Prof. Dr. Laurent Excoffier

Head of the Population Genetics division

Phone
+41 31 631 30 31
E-Mail
laurent.excoffier@iee.unibe.ch
Office
D303
Postal Address
Institute of Ecology and Evolution
University of Bern
Baltzerstrasse 6
CH-3012 Bern

Research interests

I am interested in the development of computational methods to understand evolutionary processes at the population and species level, for instance to study how past climatic and environmental changes have influenced the pattern of genetic diversity of a given species, or to detect evidence of local adaptations from genomic information.

I have been recently studying the effect of complex demography on the molecular genetic diversity of a species, for instance such as after a spatial expansion in a heterogeneous environment. I am therefore investigating how various aspects of a species genetic diversity are influenced by historical and spatial constraints, and how these effects contrast with those of selection. We are thus aiming at designing better tests of selective neutrality, taking into account the potentially complex demographic history of a species.

With Stephan Peischl, we have been recently investigating the effect of spatial range expansion on non-neutral (functional) diversity, evidencing the buildup of a mutation load due to inefficient purifying selection on wave fronts. We are testing these theoretical predictions by studying the genomic diversity of populations having gone through recent range expansions like humans and bacteria. 

I am also involved in the development of statistical methods, which rely on massive computer simulations, to reconstruct the past demography of a species from its genetic diversity, and to test among various alternative evolutionary scenarios. I have recently switched focus from Approximate Bayesian Computations (ABC) methods to composite-likelihood methods based on the Site Frequency Spectrum (SFS)  to make inference from genomic data. I have specifically developed the fastsimcoal2 software package to both simulate genomic data and perform demographic inference. These developments are mainly applied to the reconstruction of past human history, using current and ancient genomic data, but it could be applied to any other species.

I am finally still devoting quite some time to the maintenance and extension of various computer programs listed here, including the popular program Arlequin for the analysis of population genetics data.

Curriculum vitae

Publication list on ORCID ID: orcid.org/0000-0002-7507-6494

Publication list on ResearcherID: http://www.researcherid.com/rid/D-3498-2013 

2001- Professor of Population Genetics, University of Berne
2015-2018
Guest Professor, National Institute of Genetics, Mishima, Japan
2012-2014 Director of the Institute of Ecology and Evolution, University of Berne
2011 Visiting Professor, Hospital Ste-Justine, University of Montreal, Canada
2008- Group leader at the Swiss Institute of Bioinformatics (SIB)
2007- Guest Professor, Center for Computational and Evolutionary Biology, Chinese Academy of Sciences, Beijing, China
2006-2008  Head of Biology Department, University of Berne
1995-2001 Maître d'Enseignement et de Recherche, Dept.of Anthropology, University of Geneva
1991-1995 Maître assistant, Dept. of Anthropology, University of Geneva
1990-1991
Post-doc, Center for Theoretical and Applied Genetics, Rutgers University
1989-1990
Associate professor, Dept. of Biological Anthropology, Musée de l'Homme, Paris
1988-1989
Assistant, Dept.of Anthropology, University of Geneva
1983-1988
Ph.D. studies, Dept.of Anthropology, University of Geneva
1985-1986 Certificate in Numerical Computing, University of Geneva
1979-1983
Biology undergraduate studies, University of Geneva

