Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny
Copyright policy )Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny
Abstract The rooting of the SARS-CoV-2 phylogeny is important for understanding the origin and early spread of the virus. Previously published phylogenies have used different rootings that do not always provide consistent results. We investigate several different strategies for rooting the SARS-CoV-2 tree and provide measures of statistical uncertainty for all methods. We show that methods based on the molecular clock tend to place the root in the B clade, whereas methods based on outgroup rooting tend to place the root in the A clade. The results from the two approaches are statistically incompatible, possibly as a consequence of deviations from a molecular clock or excess back-mutations. We also show that none of the methods provide strong statistical support for the placement of the root in any particular edge of the tree. These results suggest that phylogenetic evidence alone is unlikely to identify the origin of the SARS-CoV-2 virus and we caution against strong inferences regarding the early spread of the virus based solely on such evidence.
- University of Copenhagen Denmark
- University of Copenhagen Denmark
- University of Copenhagen Denmark
- University of Copenhagen Denmark
- University of copenhaguen Denmark
570, Coronaviruses, Evolution, Mutation, Missense, Evolutionary biology, Genome, Viral, SARS-CoV-2 phylogeny, Evolution, Molecular, Genetic, Models, Genetics, outgroup rooting, Animals, Humans, Viral, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Discoveries, Phylogeny, Evolutionary Biology, Likelihood Functions, Genome, Models, Statistical, Models, Genetic, SARS-CoV-2, Uncertainty, Molecular, COVID-19, Bayes Theorem, Biological Sciences, Statistical, molecular clock rooting, Markov Chains, Infectious Diseases, Emerging Infectious Diseases, Biochemistry and cell biology, Mutation, RNA, RNA, Viral, Biochemistry and Cell Biology, Missense, Monte Carlo Method, Algorithms
570, Coronaviruses, Evolution, Mutation, Missense, Evolutionary biology, Genome, Viral, SARS-CoV-2 phylogeny, Evolution, Molecular, Genetic, Models, Genetics, outgroup rooting, Animals, Humans, Viral, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Discoveries, Phylogeny, Evolutionary Biology, Likelihood Functions, Genome, Models, Statistical, Models, Genetic, SARS-CoV-2, Uncertainty, Molecular, COVID-19, Bayes Theorem, Biological Sciences, Statistical, molecular clock rooting, Markov Chains, Infectious Diseases, Emerging Infectious Diseases, Biochemistry and cell biology, Mutation, RNA, RNA, Viral, Biochemistry and Cell Biology, Missense, Monte Carlo Method, Algorithms
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