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Modeling of Mutational Events in the Evolution of Viruses

Department of Biological Sciences, University of Tulsa, Tulsa, OK 74104, USA
Department of Biochemistry & Molecular Biology, Oklahoma State University, Stillwater, OK 74078-3035, USA
Author to whom correspondence should be addressed.
Viruses 2019, 11(5), 418;
Received: 4 March 2019 / Revised: 27 April 2019 / Accepted: 2 May 2019 / Published: 5 May 2019
(This article belongs to the Special Issue Plant Virus Ecology and Biodiversity)
PDF [708 KB, uploaded 5 May 2019]


Diverse studies of viral evolution have led to the recognition that the evolutionary rates of viral taxa observed are dependent on the time scale being investigated—with short-term studies giving fast substitution rates, and orders of magnitude lower rates for deep calibrations. Although each of these factors may contribute to this time dependent rate phenomenon, a more fundamental cause should be considered. We sought to test computationally whether the basic phenomena of virus evolution (mutation, replication, and selection) can explain the relationships between the evolutionary and phylogenetic distances. We tested, by computational inference, the hypothesis that the phylogenetic distances between the pairs of sequences are functions of the evolutionary path lengths between them. A Basic simulation revealed that the relationship between simulated genetic and mutational distances is non-linear, and can be consistent with different rates of nucleotide substitution at different depths of branches in phylogenetic trees. View Full-Text
Keywords: virus–host co-divergence; endogenous viral elements; virus networks; speciation virus–host co-divergence; endogenous viral elements; virus networks; speciation

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Ali, A.; Melcher, U. Modeling of Mutational Events in the Evolution of Viruses. Viruses 2019, 11, 418.

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