Gonzalez-Gonzalez, A. | bioRxiv Science

bioRxiv2020

Using changes in host demographic rates to reveal the effects of infection with hidden variable models

The impacts of disease on host vital rates can be clearly demonstrated using longitudinal studies, but these studies can be expensive and logistically challenging. We examined the utility of hidden variable models to infer the individual effects of disease, caused by infection, from population-level measurements of survival and fecundity when longitudinal studies are not possible. Our approach seeks to explain temporal changes in population-level vital rates by coupling observed changes in the infection status of individuals to an epidemiological model. We tested the approach using both single and coinfection viral challenge experiments on populations of fruit flies (Drosophila melanogaster). Specifically, we determined whether our approach yielded reliable estimates of disease prevalence and of the effects of disease on survival and fecundity rates for treatments of single infections and coinfection. We found two conditions are necessary for reliable estimation. First, diseases must drive detectable changes in vital rates, and second, there must be substantial variation in the degree of prevalence over time. This approach could prove useful for detecting epidemics from public health data in regions where standard surveillance techniques are not available, and in the study of epidemics in wildlife populations, where longitudinal studies can be especially difficult to implement.

ecology↗

bioRxiv2016

Adaptive mutations in RNA polymerase and the transcriptional terminator Rho have similar effects on Escherichia coli gene expression

Modifications to transcriptional regulators play a major role in adaptation. Here we compared the effects of multiple beneficial mutations within and between Escherichia coli rpoB, the gene encoding the RNA polymerase {beta} subunit, and rho, which encodes a transcriptional terminator. These two genes have harbored adaptive mutations in numerous E. coli evolution experiments but particularly in our previous large-scale thermal stress experiment, where the two genes characterized two alternative adaptive pathways. To compare the effects of beneficial mutations, we engineered four advantageous mutations into each of the two genes and measured their effects on fitness, growth, gene expression and transcriptional termination at 42.2{degrees}C. Among the eight mutations, two rho mutations had no detectable effect on relative fitness, suggesting they were beneficial only in the context of epistatic interactions. The remaining six mutations had an average relative fitness benefit of [~]20%. The rpoB mutations altered the expression of [~]1700 genes; rho mutations altered the expression of fewer genes, most of which were a subset of the genes altered by rpoB. Across our eight mutants, relative fitness correlated with the degree to which a mutation restored gene expression back to the unstressed, 37.0{degrees}C state. The rho mutations do not enhance transcriptional termination in known rho-terminated regions, but the genome-wide effects of mutations in both genes was to enhance termination. Although beneficial mutations in the two genes did not have identical effects on fitness, growth or gene expression, they acted predominantly through parallel phenotypic effects on gene expression and transcriptional termination.

evolutionary biology↗