different mutation types from the distribution is not consistent with the hypotheses of the three existing evolution theories (Kimuras Neutral Theory/KNT, Ohtas Nearly Neutral Theory/ONNT and the Selectionist Theory/ST), and a balance condition explains the molecular clock, thus we proposed a new theory named as Near-Neutral Balanced Selectionist Theory (NNBST). In this study, the c/{micro} analysis was extended beyond the genome to 26 TRs, 12 UTRs, and 10 TRSs (Transcriptional Regulatory Sequences) of SARS-COV-2. While L-shaped probability distributions of c/{micro} were observed for all of 49 segments, molecular clocks were observed for only 24 segments, supporting NNBST and Near-Neutral Unbalanced Selectionist Theory (NNUST) to explain the molecular evolution of 24/25 segments with/without molecular clocks. Thus, the Near-Neutral Selectionist Theory (NNST) integrates traditional neutral and selectionist theories to deepen our understanding of how mutation, selection, and genetic drift influence genomic evolution. Author SummaryThe "neutralist-selectionist" debate in molecular evolution has been unresolved for 50 years due to the three main theories of molecular evolution (Kimuras Neutral Theory/KNT, Ohtas Nearly-Neutral Theory/ONNT, Selectionist Theory/ST) disagreeing on the proportion of neutral mutations (KNT), nearly-neutral deleterious mutations (ONNT) and adaptive mutations (ST) within species. We recently developed a robust method, the c/{micro} relative substitution rate test, to quantify the proportion of each mutation type within >11K genomic sequences of SARS-COV-2 RNA virus. Our previous analysis revealed an L-shaped c/{micro} probability distribution and a constant substitution rate (e.g., molecular clock) for the SARS-COV-2 genome over 19 months, and the proportions of mutation types were inconsistent with those predicted by the three theories. We thus proposed the Near-Neutral Balanced Selectionist Theory (NNBST) to explain the molecular clock-feature and L-shaped probability distribution for SARS-COV-2. In this study, we extended this analysis to the 25 protein-coding gene segments and 24 non-protein-coding segments of SARS-COV-2. We observed that all 49 segments exhibited an L-shaped probability distribution and 24 out of the 49 segments exhibited a molecular clock, however the remaining 25 segments did not exhibit a molecular clock. We thus propose the Near-Neutral Unbalanced Selectionist Theory (NNUST) and NNBST to explain the segments without/with molecular clock features, respectively. We also coin the Near-Neutral Selectionist Theory (NNST) to combine traditional KNT, ONNT and ST to deepen our understanding of how mutation, selection, and genetic drift influence genomic evolution.