Experimental evolution | EPFL Graph Search

Experimental evolution is the use of laboratory experiments or controlled field manipulations to explore evolutionary dynamics. Evolution may be observed in the laboratory as individuals/populations adapt to new environmental conditions by natural selection. There are two different ways in which adaptation can arise in experimental evolution. One is via an individual organism gaining a novel beneficial mutation. The other is from allele frequency change in standing genetic variation already present in a population of organisms. Other evolutionary forces outside of mutation and natural selection can also play a role or be incorporated into experimental evolution studies, such as genetic drift and gene flow. The organism used is decided by the experimenter, based on the hypothesis to be tested. Many generations are required for adaptive mutation to occur, and experimental evolution via mutation is carried out in viruses or unicellular organisms wi

Male competition and the evolution of mating and ire-history traits in experimental populations of Aedes aegypti

Brian Dennis Hollis

Aedes aegypti is an important disease vector and a major target of reproductive control efforts. We manipulated the opportunity for sexual selection in populations of Ae. aegypti by controlling the number of males competing for a single female. Populations exposed to higher levels of male competition rapidly evolved higher male competitive mating success relative to populations evolved in the absence of competition, with an evolutionary response visible atter only five generations. We also detected correlated evolution in other important mating and life-history traits, such as acoustic signalling, fecundity and body size. Our results indicate that there is ample segregating variation for determinants of male mating competitiveness in wild populations and that increased male mating success trades-off with other important life-history traits. The mating conditions imposed on laboratory-reared mosquitoes are likely a significant determinant of male mating success in populations destined for release.

ROYAL SOC2019

Regulation of sedimentation rate shapes the evolution of multicellularity in a close unicellular relative of animals

Omaya Pierre Dudin

Significant increases in sedimentation rate accompany the evolution of multicellularity. These increases should lead to rapid changes in ecological distribution, thereby affecting the costs and benefits of multicellularity and its likelihood to evolve. However, how genetic and cellular traits control this process, their likelihood of emergence over evolutionary timescales, and the variation in these traits as multicellularity evolves are still poorly understood. Here, using isolates of the ichthyosporean genus Sphaeroforma-close unicellular relatives of animals with brief transient multicellular life stages-we demonstrate that sedimentation rate is a highly variable and evolvable trait affected by at least 2 distinct physical mechanisms. First, we find extensive (>300x) variation in sedimentation rates for different Sphaeroforma species, mainly driven by size and density during the unicellular-to-multicellular life cycle transition. Second, using experimental evolution with sedimentation rate as a focal trait, we readily obtained, for the first time, fast settling and multicellular Sphaeroforma arctica isolates. Quantitative microscopy showed that increased sedimentation rates most often arose by incomplete cellular separation after cell division, leading to clonal "clumping" multicellular variants with increased size and density. Strikingly, density increases also arose by an acceleration of the nuclear doubling time relative to cell size. Similar size- and density-affecting phenotypes were observed in 4 additional species from the Sphaeroforma genus, suggesting that variation in these traits might be widespread in the marine habitat. By resequencing evolved isolates to high genomic coverage, we identified mutations in regulators of cytokinesis, plasma membrane remodeling, and chromatin condensation that may contribute to both clump formation and the increase in the nuclear number-to-volume ratio. Taken together, this study illustrates how extensive cellular control of density and size drive sedimentation rate variation, likely shaping the onset and further evolution of multicellularity.

PUBLIC LIBRARY SCIENCE2022

Likelihood-free Inference of Population Genetic Parameters from Time-Sampled Genetic Data

Hyunjin Shim

This thesis consists of five papers published in peer-reviewed journals, two of which focus on method development of time-serial inference, represented by publications in methodology journals, and three others that describe collaborative data applications based on experimental evolution projects, which are published in biological journals. The first methodology publication (Chapter 2) is a comparison study of recently-introduced time-serial methods, performed using a systematic approach to evaluate, through simulation, the strengths and weaknesses of each method in quantifying selection coefficients from time-sampled data sets. The second methodology chapter (Chapter 3) introduced a novel method extending Wright-Fisher Approximate Bayesian Computation (WFABC) to detect and quantify changes in selection strength from temporal allele trajectories. This method was particularly novel in its use of simulation-based inference to detect and quantify Â€Â˜changesÂ€Â™ in evolutionary trajectories, which involved the application of Change-Point Analysis. In the first data application (Chapter 4), a time-sampled experiment of echovirus 11 evolved under the disinfectant (chlorine dioxide) was assessed on the associated genotypic and phenotypic trait in collaboration with the Environmental Chemistry Laboratory (LCE) at EPFL. This study contributes to a better understanding of disinfection resistance in waterborne viruses by identifying the mutations associated with enhanced replicative fitness. In the next application (Chapter 5), a comprehensive time-serial analysis was performed on experimental evolution data of echovirus 11 on UVC adaptation in collaboration with the Environmental Chemistry Laboratory (LCE). This study shows that the UVC adaptation of echovirus 11 is associated with a decrease in the virus mutation rate, which is an evidence of the ability of echovirus 11 to adapt to the commonly used disinfectant procedure of UVC radiation in clinical settings and water treatment plants. Additionally, a paper implementing Change-Point WFABC (CP-WFABC) to assess the experimental evolution of influenza A virus is shown in Appendix; specifically, the effects of a novel mutagenic drug (favipiravir) on adaptive allele trajectories were evaluated, with results indicating mutation meltdown under a high drug dosage.

EPFL2018