Publications associées à E. coli long-term evolution experiment

Reproductive isolation arises during laboratory adaptation to a novel hot environment

Background: Reproductive isolation can result from adaptive processes (e.g., ecological speciation and mutation-order speciation) or stochastic processes such as "system drift" model. Ecological speciation predicts barriers to gene flow between populations ...

BMC2024

Frequent asymmetric migrations suppress natural selection in spatially structured populations

Anne-Florence Raphaëlle Bitbol, Alia Abbara

Natural microbial populations often have complex spatial structures. This can impact their evolution, in particular the ability of mutants to take over. While mutant fixation probabilities are known to be unaffected by sufficiently symmetric structures, ev ...

Oxford Univ Press2023

Hydrodynamic flow and concentration gradients in the gut enhance neutral bacterial diversity

Anne-Florence Raphaëlle Bitbol

The gut microbiota features important genetic diversity, and the specific spatial features of the gut may shape evolution within this environment. We investigate the fixation probability of neutral bacterial mutants within a minimal model of the gut that i ...

National Academy of Sciences2022

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. How ...

PUBLIC LIBRARY SCIENCE2022

Exploiting Marginal Stability in Slow-Fast Quasilinear Dynamical Systems

Alessia Ferraro

The accurate investigation of many geophysical phenomena via direct numerical simulations is computationally not possible nowadays due to the huge range of spatial and temporal scales to be resolved. Therefore advances in this field rely on the development ...

EPFL2022

Towards an Evolutionary Theory of Stress Responses

Maria del Carmen Sandi Perez

All organisms have a stress response system to cope with environmental threats, yet its precise form varies hugely within and across individuals, populations, and species. While the physiological mechanisms are increasingly understood, how stress responses ...

2021

Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

Bart Deplancke

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, a ...

2020

FasR Regulates Fatty Acid Biosynthesis and Is Essential for Virulence of Mycobacterium tuberculosis

Stewart Cole, Claudia Sala

Mycobacterium tuberculosis, the etiologic agent of human tuberculosis, is the world's leading cause of death from an infectious disease. One of the main features of this pathogen is the complex and dynamic lipid composition of the cell envelope, which adap ...

Frontiers Media SA2020

Feature Learning of Virus Genome Evolution With the Nucleotide Skip-Gram Neural Network

Hyunjin Shim

Recent studies reveal that even the smallest genomes such as viruses evolve through complex and stochastic processes, and the assumption of independent alleles is not valid in most applications. Advances in sequencing technologies produce multiple time-poi ...

2019

Sexual conflict drives male manipulation of female postmating responses in Drosophila melanogaster

Laurent Keller, Brian Dennis Hollis

In many animals, females respond to mating with changes in physiology and behavior that are triggered by molecules transferred by males during mating. In Drosophila melanogaster, proteins in the seminal fluid are responsible for important female postmating ...

National Academy of Sciences2019

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 ...

EPFL2018

Experimental evolution of slowed cognitive aging in Drosophila melanogaster

Brian Dennis Hollis

Reproductive output and cognitive performance decline in parallel during aging, but it is unknown whether this reflects a shared genetic architecture or merely the declining force of natural selection acting independently on both traits. We used experiment ...

2017

The effect of overall stimulus configuration on crowding

Michael Herzog, Maya Roinishvili, Mattew Pachai

The standard framework to study vision is typically hierarchical and feedforward, which facilitates deconstructing complex mechanisms into smaller, more tractable problems. However, this framework can fail when elements are presented in context, as they ar ...

2017

Resistance of echovirus 11 to ClO2 is associated with enhanced host receptor use, altered entry routes and high fitness

Tamar Kohn, Anna Carratala Ripolles, Virginie Bachmann, Jeffrey David Jensen, Qingxia Zhong, Hyunjin Shim

Waterborne viruses can exhibit resistance to common water disinfectants, yet the mechanisms that allow them to tolerate disinfection are poorly understood. Here, we generated echovirus 11 (E11) with resistance to chlorine dioxide (ClO2) by experimental evo ...

Amer Chemical Soc2017

Energy saving glazing with a wide band-pass FSS allowing mobile communication: up-scaling and characterisation

Andreas Schueler, Olivia Valérie Charlotte Bouvard, Luc Burnier

A real case study and characterisation of modern energy efficient windows allowing mobile communication is presented. An earlier study had shown that laser scribing of energy saving coatings allows highly reducing the microwave attenuation (from 30 to 1-3d ...

Inst Engineering Technology-Iet2017

Inferring the age and strength of mutations evolving under positive selection

Nicky Louise Ormond

A fundamental goal of population genetics is to determine and quantify the interplay of mutation, natural selection, genetic drift and migration in shaping allelic frequency changes that underpin evolution-ary change. In this dissertation, I present comput ...

EPFL2017

Experimental adaptation of human echovirus 11 to ultraviolet radiation leads to tolerance to disinfection and resistance to ribavirin

Tamar Kohn, Anna Carratala Ripolles, Virginie Bachmann, Jeffrey David Jensen, Qingxia Zhong, Hyunjin Shim

Ultraviolet light in the UVC range is a commonly used disinfectant to control viruses in clinical settings and water treatment. Here, we employed an experimental evolution approach to investigate the adaptation of human echovirus 11 to disinfection by UVC, ...

2017

Optimization of Conformational Dynamics in an Epistatic Evolutionary Trajectory

Luciano Andres Abriata

The understanding of protein evolution depends on the ability to relate the impact of mutations on molecular traits to organismal fitness. Biological activity and robustness have been regarded as important features in shaping protein evolutionary landscape ...

Oxford Univ Press2016

A Statistical Guide to the Design of Deep Mutational Scanning Experiments

Jeffrey David Jensen, Claudia Bank, Sebastian Matuszewski

The characterization of the distribution of mutational effects is a key goal in evolutionary biology. Recently developed deep-sequencing approaches allow for accurate and simultaneous estimation of the fitness effects of hundreds of engineered mutations by ...

Genetics Society America2016

An Approximate Markov Model for the Wright-Fisher Diffusion and Its Application to Time Series Data

Jeffrey David Jensen, Anna Ferrer Admetlla

The joint and accurate inference of selection and demography from genetic data is considered a particularly challenging question in population genetics, since both process may lead to very similar patterns of genetic diversity. However, additional informat ...

Genetics Society America2016