Selected publications

Journal articles

  • Sikora Martin, Seguin-Orlando Andaine, Sousa Vitor C, Albrechtsen Anders, Korneliussen Thorfinn, Ko Amy, Rasmussen Simon, Dupanloup Isabelle, Nigst Philip R, Bosch Marjolein D, Renaud Gabriel, Allentoft Morten E, Margaryan Ashot, Vasilyev Sergey V, Veselovskaya Elizaveta V, Borutskaya Svetlana B, Deviese Thibaut, Comeskey Dan, Higham Tom, Manica Andrea, Foley Robert, Meltzer David J, Nielsen Rasmus, Excoffier Laurent, Lahr Marta Mirazon, Orlando Ludovic & Willerslev Eske (2017) Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science early online publication [Abstract and pdf]
  • Bosshard L, Dupanloup I, Tenaillon O, Bruggmann R, Ackermann M, Peischl S & Excoffier L (2017) Accumulation of deleterious mutations during bacterial range expansions. Genetics 207: 669-684 [Abstract and pdf]
  • Gouy A, Daub JT & Excoffier L (2017) Detecting gene subnetworks under selection in biological pathways. Nucleic Acids Research 45(16): e149 [Abstract and pdf]
  • Meier JI, Marques DA, Mwaiko S, Wagner CE, Excoffier L & Seehausen O (2017) Ancient hybridization fuels rapid cichlid fish adaptive radiations Nature Communications 8: 14363 [Abstract and pdf]
  • de Manuel M, Kuhlwilm M, Frandsen P, Sousa VC, Desai T, Prado-Martinez J, Hernandez-Rodriguez J, Dupanloup I, Lao O, Hallast P, Schmidt JM & et al. (2016) Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science 354: 477-481 [Abstract and pdf]
  • Malaspinas AS, Westaway MC, Muller C, Sousa VC, Lao O, Alves I, Bergstrom A, Athanasiadis G, Cheng JY, Crawford JE, Heupink TH & et al. (2016) A genomic history of Aboriginal Australia. Nature 538: 207-214 [Abstract and pdf]
  • Peischl S, Dupanloup I, Bosshard L & Excoffier L (2016) Genetic surfing in human populations: from genes to genomes. Current Opinion in Genetics and Development 41: 53-61 [Abstract and pdf]
  • Foote AD, Vijay N, Ávila-Arcos MC, Baird RW, Durban JW, Fumagalli M, Gibbs RA, Bradley Hanson M, Korneliussen TS, Martin MD, Robertson KM, Sousa VC, Vieira FG, Vinař T, Wade P, Worley KC, Excoffier L, Morin PA, Gilbert MTP & Wolf JBW (2016) Genome-culture coevolution promotes rapid divergence of killer whale ecotypes. Nature Communications 7: 11693 [Abstract and pdf]
  • Henn BM, Botigue LR, Peischl S , Dupanloup I, Lipatov M , Maples BK , Martin AR , Musharoff S, Cann H , Snyder M , Excoffier L , Kidd JM & Bustamante CD (2016) Distance from Sub-Saharan Africa Predicts Mutational Load in Diverse Human Genomes. PNAS 113: E440-9 [Abstract and pdf]
  • Alves I, Arenas M, Currat M, Sramkova Hanulova A, Sousa VC, Ray N & Excoffier L (2016) Long distance dispersal shaped patterns of human genetic diversity in Eurasia. Molecular Biology and Evolution 33: 946–958 [Abstract and pdf]
  • Marques DA , Lucek K, Meier JI Mwaiko S Wagner CE , Excoffier L & Seehausen O (2016) Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback. PLoS Genetics 12: e1005887 [Abstract and pdf]
  • Daub JT, Dupanloup I Robinson-Rechavi M & Excoffier L (2015) Inference of evolutionary forces acting on human biological pathways. Genome Biology and Evolution 7: 1546–1558 [Abstract and pdf]
  • Peischl S & Excoffier L (2015) Expansion load: recessive mutations and the role of standing genetic variation. Molecular Ecology 24: 2084-2094 [Abstract and pdf]
  • Peischl S, Kirkpatrick M & Excoffier L (2015) Expansion load and the evolutionary dynamics of a species range. American Naturalist 185: E81-E93 [Abstract and pdf]
  • Schubert M, Jonsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A, Albrechtsen A, Dupanloup I, Foucal A, Petersen B, Fumagalli M & et al. (2014) Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proceedings of the National Academy of Sciences, USA 111(52): E5661-9
  • Perry GH, Foll M, Grenier JC, Patin E, Nedelec Y, Pacis A, Barakatt M, Gravel S, Xiang Zhou, Nsobya S, Excoffier L, Quintana-Murci L, Dominy NJ & Barreiro LB (2014) Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers. Proceedings of the National Academy of Sciences, USA 111: E3596-3603 [Abstract and pdf]
  • Foll M, Gaggiotti O, Daub JT, Vatsiou A & Excoffier L (2014) Widespread Signals of Convergent Adaptation to High Altitude in Asia and America. American Journal of Human Genetics 95: 394–407 [Abstract and pdf]
  • Sousa V , Peischl S & Excoffier L (2014) Impact of range expansions on current human genomic diversity. Current Opinion in Genetics and Development 29: 22-30 [Abstract]
  • Excoffier L, Dupanloup I, Huerta-Sanchez E, Sousa VC & Foll M (2013) Robust demographic inference from genomic and SNP data. PLOS Genetics 9: e1003905 [Abstract and pdf]
  • Peischl S, Dupanloup I, Kirkpatrick M & Excoffier L (2013) On the accumulation of deleterious mutations during range expansions. Molecular Ecology 22: 5972-5982 [Abstract and pdf]
  • Daub JT, Hofer T, Cutivet E, Dupanloup I, Quintana-Murci L, Robinson-Rechavi M & Excoffier L (2013) Evidence for Polygenic Adaptation to Pathogens in the Human Genome Molecular Biology And Evolution 30 (7): 1544-1558 [Abstract]
  • Arenas M, Francois O, Currat M, Ray N & Excoffier L (2013) Influence of Admixture and Paleolithic Range Contractions on Current European Diversity Gradients. Molecular Biology and Evolution 30: 57-61 [Abstract and pdf]