Biology subjects

Bailey, S. F.

Publications and source records attributed to Bailey, S. F..

3 recordsLinked to original sources

bioRxiv2024

Agar concentration affects the evolution of antibiotic resistance and population genomics in experimental populations Pseudomonas aeruginosa

Bacteria live in a diversity of spatially structured environments, which can impact their evolutionary dynamics via local interactions and environmental variation. Spatial structure is expected to slow the rate of adaptive evolution, increase the amount of clonal competition and so increase diversity of evolutionary trajectories explored as a population evolves. In the lab, agar is a common way in which we add spatial structure to bacterial growth environments. In this study we explored the effects of agar concertation on experimental populations of Pseudomonas aeruginosa evolved in the presence/ absence of a sub-lethal concentration of an antibiotic, ciprofloxacin. We varied agar across four different concentrations which modified viscosity and so the rate at which bacteria move through their environment, as well as potentially shifting the mode of motility. We saw that increasing agar concentration decreased the rate of adaptation, and that the presence of antibiotics, amplified this effect. The number and frequency of evolved mutations also varied with agar concentration and the direction of the effect changed in the presence/ absence of antibiotics - for example, the number of high frequency mutation increased with agar concentration when antibiotics were absent but decreased when antibiotics were present. We also saw an increase in the degree of parallel evolution in populations evolved in the presence of antibiotics and even more so in higher concentrations of agar. Thus, we show that agar concentration, and so spatial structure, can be an important driver of evolutionary dynamics with important impacts on antibiotic resistance evolution including the rate and predictability of adaptation.

evolutionary biology↗

bioRxiv2021

Spatial structure affects evolutionary dynamics and drives genomic diversity in experimental populations of Pseudomonas fluorescens

Most populations live in spatially structured environments and that structure has the potential to impact the evolutionary dynamics in a number of important ways. Theoretical models tracking evolution in structured environments using a range of different approaches, suggest that local interactions and spatial heterogeneity can increase the adaptive benefits of motility, impact both the rate and extent of adaptation, and increase the probability of parallel evolution. We test these general predictions in a microbial evolution experiment tracking phenotypic and genomic changes in replicate populations of Pseudomonas fluorescens evolved in both well-mixed and spatially-structured environments, where spatial structure was generated through the addition of semi-solid agar. In contrast to the well-mixed environment, populations evolved in the spatially-structured environment adapted more slowly, retained the ability to disperse more rapidly, and had a greater putatively neutral population genomic diversity. The degree of parallel evolution measured at the gene-level, did not differ across these two types of experimental environments, perhaps because the populations had not evolved for long enough to near their fitness optima. These results confirm important general impacts of spatial structure on evolutionary dynamics at both the phenotypic and genomic level.

evolutionary biology↗

bioRxiv2017

Identifying drivers of parallel evolution: A regression model approach

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100045). Parallel evolution, defined as identical changes arising in independent populations, is often attributed to similar selective pressures favoring the fixation of identical genetic changes. However, some level of parallel evolution is also expected if mutation rates are heterogeneous across regions of the genome. Theory suggests that mutation and selection can have equal impacts on patterns of parallel evolution, however empirical studies have yet to jointly quantify the importance of these two processes. Here, we introduce several statistical models to examine the contributions of mutation and selection heterogeneity to shaping parallel evolutionary changes at the gene-level. Using this framework we analyze published data from forty experimentally evolved Saccharomyces cerevisiae populations. We can partition the effects of a number of genomic variables into those affecting patterns of parallel evolution via effects on the rate of arising mutations, and those affecting the retention versus loss of the arising mutations (i.e. selection). Our results suggest that gene-to-gene heterogeneity in both mutation and selection, associated with gene length, recombination rate, and number of protein domains drive parallel evolution at both synonymous and nonsynonymous sites. While there are still a number of parallel changes that are not well described, we show that allowing for heterogeneous rates of mutation and selection can provide improved predictions of the prevalence and degree of parallel evolution.\n\nData archival locationDryad, doi to be included later

evolutionary biology↗