Sindbis virus Raw sequence reads

Understanding the dynamics of molecular evolution is a fundamental goal of evolutionary biology. Experimental evolution in microbial populations provides a tractable model in which to study these dynamics. In this study, we used next-generation sequencing to map adaptive walks in experimentally evolved Sindbis virus (SINV) populations. Virus populations were allowed to evolve in one of two tissue culture treatments: an environment in which they were shifted suddenly onto a novel host cell type and propagated on solely the novel host, or in a mixed-cell environment where the prevalence of the novel host increased gradually over time. Virus populations were sampled at time points over the course of their evolution, and whole-genome population-level sequencing was used to track allele frequencies at each time point. This produces a high-resolution map of how new alleles enter the populations and change in frequency over time. These data were used to answer questions related to how the rate of environmental change affects the distribution of fixed mutational effect sizes, the degree of clonal interference, and the number of mutations that fix in each fixation event.