Publications by Matthieu Foll | EPFL Graph Search

Linking a mutation to survival in wild mice

Jeffrey David Jensen, Matthieu Foll, Stefan Jean Laurent, Susanne Petra Pfeifer

Adaptive evolution in new or changing environments can be difficult to predict because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these explicit connections by combining field and laboratory experiments i ...

American Association for the Advancement of Science2019

The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene Flow

Jeffrey David Jensen, Matthieu Foll, Stefan Jean Laurent, Susanne Petra Pfeifer

2018

Detecting and Quantifying Changing Selection Intensities from Time-Sampled Polymorphism Data

Hyunjin Shim, Jeffrey David Jensen, Matthieu Foll, Stefan Jean Laurent, Sebastian Matuszewski

During his well-known debate with Fisher regarding the phenotypic dataset of Panaxia dominula, Wright suggested fluctuating selection as a potential explanation for the observed change in allele frequencies. This model has since been invoked in a number of ...

Genetics Society of America2016

An experimental evaluation of drug-induced mutational meltdown as an antiviral treatment strategy

Hyunjin Shim, Jeffrey David Jensen, Claudia Bank, Matthieu Foll, Sebastian Matuszewski

The rapid evolution of drug resistance remains a critical public health concern. The treatment of influenza A virus (IAV) has proven particularly challenging, due to the ability of the virus to develop resistance against current antivirals and vaccines. He ...

Wiley-Blackwell2016

Inferring the age of a fixed beneficial allele

Jeffrey David Jensen, Nicky Louise Ormond, Gregory Bruce Ewing, Matthieu Foll, Susanne Petra Pfeifer

Estimating the age and strength of beneficial alleles is central to understanding how adaptation proceeds in response to changing environmental conditions. Several haplotype-based estimators exist for inferring the age of segregating beneficial mutations. ...

Wiley-Blackwell2016

The past, present and future of genomic scans for selection INTRODUCTION

Jeffrey David Jensen, Matthieu Foll

Wiley-Blackwell2016

Neutral and Adaptive Drivers of Microgeographic Genetic Divergence within Continuous Populations: The Case of the Neotropical Tree Eperua falcata (Aubl.)

Matthieu Foll

Background In wild plant populations, genetic divergence within continuous stands is common, sometimes at very short geographical scales. While restrictions to gene flow combined with local inbreeding and genetic drift may cause neutral differentiation amo ...

Public Library of Science2015

Detection of Convergent Genome-Wide Signals of Adaptation to Tropical Forests in Humans

Matthieu Foll

Tropical forests are believed to be very harsh environments for human life. It is unclear whether human beings would have ever subsisted in those environments without external resources. It is therefore possible that humans have developed recent biological ...

Public Library of Science2015

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

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

Jeffrey David Jensen, Matthieu Foll, Valeria Montano

Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of pa ...

Genetics Society America2015

Positive Selection Drives Preferred Segment Combinations during Influenza Virus Reassortment

Jeffrey David Jensen, Matthieu Foll

Influenza A virus (IAV) has a segmented genome that allows for the exchange of genome segments between different strains. This reassortment accelerates evolution by breaking linkage, helping IAV cross species barriers to potentially create highly virulent ...

Oxford University Press2015

Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective

Hyunjin Shim, Jeffrey David Jensen, Claudia Bank, Gregory Bruce Ewing, Matthieu Foll, Anna Ferrer Admetlla

Author Summary In recent years, considerable attention has been given to the evolution of drug resistance in the influenza A H1N1 strain. As a major annual cause of morbidity and mortality, combined with the rapid global spread of drug resistance, influenz ...

Public Library of Science2014

Continental-Scale Footprint of Balancing and Positive Selection in a Small Rodent (Microtus arvalis)

Matthieu Foll

Genetic adaptation to different environmental conditions is expected to lead to large differences between populations at selected loci, thus providing a signature of positive selection. Whereas balancing selection can maintain polymorphisms over long evolu ...

Public Library of Science2014

Widespread Signals of Convergent Adaptation to High Altitude in Asia and America

Matthieu Foll

Living at high altitude is one of the most difficult challenges that humans had to cope with during their evolution. Whereas several genomic studies have revealed some of the genetic bases of adaptations in Tibetan, Andean, and Ethiopian populations, relat ...

Cell Press2014

Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers

Matthieu Foll, Xin Zhou

The evolutionary history of the human pygmy phenotype (small body size), a characteristic of African and Southeast Asian rainforest hunter-gatherers, is largely unknown. Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions th ...

National Academy of Sciences2014

Thinking too positive? Revisiting current methods of population genetic selection inference

Jeffrey David Jensen, Claudia Bank, Gregory Bruce Ewing, Matthieu Foll

In the age of next-generation sequencing, the availability of increasing amounts and improved quality of data at decreasing cost ought to allow for a better understanding of how natural selection is shaping the genome than ever before. However, alternative ...

Elsevier Science London2014

Robust Demographic Inference from Genomic and SNP Data

Matthieu Foll

We introduce a flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets. We show that our composite-likelihood approach allows one to study evolutionary models ...

Public Library of Science2013