Exceptional Convergent Evolution in a Virus

Abstract

Replicate lineages of the bacteriophage ϕX 174 adapted to growth at high temperature on either of two hosts exhibited high rates of identical, independent substitutions. Typically, a dozen or more substitutions accumulated in the 5.4-kilobase genome during propagation. Across the entire data set of nine lineages, 119 independent substitutions occurred at 68 nucleotide sites. Over half of these substitutions, accounting for one third of the sites, were identical with substitutions in other lineages. Some convergent substitutions were specific to the host used for phage propagation, but others occurred across both hosts. Continued adaptation of an evolved phage at high temperature, but on the other host, led to additional changes that included reversions of previous substitutions. Phylogenetic reconstruction using the complete genome sequence not only failed to recover the correct evolutionary history because of these convergent changes, but the true history was rejected as being a significantly inferior fit to the data. Replicate lineages subjected to similar environmental challenges showed similar rates of substitution and similar rates of fitness improvement across corresponding times of adaptation. Substitution rates and fitness improvements were higher during the initial period of adaptation than during a later period, except when the host was changed.

Slow Fitness Recovery in a Codon-Modified Viral Genome

“…Two short-term adaptations, denoted S1 and S2, each consisted of 20 h of serial transfer. A longer adaptation was carried out (L1) first by growth in a continuous flow system for 265 h and then by serial transfer for 11-12 h. This continuous flow system used a cell-only tube that fed unidirectionally into a tube with phage (Bull et al 1997;Wichman et al 2005). Volumes and flow rates were adjusted to maintain phage densities in the range of 10 6 -10 8 .…”

Ecological Approach to Understanding Superinfection Inhibition in Bacteriophage

“…Fitness assays were designed to measure phage fitness as the number of phage doublings per hour in a homogeneous liquid culture. This low-density assay for growth rate has been described previously [ 32 ]. High-density assays were found to be unreliable and inconsistent.…”

“…Cells and media then flowed into the second test tube, which contained the phage population. From there, media, cells, and phage were pulled out using an aquarium pump into a waste container to maintain a continuous population volume [32,33]. Both the bacteria and phage tubes were submerged in a water bath held at 37 • C. The lids of both tubes contained a port to allow for the inoculation of each tube, and the second tube also contained a port for the collection of samples.…”

Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution

“…Microbial populations that evolve and adapt to novel environments under strong selection pressures typically show a pattern of evolutionary convergence (Bull et al, 1997;Tenaillon et al, 2012). Laboratory mutation accumulation experiments combined with high-throughput sequencing are one of the best methods to estimate mutation rates, determine how they vary along the genome (Lynch et al, 2016) and study the extent to which convergent evolution occurs (Bull et al, 1997).…”

“…Microbial populations that evolve and adapt to novel environments under strong selection pressures typically show a pattern of evolutionary convergence (Bull et al, 1997;Tenaillon et al, 2012). Laboratory mutation accumulation experiments combined with high-throughput sequencing are one of the best methods to estimate mutation rates, determine how they vary along the genome (Lynch et al, 2016) and study the extent to which convergent evolution occurs (Bull et al, 1997). With an experimental evolution design where sequential propagation of the SARS-CoV-2 virus occurs under strong bottlenecks and at low multiplicity of infection (MOI), the intensity of selection is minimized (Chao, 1990;Duarte et al, 1992).…”