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Articles by Simon Boitard
A matrix-analytical sampling formula for time-homogeneous coalescent processes under the infinite sites mutation model
Article Dans Une Revue Theoretical Population Biology Année : 2025 A matrix-analytical sampling formula for time-homogeneous coalescent processes under the infinite sites mutation model Fichier principal 1-s2.0-S004058092500019X-main.pdf (843) Télécharger le fichier hal-05030389 , version 1 (11-04-2025) Asger Hobolth, Simon Boitard, Andreas Futschik, Raphael Leblois. A matrix-analytical sampling formula for time-homogeneous coalescent processes under the infinite sites mutation model.
Extending the IICR to complex non-stationary structured models
Abstract Population genetic studies use genetic data to understand aspects of the evolutionary history of species, particularly to infer their demography. Here, we extend the non-stationary structured coalescent framework to complex models where the parameters of the model, and thus the state space, change between stationary periods.
Predicting species invasiveness with genomic data: Is genomic offset related to establishment probability?
1 INTRODUCTION Predicting how natural species adapt to environmental change is crucial in evolutionary biology. This knowledge not only furthers our understanding of evolutionary processes involved in adaptation but also holds practical implications, particularly in the current context of global changes.
Predicting species invasiveness with genomic data: is Genomic Offset related to establishment probability?
Abstract Predicting the risk of establishment and spread of populations outside their native range represents a major challenge in evolutionary biology. Various methods have recently been developed to estimate population (mal)adaptation to a new environment with genomic data via so-called Genomic Offset (GO) statistics. These approaches are particularly promising for studying invasive species, but have still rarely been used in this context.
Exact calculation of the expected SFS in structured populations
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The quail as an avian model system: its genome provides insights into social behaviour, seasonal biology and infectious disease response
The quail as an avian model system: its genome provides insights into social behaviour, seasonal biology and infectious disease response Katrina Morris, Matthew M Hindle, Simon Boitard, David W Burt, Angela F Danner, Lel Eory, Heather L Forrest, David Gourichon, Jerome Gros, LaDeana Hillier, Thierry Jaffredo, Hanane Khoury, Rusty Lansford, Christine Leterrier, Andrew Loudon, Andrew S Mason, Simone L Meddle, Francis Minvielle, Patrick Minx, Frederique Pitel, J Patrick Seiler, Tsuyoshi...
An ABC method for whole-genome sequence data: inferring paleolithic and neolithic human expansions
AbstractSpecies generally undergo a complex demographic history, consisting, in particular, of multiple changes in population size. Genome-wide sequencing data are potentially highly informative for reconstructing this demographic history. A crucial point is to extract the relevant information from these very large datasets. Here we designed an approach for inferring past demographic events from a moderate number of fully sequenced genomes.
Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection
Citation: Kijas JW, Lenstra JA, Hayes B, Boitard S, Porto Neto LR, San Cristobal M, et al. (2012) Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection. PLoS Biol 10(2): e1001258. doi:10.1371/journal.pbio.1001258 Copyright: © 2012 Kijas et al.
Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach
Reconstructing the ancestral dynamics of effective population size is important in several contexts. From a long term evolutionary perspective, the history of population size changes can be related to various climatic or geological events, and reconstructing this history allows studying the impact of such events on natural species [1]. This demographic history also provides a statistical null model of neutral evolution that can subsequently be used for detecting loci under selection [2, 3].
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