Modeling of Mutational Events in the Evolution of Viruses.

Akhtar Ali,Ulrich Melcher

doi:10.3390/v11050418

Abstract

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.

Highlights

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
We defined the phylogenetic distance as the number of loci that differ between the two sequences and evolutionary distances, as the number of modeled mutations used to transition between the two sequences, given the mutation, replication, and selection processes
Theofmean numbers of of string elements. It established that varying the positions of the elements of the seed evolutionary cycles needed to increase the fitness index from a given level to the various higher and target strings was without effect numbersrevealed of simulation cycles

Summary

Introduction

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. Each of these factors may contribute to this time dependent rate phenomenon, a more fundamental cause should be considered. 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. The typical substitution frequencies observed by such techniques are 10−3 to 10−4 substitutions per residue per year

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Conclusion