A. Tellier

Patterns of presence-absence variation of NLRs across populations of Solanum chilense are clade-dependent and mainly shaped by past demographic history.

The paper examines NLR presence-absence variation in Solanum chilense populations, finding it shaped by demographic history rather than selection or environmental factors.

Copy number variation shapes structural genomic diversity associated with ecological adaptation in the wild tomato Solanum chilense

This study identifies CNVs in wild tomato Solanum chilense linked to ecological adaptation, showing gene loss and gain associated with stress response and climate variables.

Inference of host-pathogen interaction matrices from genome-wide polymorphism data

This paper develops a Bayesian method to infer host-pathogen interaction matrices from genome-wide polymorphism data and applies it to HCV-infected humans to identify new resistance genes and GxG interactions.

Improved inference of population histories by integrating genomic and epigenomic data

This paper improves population history inference by integrating genomic and epigenomic data using an extended SMC framework, revealing new insights into demographic events in A. thaliana.

Evolution of two gene networks underlying adaptation to drought stress in the wild tomato Solanum chilense

The paper studies the evolution of two gene networks in Solanum chilense under drought stress, finding that the metabolic network is younger and under recent selection, while the cell-cycle network is ancient and conserved.

Local adaptation to novel habitats and climatic changes in a wild tomato species via selective sweeps.

The paper identifies selective sweeps in Solanum chilense populations linked to adaptation to different altitudes and climates.

Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population

This paper introduces an ABC framework to infer demographic and genetic parameters from time series population genetic data, showing high accuracy in estimating parameters during rapid adaptation.

Neutral genetic structuring of pathogen populations during rapid adaptation

This study models pathogen population dynamics during adaptation to new hosts and identifies genetic signatures of rapid adaptation events using time-series clustering.

Inference of evolutionary transitions to self-fertilization using whole-genome sequences

This paper develops two methods to infer the timing of transitions from outcrossing to selfing using whole-genome polymorphism data, applied to Arabidopsis thaliana.

Weak seed banks influence the signature and detectability of selective sweeps

This study introduces a simulation tool to examine how weak seed banks affect the genomic signatures and detectability of selective sweeps in species with seed banking.

Approximate Bayesian computation untangles signatures of contemporary and historical hybridization between two endangered species

This study uses Approximate Bayesian computation to analyze gene flow history between two endangered plant species, revealing long-term isolation followed by recent hybridization.

Cross-Species association statistics for genome-wide studies of host and parasite polymorphism data

This study develops and evaluates statistical indices to identify coevolving loci between hosts and parasites using cross-species genome-wide association analyses.

Inference of coevolutionary dynamics and parameters from host and parasite polymorphism data of repeated experiments

This paper develops a method to infer coevolutionary parameters from host and parasite polymorphism data using ABC, showing high accuracy in distinguishing coevolving loci from neutral ones.

Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data

This paper introduces a novel SMC-based method to infer demographic history and life-history traits like self-fertilization and seed/egg-bank rates from whole genome sequences, validated on simulated data and applied to Arabidopsis thaliana and Daphnia pulex.

Strengths and potential pitfalls of hay-transfer for ecological restoration revealed by RAD-seq analysis in floodplain Arabis species

This study uses RAD-seq to assess how hay-transfer affects genetic diversity in floodplain Arabis species, showing it maintains diversity but with species-specific outcomes.

A small subset of NLR genes drives local adaptation to pathogens in wild tomato

The paper identifies a small subset of NLR genes driving local adaptation to pathogens in wild tomato by analyzing genetic differentiation and selection signatures across populations.

The de novo reference genome and transcriptome assemblies of the wild tomato species Solanum chilense

This study generates the first genome and transcriptome assembly for Solanum chilense, a wild tomato species, and demonstrates its utility in comparative genomics and stress adaptation research.

Neutral genomic signatures of host-parasite coevolution.

The paper models host-parasite coevolution and shows that parasite population size changes can be detected in neutral polymorphism data, while host changes cannot due to differing mutation and drift dynamics.

Host-parasite coevolution can promote the evolution of seed banking as a bet-hedging strategy

This study shows host-parasite coevolution can drive the evolution of seed banking as a bet-hedging strategy under certain genetic and environmental conditions.