(NB: I am coorganisator of the molecular evolution in Paris region 'evolmol' seminar group.)

Research interests

Keywords: population genetics, molecular evolution, coalescence, molecular polymorphism.

I make inferences from molecular polymorphism data on the evolutionary history of populations.

Our null hypothesis of molecular polymorphism is based on neutral model, which describe molecular evolution under mutation drift equilibrium.

I model such stochastic process with the help of coalescent simulations, i.e. random genealogies describing the genetic history of a gene sample.

I am primarily interested in nucleotide polymorphism, which obeys reasonably to the infinite many site (ISMM) mutational model, the most powerful one to make inferences.

I develop statistical tests based on this approach.

Such tests can be applied to nucleotide polymorphism data to detect and ideally disentangle, various factor that can alter evolution compared to standard models. :

Demographic effects: bottlenecks, population structure, isolation by distance...

Natural selection, and in particular hitchhiking (selective sweep ).

Genetic effects: recombination, mutational biases.

In particular, I have been working on time series data (measurably evolving populations): datasets with various sampling time where mutation cannot be neglected between sampling time points. This allows following the evolution as a real time process and for instance separating the mutation rate from the effective size and thus scaling time for corresponding inferences or assessing the demographic trajectory.

Such range of applications include ancient DNA data. I have been collaborating with Ludovic Orlando and Catherine Hänni (ENS Lyon and LECA Grenoble I), with applications on cave bear data. I showed that classic molecular population genetics statistics were substantially influenced by time structure in the dataset, with inflated polymorphism and divergence most generally with spurious population expansion signal.

On a more recent absolute time scale, time structure may concern the most fast viral evolution, with high mutation rates and short generation time. I have been collaborating with Antoine Chaillon, Francis Barin et al. from a virology lab in Tours (FR) on HIV within host evolution and mother to child transmission (in a Thai population) we used time series sequence data in the first infant years and their variation level to infer the transmission timing. This separates most finely cases with transmission during pregnancy from those occurring at birth.

I have also been working with Catherine Gaudy-Graffin from the same virology lab on C hepatitis within host evolution. I used phylogenetic methods based on non synonymous to synonymous substitution ratio to detect codons target for selection (immune response or treatment). My main interest is to adapt such methods intended for large time scale or between species evolution to short time scale or within species evolution and in particular the impact of gene exchanges such as recombination.

Finally I am working with Sandrine Adiba from our group on experimental evolution data from bacteria Escherichia coli. We followed the frequency trajectories of a neutral marker. It may however be correlatively affected by selection on linked loci (hitchhiking) and we try to separate such selective effects from neutral random ones (genetic drift). In contrast with the above case, on such a laboratory time scale, mutation of a neutral marker may be neglected. To address how robust are simple selective models to more natural varying biotic pressure, we manipulate predation from an ameoba Dictyostellium discoideum, together with spatial structure (non agitated vs agitated liquid media).

Classes

Molecular Evolution 2021 ppsx (+ anim)

Molecular Evolution 2021 pdf (-anim)

Coalescence class 2021 ppsx (+ anim)

Coalescence class 2021 pdf (-anim)

MCMC ABC class 2022 ppsx (+ anim)

MCMC ABC class 2022 pdf (- anim)

Publications

Depaulis F. Détecter les effets de la sélection naturelle sur l'ADN par intelligence artificielle. Planet-Vie, 2 avril 2019.

Navascués M, Legrand D, Campagne C, Cariou ML, Depaulis F 2014. Distinguishing migration from isolation using genes with intragenic recombination: detecting introgression in the Drosophila simulans species complex. BMC Evolutionary Biology 14: 89.

Chaillon A, Samleerat T, Zoveda F, Ballesteros S, Moreau A, Ngo-Giang-Huong N, Jourdain G, Gianella S, Lallemant M, Depaulis F, Barin F 2014. Estimating the Timing of Mother-to-Child Transmission of the Human Immunodeficiency Virus Type 1 Using a Viral Molecular Evolution Model. PLoS ONE 9: e90421.

Esteban-Riesco L, Depaulis F, Moreau A, Bacq Y, Dubois F, Goudeau A, Gaudy-Graffin C 2013. Rapid and sustained autologous neutralizing response leading to early spontaneous recovery after HCV infection. Virology 444: 90-99.

