Population Genetics

Team

Prof. Dr. Laurent Excoffier

Head of the Division Population Genetics

Phone
+41 31 684 30 31
E-Mail
laurent.excoffier@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 

Year Activity
2001-  Professor of Population Genetics, University of Berne
2020-2022 Director of the Institute of Ecology and Evolution, University of Berne
2017.11 - 2018.02 Miller Visiting Professor at UC Berkeley, USA
2017.08 - 2017.11 Visiting Professor at the Institut Pasteur, Paris
2015-2018 Guest Professor, National Institute of Genetics, Mishima, Japan (annual one week visits).
2012-2014 Director of the Institute of Ecology and Evolution, University of Berne
2011.01 - 2011.07 Visiting Professor, Hospital Ste-Justine, University of Montreal, Canada
2008- Group leader at the Swiss Institute of Bioinformatics (SIB)
2007-2011 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, USA
1989-1990
Associate professor, Dept. of Biological Anthropology, Musée de l'Homme, Paris,France
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

  • Marchi N, Kapopoulou A & Excoffier L (2023) Demogenomic inference from spatially and temporally heterogeneous samples. Molecular Ecology Resources online version [Abstract and pdf]
  • Schlichta N, Moinet A, Peischl S & Excoffier L (2022) The impact of genetic surfing on neutral genomic diversity. Molecular Biology and Evolution 39: msac249 [Abstract and pdf]
  • Marchi N, Winkelbach L, Schulz I, Brami M, Hofmanova Z, Blocher J, Reyna-Blanco CS, Diekmann Y, Thiery A, Kapopoulou A, Link V & et al. (2022) The genomic origins of the world’s first farmers. Cell 185: 1842–1859 [Abstract and pdf]
  • Moinet A, Schlichta F, Peischl S & Excoffier L (2022) Strong neutral sweeps occurring during a population contraction. Genetics 220: 1-10 [Abstract and pdf]
  • Choin J, Mendoza-Revilla J, Arauna LR, Cuadros-Espinoza S, Cassar O, Larena M, Ko AM-S, Harmant C, Laurent R, Verdu P Laval G, Boland A, Olaso R, Deleuze J-F, Valentin F, Ko Y-C, Jakobsson M, Gessain A, Excoffier L, Stoneking M, Patin E & Quintana-Murci L (2021) Genomic insights into population history and biological adaptation in Oceania. Nature 592: 583–589 [Abstract and pdf]
  • Armstrong EE, Khan A, Taylor RW, Gouy A, Greenbaum G, Thiéry A, Kang JTL, Redondo SA, Prost S, Barsh G, Kaelin C, Phalke S, Chugani A, Gilbert M, Miquelle D, Zachariah A, Borthakur U, Reddy A, Louis E, Ryder OA, Jhala YV, Petrov D, Excoffier L, Hadly E & and Ramakrishnan U (2021) Recent evolutionary history of tigers highlights contrasting roles of genetic drift and selection. Molecular Biology and Evolution 38: 2366-2379 [Abstract and pdf]
  • Marchi N, Schlichta F & Excoffier L (2021) Demographic inference. Current Biology 31: R267–R281 [Abstract and pdf]
  • Marchi N & Excoffier L (2020) Gene flow as a simple cause for an excess of high‐frequency‐derived alleles Evolutionary Applications 13: 2254-2263 [Abstract and pdf]
  • Gouy A & Excoffier L (2020) Polygenic patterns of adaptive introgression in modern humans are mainly shaped by response to pathogens. Molecular Biology and Evolution 37: 1420-1433 [Abstract and pdf]
  • Gilbert KJ, Pouyet F, Excoffier L & Peischl S (2020) Transition from Background Selection to Associative Overdominance Promotes Diversity in Regions of Low Recombination. Current Biology 30: 101-107 [Abstract and pdf]
  • Kuhlwilm M, Han S, Sousa VC, Excoffier L & Marques-Bonet T (2019) Ancient admixture from an extinct ape lineage into bonobos. Nature Ecology & Evolution 3: 957–965 [Abstract and pdf]
  • