BOITARD S - cbgp

simon.boitard@inrae.fr

+33 4 99 62 33 70

All members

Simon BOITARD

Research Director, INRAE

Area(s)

4 - Contemporary evolution of populations

Technical platform(s)

Calculation and data management

Collective responsibility(ies)

Head of Area 4
Scientific manager of the TP Calculation
Member of the Scientific Council and Bureau of the GDR "Approche Interdisciplinaire en Évolution Moléculaire" (IAME - Interdisciplinary Approach to Molecular Evolution)

My research project focuses on developing statistical methods to reconstruct the evolutionary history of a species using high-throughput genomic data from individuals of that species. The first part of the project focuses on estimating the demographic (or neutral) aspects of this evolution, such as variations in effective population size or the organisation of the species into populations (time of divergence, gene flow, etc.). The second part focuses on identifying regions of the genome whose evolution results not only from these neutral processes, but also from adaptive pressures. Alongside this general research, which can be applied to a wide range of animal and plant species, I am specifically interested in characterising and predicting biological invasions and the adaptation of insect pests to their host plants. In particular, I am involved in research conducted at the CBGP on Drosophila suzukii and Harmonia axyridis.

Keywords: population history, genetic basis of adaptation, genomic prediction, biological invasions, insect pests.

Arredondo A., Corujo J., Nous C., Boitard S., Chikhi L. & Mazet O. 2025. Exact calculation of the expected SFS in structured populations. Theoretical Population Biology 163 : 50-61. (https://dx.doi.org/10.1016/j.tpb.2025.03.003)

Camus* L., Rode N.O., Serga S., Loiseau A., Chen X., Iampietro C., Kenis M., Marande W., Mensch J., Parinello H., Savic Veselinovic M., Valiere S., Zhang J., Estoup A., Boitard S. & Gautier M. 2025. Adaptive challenges of past and future invasion of Drosophila suzukii: insights from novel genomic resources and statistical methods combining individual and pool sequencing data. Molecular Ecology 34 : e70192. (https://dx.doi.org/10.1111/mec.70192)

Hobolth A., Boitard S., Futschik A. & Leblois R. 2025. A matrix-analytical sampling formula for time-homogeneous coalescent processes under the infinite sites mutation model. Theoretical Population Biology 163 : 62-79. (https://dx.doi.org/10.1016/j.tpb.2025.03.002)

Uhl* M., Bunel* P., de Navascués M., Boitard S. & Servin B. 2025. SelNeTime: a python package inferring effective population size and selection intensity from genomic time series data. PCI Mathematical and Computational Biology na : na. (https://dx.doi.org/10.1101/2024.11.06.622284)

Camus* L., Gautier M. & Boitard S. 2024. Predicting species invasiveness with genomic data: Is genomic offset related to establishment probability?. Evolutionary Applications 17 : e13709. (https://dx.doi.org/10.1111/eva.13709)

Soubeyrand S., Estoup A., Cruaud A., Malembic-Maher S., Meynard C., Ravigné V., Barbier M., Barrès B., Berthier K., Boitard S., Dallot S., Gaba S., Grosdidier M., Hannachi M., Jacques M.A., Leclerc M., Lucas P., Martinetti D., Mougel C., Robert C., Roques A., Rossi J.-P., Suffert F., Abad P., Auger-Rozenberg M.-A., Ay J.S., Bardin M., Bernard H., Bohan D.A., Candresse T., Castagnone-Sereno P., Danchin E.G.J., Delmas C.E.L., Ezanno P., Fabre F., Facon B., Gabriel E., Gaudin J., Gauffre B., Gautier M., Guinat C., Lavigne C., Lemaire O., Martinez C., Michel L., Moury B., Nam K., Nédellec C., Ogliastro M., Papaïx J., Parisey N., Poggi S., Radici A., Rasplus J.-Y., Reboud X., Robin C., Roche M., Rusch A., Sauvion N., Streito J.-C., Verdin E., Walker A.S., Xuéreb A., Thébaud G. & Morris C.E. 2024. Building integrated plant health surveillance: a proactive research agenda for anticipating and mitigating disease and pest emergence. CABI Agriculture and Bioscience 5 : 72. (https://dx.doi.org/10.1186/s43170-024-00273-8)

Boitard S., Liaubet L., Paris C., Feve K., Dehais P., Bouquet A., Riquet J. & Mercat M.J. 2023. Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines. Genetics, Selection, Evolution 55 : 13. (https://dx.doi.org/10.1186/s12711-023-00789-z)

Boitard S., Arredondo A., Chikhi L. & Mazet O. 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 : iyac008. (https://dx.doi.org/10.1093/genetics/iyac008)

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 : 85. (https://dx.doi.org/10.1186/s40168-022-01280-5)

Arredondo A., Mourato B., Nguyen K., Boitard S., Rodríguez W., Noûs C., Mazet O. & Chikhi L. 2021. Inferring number of populations and changes in connectivity under the n-island model. Heredity 126 : 896-912. (https://dx.doi.org/10.1038/s41437-021-00426-9)