Publications associées à Alternative Restart Strategies for CMA-ES

Impact of population size on early adaptation in rugged fitness landscapes

Anne-Florence Raphaëlle Bitbol, Richard Marie Servajean

Owing to stochastic fluctuations arising from finite population size, known as genetic drift, the ability of a population to explore a rugged fitness landscape depends on its size. In the weak mutation regime, while the mean steady-state fitness increases ...

ROYAL SOC2023

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

On the relation between transversal and longitudinal scaling in cities

João Vitor Meirelles de Miranda

Does the scaling relationship between population sizes of cities with urban metrics like economic output and infrastructure (transversal scaling) mirror the evolution of individual cities in time (longitudinal scaling)? The answer to this question has impo ...

2020

Adapt or Perish: Evolutionary Rescue in a Gradually Deteriorating Environment

Loïc Marrec, Anne-Florence Raphaëlle Bitbol

We investigate the evolutionary rescue of a microbial population in a gradually deteriorating environment, through a combination of analytical calculations and stochastic simulations. We consider a population destined for extinction in the absence of mutan ...

2020

Limits on amplifiers of natural selection under death-Birth updating

Andreas Pavlogiannis

The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advanta ...

2020

Computational and Statistical analyses of Molecular Evolution and Demography using Large-scale Sequencing Data

Adamantia Kapopoulou

Evolution can be described as the change of allele frequencies over time. Four forces - mutation, migration, genetic drift, and selection, drive this change. The aim of my thesis was to accurately estimate and differentiate the parameters governing each of ...

EPFL2018

Evolution of urban scaling: Evidence from Brazil

João Vitor Meirelles de Miranda, Claudia Rebeca Binder Signer

During the last years, the new science of cities has been established as a fertile quantitative approach to systematically understand the urban phenomena. One of its main pillars is the proposition that urban systems display universal scaling behavior rega ...

2018

Persistence of butterfly populations in fragmented habitats along urban density gradients: motility helps

Stéphane Joost, Estelle Rochat, Ivo Widmer

In a simulation study of genotypes conducted over 100 generations for more than 1600 butterfly’s individuals, we evaluate how the increase of anthropogenic fragmentation and reduction of habitat size along urbanisation gradients (from 7% to 59% of impervio ...

Nature Publishing Group2017

The consequences of not accounting for background selection in demographic inference

Jeffrey David Jensen, Gregory Bruce Ewing

Recently, there has been increased awareness of the role of background selection (BGS) in both data analysis and modelling advances. However, BGS is still difficult to take into account because of tractability issues with simulations and difficulty with no ...

Wiley-Blackwell2016

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

Coalescent inferences in conservation genetics: should the exception become the rule?

Valeria Montano

Genetic estimates of effective population size (Ne) are an established means to develop informed conservation policies. Another key goal to pursue the conservation of endangered species is keeping the connectivity across fragmented environments, to which g ...

Royal Soc2016

The Impact of Linked Selection in Chimpanzees: A Comparative Study

Jeffrey David Jensen, Susanne Petra Pfeifer

Levels of nucleotide diversity vary greatly across the genomes of most species owing to multiple factors. These include variation in the underlying mutation rates, as well as the effects of both direct and linked selection. Fundamental to interpreting the ...

Oxford University Press (OUP)2016

WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data

Hyunjin Shim, Jeffrey David Jensen, Matthieu Foll

With novel developments in sequencing technologies, time-sampled data are becoming more available and accessible. Naturally, there have been efforts in parallel to infer population genetic parameters from these data sets. Here, we compare and analyse four ...

Wiley-Blackwell2015

Periodic versus Intermittent Adaptive Cycles in Quasispecies Coevolution

Alexander Kevin Seeholzer

We study an abstract model for the coevolution between mutating viruses and the adaptive immune system. In sequence space, these two populations are localized around transiently dominant strains. Delocalization or error thresholds exhibit a novel interdepe ...

American Physical Society2014

Population Sensing Using Mobile Devices : a Statistical Opportunity or a Privacy Nightmare?

Farid Movahedi Naini

In our daily lives, our mobile phones sense our movements and interactions via a rich set of embedded sensors such as a GPS, Bluetooth, accelerometers, and microphones. This enables us to use mobile phones as agents for collecting spatio-temporal data. The ...

EPFL2014

Analysis of Fitness Noise in Particle Swarm Optimization: From Robotic Learning to Benchmark Functions

Alcherio Martinoli, Inaki Navarro Oiza, Ezequiel Leonardo Di Mario

Population-based learning techniques have been proven to be effective in dealing with noise and are thus promising tools for the optimization of robotic controllers, which have inherently noisy performance evaluations. This article discusses how the result ...

2014

On the Prospect of Identifying Adaptive Loci in Recently Bottlenecked Populations

Jeffrey David Jensen

Identifying adaptively important loci in recently bottlenecked populations - be it natural selection acting on a population following the colonization of novel habitats in the wild, or artificial selection during the domestication of a breed - remains a ma ...

Public Library of Science2014

Competing islands limit the rate of adaptation in structured populations

Cornelia Pokalyuk

Beneficial mutations can co-occur when population structure slows down adaptation. Here, we consider the process of adaptation in asexual populations distributed over several locations ("islands"). New beneficial mutations arise at constant rate u(b), and ...

Elsevier2013

Intensive Surrogate Model Exploitation in Self-adaptive Surrogate-assisted CMA-ES (saACM-ES)

Ilya Loshchilov

This paper presents a new mechanism for a better exploitation of surrogate models in the framework of Evolution Strategies (ESs). This mechanism is instantiated here on the self-adaptive surrogate-assisted Covariance Matrix Adaptation Evolution Strategy (( ...

Assoc Computing Machinery2013

Rapid Intrahost Evolution of Human Cytomegalovirus Is Shaped by Demography and Positive Selection

Jeffrey David Jensen

Populations of human cytomegalovirus (HCMV), a large DNA virus, are highly polymorphic in patient samples, which may allow for rapid evolution within human hosts. To understand HCMV evolution, longitudinally sampled genomic populations from the urine and p ...

Public Library of Science2013