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INRAE

24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

Simon Boitard

I am interested in the development of inference methods for population genetics. The methods I develop aim at reconstructing the evolution history of species based on high-density genomic data observed in these species. They concern both neutral (population size history, population structure ...) and adaptive (detection of locus under selection, estimation of selection history ...) aspects of this evolution. These methods are generic and can be applied to a wide range of plant and animal species. Until 2019, I have mainly focused on farm animal species, studying both the domestication process and the recent period of intensive breeding. In 2020 I joined the CBGP and started to contribute to ongoing projects concerning the invasive species Drosophila suzukii and Harmonia axyridis.

Ongoing projects

- Development and applications of methods for the management and conservation of natural populations using genomic data (DevOCGen). Funded by Région Occitanie in the context of the BiodivOc call undertaken by Montpellier University. Co-coordinator with Raphaël Leblois. https://biodivoc.edu.umontpellier.fr/recherche/projets-consortium/projet-de-consortium-devocgen/

To work on this project, we are looking for two PhD students starting in september 2022 on the following subjects: "inference of recent evolutionary history from genomic time series data" and "Inference of recent demographic history in continuous spatially structured populations using genomic data".

- Genomic prediction of the adaptive potentiel of populations. PhD project of Louise Camus (2021-2024), co-supervised with Mathieu Gautier.

- Genomics of the invasion of the ladybird Harmonia axyridis (ANR GANDHI, leader A. Estoup).

Software

Pool-HMM & Freq-HMM, https://forge-dga.jouy.inra.fr/projects/pool-hmm

PopSizeABC, https://forge-dga.jouy.inra.fr/projects/popsizeabc

Recent publications (2019-2021)

Fallet M., Montagnani C., Petton B., Dantan L., de Lorgeril J., Comarmond S., Chaparro C., Toulza E., Boitard S., Escoubas J.M., Vergnes A., Le Grand J., Bulla I., Gueguen Y., Vidal-Dupiol J., Grunau C., Mitta G. & Cosseau C. 2022. Early life microbial exposures shape the Crassostrea gigas immune system for lifelong and intergenerational disease protection. Microbiome 10(1): 85.

A. Ouhrouch, S. Boitard, F. Boyer, B. Servin, A. Da Silva, F. Pompanon, A. Haddioui & B. Benjelloun (2021). Genomic Uniqueness of Local Sheep Breeds From Morocco. Frontiers in genetics, 12: 723599.

S. Boitard, A. Arredondo, C. Noûs, L. Chikhi, O. Mazet (2022). Heterogeneity in effective size across the genome: effects on the Inverse Instantaneous Coalescence Rate (IICR) and implications for demographic inference under linked selection. Genetics, 220(3), iyac008.

Boitard, S., Paris, C., Sevane, N., Servin, B & Dunner, S. (2021). Gene banks as reservoirs to detect recent selection: the example of the Asturiana de los Valles bovine breed. Frontiers in Genetics, 12:575405.

Soto, A. A., Mourato, B., Nguyen, K., Boitard, S., Valcarce, W. R. R., Noûs, C., ... & Chikhi, L. (2021). Inferring number of populations and changes in connectivity under the n-island model. Heredity, 1-17.

Morris, K. M., Hindle, M. M., Boitard, S., Burt, D. W., Danner, A. F., Eory, L., ... & Jaffredo, T. (2020). The quail genome: insights into social behaviour, seasonal biology and infectious disease response. BMC biology, 18(1), 1-18.

C. Paris, B. Servin & S. Boitard (2019). Inference of selection from genetic time series using various parametric approximations to the Wright-Fisher model. G3: Genes, Genomes, Genetics, 9(12), 4073-4086.

A. Vignal, S. Boitard, N. Thebault, G. K. Dayo, V. Yapi‐Gnaore, I. Youssao Abdou Karim, ... & W. C. Warren (2019). A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes. Molecular ecology resources 19: 997– 1014.

F. Jay, S. Boitard, & F. Austerlitz (2019). An ABC method for whole-genome sequence data: inferring paleolithic and neolithic human expansions. Molecular biology and evolution, 36(7), 1565-1579.

Selection of more ancient publications

M.I. Fariello, S. Boitard, S. Mercier, D. Robelin, T. Faraut, C. Arnould, J. Recoquillay, O. Bouchez, G. Salin, P. Dehais, D. Gourichon, S. Leroux, F. Pitel, C. Leterrier and M. SanCristobal (2017). Accounting for Linkage Disequilibrium in genome scans for selection without individual genotypes: the local score approach. Mol Ecol 26:3700–3714.

S. Boitard, W. Rodríguez, F. Jay, S. Mona and F. Austerlitz (2016). Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach. PLoS Genet 12(3): e1005877.

S. Boitard, M. Boussaha, A. Capitan, D. Rocha and B. Servin (2016). Uncovering Adaptation from Sequence Data: Lessons from Genome Resequencing of Four Cattle Breeds. Genetics 203(1), 433-450.

O. Mazet, W. Rodríguez, S. Grusea, S. Boitard and L. Chikhi (2015). On the importance of being structured: instantaneous coalescence rates and human evolution-lessons for ancestral population size inference? Heredity116(4):362-71.

M. I. Fariello, S. Boitard, H. Naya, M. SanCristobal and B. Servin (2013). Detecting signatures of selection through haplotype differentiation among hierarchically structured populations. Genetics 193 (3), 929-941.

S. Boitard, C. Schltterer, V. Nolte, R. V. Pandey and A. Futschik (2012). Detecting selective sweeps from pooled next generation sequencing samples. Mol. Biol. Evol. 29(9): 2177-2186.