Stochastic Models for the Inference of Life Evolution

Guillaume Achaz

Permanent member

Collège de France
11, place Marcellin Berthelot
75005 Paris
Catch me if you can:
CdF: +33-1-44-27-13-91
MNHN: +33-1-40-79-57-68

Professor at Université Paris-Cité
Co-head of research group SMILE (Collège de France)
Director of the GDR network AIEM (CNRS)
Lecturer in population genetics (Ecole Normale Supérieure)
affiliated to research group Anthropologie génétique (Musée de l'Homme)
affiliated to research group Atelier de BioInformatique (Muséum)

Interests in Biology


Theoretical Biology, Molecular Evolution, Bioinformatics.



I have been working on properties of fitness landscapes. We are trying to characterize the models that fits the best experimental fitness landscapes. We also have developped a tool to explore visually fitness landscapes, that is accessible from the Magellan webpage. In the last years, we have been working on detecting and characterizing correlated evolution using a phylogenetic approach Related softwares are Epics and Epocs.

Coalescent Theory

 I have developped tests for neutrality related to the famous Tajima's D. In an attempt to correct for sequencing errors, I built new tests that exclude singletons. I also have also develop a unifying framework that encompasses all neutrality tests based on the frequency spectrum and makes easy the creation of new ones. To compute these new tests (and the previous ones), please visit the online neutrality tests. I also did some work on the SFS decomposition and on alternative models to that generate U-shaped SFS.

Species Delineation

I worked on a method that delineate species from a genetic dataset (aligned sequences) and propose partitions into a priori species. The method was develop in collaboration with N Puilandre (MNHN), A Lambert (UPMC, UFR Maths) and S Brouillet (ABI). The Automatic Barcod Gap Discovery method (ABGD) can be used from here. A new (2021) software, ASAP is accessible from here.


 I am currently working on methods to assess very recent demography using information from linkage disiquilibrium.


Main Lectures

  • Basics in mathematics (Bachelor)
  • Bioinformatics (Master)
  • Population genetics (Bachelor and Master). French readers interested in an introductory text in coalescent theory could cast a glance coalescence.pdf.

Where and when

  • 2019-now : professor (Univ Paris-Cité).
  • 2009-2010: delegation CNRS (sabbatical at Kyoto Univ).
  • 2005-2019 : maître de conférences (UPMC / Sorbonne Université).
  • 2005         : bioinformatics engineering (Modul-Bio, Marseille).
  • 2002-2005: postdoc with John Wakeley (Harvard University).
  • 1999-2002: PhD with Eric Coissac & Pierre Netter (UPMC ; IJM).


