Simon Boitard

SelNeTime: a python package inferring effective population size and selection intensity from genomic time series data

SelNeTime infers effective population size and selection intensity from genomic time series data using an improved HMM approach with Beta with Spikes approximation.

Extending the IICR to complex non-stationary structured models

This paper extends the non-stationary structured coalescent framework to models with changing parameters, showing that IICR curves can be misleading and highlighting the impact of deme changes on population genetic inferences.

Adaptive challenges of past and future invasion of Drosophila suzukii: insights from novel genomic resources and statistical methods combining individual and pool sequencing data

This study uses genomic data and statistical methods to analyze adaptation in Drosophila suzukii during past and future invasions, identifying genomic regions associated with invasion success and predicting future invasion risks.

Exact calculation of the expected SFS in structured populations

The paper presents an algorithm to calculate the expected Site Frequency Spectrum (SFS) in structured populations, enabling demographic parameter inference in the symmetrical n-island model.

Extending the IICR to multiple genomes and identification of limitations of some demographic inferential methods

This paper extends the IICR to larger sample sizes and identifies limitations of demographic inferential methods using simulations and real data.

Predicting species invasiveness with genomic data: is Genomic Offset related to establishment probability?

This study evaluates Genomic Offset (GO) as a predictor of establishment probability in invasive species using simulations and empirical data from Bactrocera tryoni.

Heterogeneity in effective size across the genome: effects on the Inverse Instantaneous Coalescence Rate (IICR) and implications for demographic inference under linked selection.

The paper examines how genomic variations in effective population size due to linked selection affect coalescence time distributions and demographic inference.

The quail as an avian model system: its genome provides insights into social behaviour, seasonal biology and infectious disease response

The paper presents a high-quality quail genome and uses it to study social behavior, photoperiodism, and immune response to H5N1 influenza.

Inference of selection from genetic time series using various parametric approximations to the Wright-Fisher model

The paper compares parametric approximations to the Wright-Fisher model for inferring selection from genetic time series and finds the Beta-with-Spikes model performs best.

On the importance of being structured: instantaneous coalescence rates and a re-evaluation of human evolution

The paper shows that ignoring population structure in demographic inference leads to misleading population size changes, using human genomic data to demonstrate this issue.

Selection signatures in worldwide Sheep populations

This study re-analyzes the Sheep Hapmap dataset to identify selection signatures in worldwide sheep populations, distinguishing between recent and older selection pressures.