[ Depaulis F, Enard D 2013. Sélection récurrente dans les génomes de primates. Focus 9-1 dans Génomique environnementale. Paris: D Faure, D Joly, Cahiers prospectives de l'INEE du CNRS n° 5, 96p . ]

Lakis G, Navascués M, Rekima S, Simon M, Remigereau MS, Leveugle M, Takvorian N, Lamy F, Depaulis F, Sarr A, Robert T 2012. Evolution Of Neutral And Flowering Genes along Pearl Millet (Pennisetum glaucum) domestication. PLoS ONE 7: e36642.

Adiba S, Nizak C, van Baalen M, Denamur E, Depaulis F 2010. From Grazing Resistance to Pathogenesis: The Coincidental Evolution of Virulence Factors. PLoS ONE 5: e11882.

Navascués M, Depaulis F, Emerson BC 2010. Combining contemporary and ancient DNA in population genetic and phylogeographic studies. Molecular Ecology Resources 10: 760-772.

Enard D, Depaulis F, Roest Crolluis H 2010. Human and non-human primate genomes share hotspots of positive selection. PLoS Genet 6:e1000840.

Depaulis F, Orlando L, Hanni C 2009. Using classical population genetics tools with heterochroneous data: time matters! PLoS One 4: e5541.

Raquin AL, Depaulis F, Lambert A, Galic N, Brabant P, Goldringer I 2008. Experimental estimation of mutation rates in a wheat population with gene genealogy approach. Genetics 179:2195-2211.

Gallet R, Alizon S, Comte PA, Gutierrez A, Depaulis F, van Baalen M, Michel E, Müller-Graf CDM 2007. Predation and Disturbance Interact to Shape Prey Species Diversity. Am Nat 170:143-154.

2005. 33rd European Mathematical Genetics Meeting, EMGM2005, Le Kremlin-Bicêtre, France, April 1st-2nd 2005. Annals of Human Genetics 69:764-774.

Depaulis F, Mousset S, Veuille M 2005. Detecting selective sweeps with haplotype tests in D. Nurminsky, ed. Selective Sweep. Landes Bioscience, Georgetown, USA.

Baudry E, Depaulis F. 2003. Effect of misoriented sites on neutrality tests with outgroup. Genetics 165:1619-1622.

Mousset S, Brazier L, Cariou ML, Chartois F, Depaulis F, Veuille M 2003. Evidence of a High Rate of Selective Sweeps in African Drosophila melanogaster. Genetics 163:599-609.

Depaulis F, Mousset S, Veuille M 2003. Power of neutrality tests to detect bottlenecks and hitchhiking. J Mol Evol 57 Suppl 1:S190-200.

Barton NH, Depaulis F, Etheridge AM 2002. Neutral evolution in spatially continuous populations. Theoretical Population Biology 61 :31-48.

Depaulis F, Mousset S, Veuille M 2001. Haplotype tests using coalescent simulations conditional on the number of segregating sites. Molecular Biology and Evolution 18: 1136-1138.

Andolfatto P, Depaulis F, Navarro A 2001. Inversion polymorphism and nucleotide variability in Drosophila. Genetical Research 77 :1-8.

Depaulis F, Brazier L, Mousset S, Turbé A, Veuille M 2000. Selective sweep near the In(2L)t inversion breakpoint in an African population of Drosophila melanogaster. Genetical research 76 :149-158.

Galtier N, Depaulis F, Barton NH 2000. Detecting bottlenecks and selective sweeps from DNA sequence polymorphism. Genetics 155 :981-987.

Kliman RM, Andolfatto P, Coyne JA, Depaulis F, Kreitman M, Berry AJ, McCarter J, Wakeley J, Hey J 2000. The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics 156 :1913-1931.

Depaulis F, Brazier L, Veuille M 1999. Selective sweep at the Drosophila melanogaster Suppressor of Hairless locus, and its association with the In(2L)t inversion polymorphism. Genetics 152 : 1017-1024.

Bénassi V, Depaulis F, Meghlaoui GK, Veuille M 1999. Partial sweeping of variation at the Fbp2 locus, in a highly recombining region of the Drosophila melanogaster Genome. Molecular Biology and Evolution. 16 : 347-353.

Depaulis F, Veuille M 1998. Neutrality tests based on the distribution of haplotypes under an infinite site model. Molecular Biology and Evolution 15 : 1788-1790.

Veuille, M, Bénassi V, Aulard S, Depaulis F 1998. Allele-specific population structure of Drosophila melanogaster Alcohol-dehydrogenase at the molecular level. Genetics 149 : 971-981.