Biology subjects

Ghenu, A.-H.

Publications and source records attributed to Ghenu, A.-H..

3 recordsLinked to original sources

bioRxiv2022

Epistasis decreases with increasing antibiotic pressure but not temperature

Predicting mutational effects is essential for the control of antibiotic resistance (ABR). Predictions are difficult when there are strong genotype-by-environment (GxE), gene-by-gene (GxG or epistatic), or gene- by-gene-by-environment (GxGxE) interactions. We quantified GxGxE effects in Escherichia coli across environmental gradients. We created intergenic fitness landscapes using gene knock-outs and single nucleotide ABR mutations previously identified to vary in the extent of GxE effects in our environments of interest. Then, we measured competitive fitness across a complete combinatorial set of temperature and antibiotic dosage gradients. In this way, we assessed the predictability of 15 fitness landscapes across 12 different but related environments. We found GxG interactions and rugged fitness landscapes in the absence of antibiotic, but as antibiotic concentration increased, the fitness effects of ABR genotypes quickly overshadowed those of gene knock-outs, and the landscapes became smoother. Our work reiterates that some single mutants, like those conferring resistance or susceptibility to antibiotics, have consistent effects across genetic backgrounds in stressful environments. Thus, although epistasis may reduce the predictability of evolution in benign environments, evolution may be more predictable in adverse environments.

evolutionary biology↗

bioRxiv2022

Challenges and pitfalls of inferring microbial growth rates from lab cultures

After more than 100 years of generating monoculture batch culture growth curves, microbial ecologists and evolutionary biologists still lack a reference method for inferring growth rates. Our work highlights the challenges of estimating the growth rate from growth curve data and shows that inaccurate estimates of growth rates significantly impact the estimated relative fitness, a principal quantity in evolution and ecology. First, we conducted a literature review and found which different types of methods are currently used to estimate growth rates. These methods differ in the meaning of the estimated growth rate parameter. Kinetic models estimate the intrinsic growth rate {micro} whereas statistical methods - both model-based and model-free - estimate the maximum per capita growth rate {micro}max. Using math and simulations, we show the conditions in which {micro}max is not a good estimator of {micro}. Then, we demonstrate that inaccurate absolute estimates of {micro} is not overcome by calculating relative values. Importantly, we find that poor approximations for {micro} sometimes lead to wrongly classifying a beneficial mutant as deleterious. Finally, we re-analyzed four published data-sets using most of the methods found by our literature review. We detected no single best-fitting model across all experiments within a data-set and found that the Gompertz models, which were among the most commonly used, were often among the worst fitting. Our study provides suggestions for how experimenters can improve their growth rate and associated relative fitness estimates and highlights a neglected but fundamental problem for nearly everyone who studies microbial populations in the lab.

microbiology↗

bioRxiv2017

Conflict between heterozygote advantage and hybridincompatibility in haplodiploids (and sex chromosomes)

In many diploid species the sex chromosomes play a special role in mediating reproductive isolation. In haplodiploids, where females are diploid and males haploid, the whole genome behaves similarly to the X/Z chromosomes of diploids. Therefore, haplodiploid systems can serve as a model for the role of sex chromosomes in speciation and hybridization. A previously described population of Finnish Formica wood ants displays genome-wide signs of ploidally and sexually antagonistic selection resulting from hybridization. Here, hybrid females have increased survivorship but hybrid males are inviable. To understand how the unusual hybrid population may be maintained, we developed a mathematical model with hybrid incompatibility, female heterozygote advantage, recombination, and assortative mating. The rugged fitness landscape resulting from the co-occurrence of heterozygote advantage and hybrid incompatibility results in a sexual conflict in haplodiploids, which is caused by the ploidy difference. Thus, whereas heterozygote advantage always promotes long-term polymorphism in diploids, we find various outcomes in haplodiploids in which the population stabilizes either in favor of males, females, or via maximizing the number of introgressed individuals. We discuss these outcomes with respect to the potential long-term fate of the Finnish wood ant population, and provide approximations for the extension of the model to multiple incompatibilities. Moreover, we highlight the general implications of our results for speciation and hybridization in haplodiploids versus diploids, and how the described fitness relationships could contribute to the outstanding role of sex chromosomes as hotspots of sexual antagonism and genes involved in speciation.

evolutionary biology↗