Freund, F., Kerdoncuff, E., Matuszewski, S., Lapierre, M., Hildebrandt, M., Jensen, J. D., Ferretti, L., Lambert, A., Sackton, T. B., Achaz, G. (2022)
Interpreting the pervasive observation of u-shaped site frequency spectra
Behdenna, A., Godfroid, M., Petot, P., Pothier, J., Lambert, A., Achaz, G. (2022)
A minimal yet flexible likelihood framework to assess correlated evolution
Systematic Biology 71 823-838
Cury, J., Haller, B. C., Achaz, G., Jay, F. (2022)
Simulation of bacterial populations with slim
Peer Community Journal 2
Achaz, G., Gangloff, S., Arcangioli, B. (2022)
The quiescent x, the replicative y and the autosomes
Peer Community Journal 2
Fedosov, A., Achaz, G., Gontchar, A., Puillandre, N. (2022)
Mold, a novel software to compile accurate and reliable dna diagnoses for taxonomic descriptions
Molecular Ecology Resources
Guez, J., Achaz, G., Bienvenu, F. C., Cury, J., Toupance, B., Heyer, \., Jay, F., Austerlitz, F. (2022)
Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies and demographic inferences
Puillandre, N., Brouillet, S., Achaz, G. (2021)
Asap: assemble species by automatic partitioning
Molecular Ecology Resources 21 609-620
Van Helden, J., Butler, C. D., Achaz, G., Canard, B., Casane, D., Claverie, J., Colombo, F., Courtier, V., Ebright, R. H., Graner, F., others, . (2021)
An appeal for an objective, open, and transparent scientific debate about the origin of sars-cov-2
The Lancet 398 1402-1404
Kerdoncuff, E., Lambert, A., Achaz, G. (2020)
Testing for population decline using maximal linkage disequilibrium blocks
Theoretical Population Biology 134 171 - 181
Achaz, G., Lambert, A., Schertzer, E. (2018)
The sequential loss of allelic diversity
Advances in Applied Probability 50 13-29
Marin, J., Achaz, G., Crombach, A., Lambert, A. (2018)
The genomic view of diversification
Delaporte, C., Achaz, G., Lambert, A. (2016)
Mutational pattern of a sample from a critical branching population
Journal of Mathematical Biology 1-38
Lapierre, M., Blin, C., Lambert, A., Achaz, G., Rocha, E. P. C. (2016)
The impact of selection, gene conversion, and biased sampling on the assessment of microbial demography
Behdenna, A., Pothier, J., Abby, S. S., Lambert, A., Achaz, G. (2016)
Testing for independence between evolutionary processes
Systematic biology 65 812-823
Ferretti, L., Schmiegelt, B., Weinreich, D., Yamauchi, A., Kobayashi, Y., Tajima, F., Achaz, G. (2016)
Measuring epistasis in fitness landscapes: the correlation of fitness effects of mutations
Journal of theoretical biology 396 132-143
Regnier, C., Achaz, G., Lambert, A., Cowie, R. H., Bouchet, P., Fontaine, B. (2015)
Mass extinction in poorly known taxa
Proceedings of the National Academy of Sciences of the United States of America 112 7761-7766
Suez, M., Behdenna, A., Brouillet, S., Graça, P., Higuet, D., Achaz, G. (2015)
Micness: genotyping microsatellite loci from a collection of (ngs) reads
Molecular Ecology Resources
Brouillet, S., Annoni, H., Ferretti, L., Achaz, G. (2015)
Magellan: a tool to explore small fitness landscapes
Ledda, A., Achaz, G., Wiehe, T., Ferretti, L. (2015)
Decomposing the site frequency spectrum: the impact of tree topology on neutrality tests
arXiv preprint arXiv:1510.06748
Achaz, G., Rodriguez-Verdugo, A., Gaut, B. S., Tenaillon, O. (2014)
The reproducibility of adaptation in the light of experimental evolution with whole genome sequencing
Advances in Experimental Medicine and Biology 781 211-231
Blanquart, F., Achaz, G., Bataillon, T., Tenaillon, O. (2014)
Properties of selected mutations and genotypic landscapes under fisher’s geometric model
Evolution; international journal of organic evolution 68 3537-3554
Ishida, S., Picard, F., Rudolf, G., Noé, E., Achaz, G., Thomas, P., Genton, P., Mundwiller, E., Wolff, M., Marescaux, C., Miles, R., Baulac, M., Hirsch, E., Leguern, E., Baulac, S. (2013)
Mutations of depdc5 cause autosomal dominant focal epilepsies
Nature Genetics 45 552-555
Loire, E., Higuet, D., Netter, P., Achaz, G. (2013)
Evolution of coding microsatellites in primate genomes
Genome Biology and Evolution 5 283-295
Puillandre, N., Lambert, A., Brouillet, S., Achaz, G. (2012)
Abgd automatic barcode gap discovery for primary species delimitation
Molecular Ecology 21 1864-1877
Kobayashi, Y., Achaz, G., Telschow, A. (2011)
Effect of parasitic sex-ratio distorters on host gene frequencies in a mainland-island context
Journal of Evolutionary Biology 24 1695-1705
Kutty, G., Achaz, G., Maldarelli, F., Varma, A., Shroff, R., Becker, S., Fantoni, G., Kovacs, J. A. (2010)
Characterization of the meiosis-specific recombinase dmc1 of pneumocystis
The Journal of Infectious Diseases 202 1920-1929
Pellet, J., Tafforeau, L., Lucas-Hourani, M., Navratil, V., Meyniel, L., Achaz, G., Guironnet-Paquet, A., Aublin-Gex, A., Caignard, G., Cassonnet, P., Chaboud, A., Chantier, T., Deloire, A., Demeret, C., Le Breton, M., Neveu, G., Jacotot, L., Vaglio, P., Delmotte, S., Gautier, C., Combet, C., Deleage, G., Favre, M., Tangy, F., Jacob, Y., Andre, P., Lotteau, V., Rabourdin-Combe, C., Vidalain, P. O. (2010)
Viralorfeome: an integrated database to generate a versatile collection of viral orfs
Nucleic Acids Research 38
Loire, E., Praz, F., Higuet, D., Netter, P., Achaz, G. (2009)
Hypermutability of genes in homo sapiens due to the hosting of long mono-ssr
Molecular Biology and Evolution 26 111-121
Treangen, T. J., Darling, A. E., Achaz, G., Ragan, M. A., Messeguer, X., Rocha, E. P. C. (2009)
A novel heuristic for local multiple alignment of interspersed dna repeats
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 6 180-189
Achaz, G. (2008)
Testing for neutrality in samples with sequencing errors
Genetics 179 1409-1424
Kutty, G., Maldarelli, F., Achaz, G., Kovacs, J. A. (2008)
Variation in the major surface glycoprotein genes in pneumocystis jirovecii
The Journal of Infectious Diseases 198 741-749
Nicolas, P., Mondot, S., Achaz, G., Bouchenot, C., Bernardet, J., Duchaud, E. (2008)
Population structure of the fish-pathogenic bacterium flavobacterium psychrophilum
Applied and Environmental Microbiology 74 3702-3709
Achaz, G., Boyer, F., Rocha, E. P. C., Viari, A., Coissac, E. (2007)
Repseek, a tool to retrieve approximate repeats from large dna sequences
Bioinformatics (Oxford, England) 23 119-121
Rual, J., Klitgord, N., Achaz, G. (2007)
Novel insights into rnai off-target effects using c. elegans paralogs
BMC genomics 8