Publications de Jeffrey David Jensen

The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards

Jeffrey David Jensen, Kristen Kay Irwin, Stefan Jean Laurent, Susanne Petra Pfeifer

By combining well-established population genetic theory with high-throughput sequencing data from natural populations, major strides have recently been made in understanding how, why, and when vertebrate populations evolve crypsis. Here, we focus on backgr ...

NATURE PUBLISHING GROUP2020

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

Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares

Jeffrey David Jensen

American Association for the Advancement of Science2018

Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography

Jeffrey David Jensen, Sebastian Matuszewski

2018

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

The Demographic History of African Drosophila melanogaster

Adamantia Kapopoulou, Jeffrey David Jensen, Stefan Jean Laurent, Susanne Petra Pfeifer

As one of the most commonly utilized organisms in the study of local adaptation, an accurate characterization of the demographic history of Drosophila melanogaster remains as an important research question. This owes both to the inherent interest in charac ...

OXFORD UNIV PRESS2018

The fitness landscape of the codon space across environments

Jeffrey David Jensen, Claudia Bank, Sebastian Matuszewski

Fitness landscapes map the relationship between genotypes and fitness. However, most fitness landscape studies ignore the genetic architecture imposed by the codon table and thereby neglect the potential role of synonymous mutations. To quantify the fitnes ...

NATURE PUBLISHING GROUP2018

Two sides of the same coin: A population genetics perspective on lethal mutagenesis and mutational meltdown

Jeffrey David Jensen, Claudia Bank, Nicky Louise Ormond, Sebastian Matuszewski

The extinction of RNA virus populations upon application of a mutagenic drug is frequently referred to as evidence for the existence of an error threshold, above which the population cannot sustain the mutational load. To explain the extinction process aft ...

Oxford Univ Press2017

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

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

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

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

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

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

Characterizing human cytomegalovirus reinfection in congenitally infected infants: an evolutionary perspective

Jeffrey David Jensen, Cornelia Pokalyuk, Kristen Kay Irwin, Susanne Petra Pfeifer

Given the strong selective pressures often faced by populations when colonizing a novel habitat, the level of variation present on which selection may act is an important indicator of adaptive potential. While often discussed in an ecological context, this ...

Wiley2017

On the Analysis of Intrahost and Interhost Viral Populations: Human Cytomegalovirus as a Case Study of Pitfalls and Expectations

Jeffrey David Jensen, Sebastian Matuszewski, Susanne Petra Pfeifer

Intrahost and interhost assessments of viral diversity are often treated as measures of separate and distinct evolutionary processes, with numerous investigations reporting seemingly incompatible results between the two. For example, in human cytomegalovir ...

American Society for Microbiology2017

The Combined Effect of Oseltamivir and Favipiravir on Influenza A Virus Evolution

Jeffrey David Jensen, Claudia Bank, Nicky Louise Ormond, Sebastian Matuszewski

Influenza virus inflicts a heavy death toll annually and resistance to existing antiviral drugs has generated interest in the development of agents with novel mechanisms of action. Favipiravir is an antiviral drug that acts by increasing the genome-wide mu ...

Oxford University Press (OUP)2017

CRISPR-Cas9-mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy

Jeffrey David Jensen, Sebastian Matuszewski

Developing tools to accurately predict the clinical prevalence of drug-resistant mutations is a key step toward generating more effective therapeutics. Here we describe a high-throughput CRISPR-Cas9-based saturated mutagenesis approach to generate comprehe ...

National Academy of Sciences2017

Antiviral drug resistance as an adaptive process

Jeffrey David Jensen, Kristen Kay Irwin

Antiviral drug resistance is a matter of great clinical importance that, historically, has been investigated mostly from a virological perspective. Although the proximate mechanisms of resistance can be readily uncovered using these methods, larger evoluti ...

Oxford University Press2016

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

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

Jeffrey David Jensen, Matthieu Foll

Wiley-Blackwell2016

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

The evolution of gene expression and binding specificity of the largest transcription factor family in primates

Didier Trono, Adamantia Kapopoulou, Jeffrey David Jensen, Lisha Mathew

The KRAB-containing zinc finger (KRAB-ZF) proteins represent the largest family of transcription factors (TFs) in humans, yet for the great majority, their function and specific genomic target remain unknown. However, it has been shown that a large fractio ...

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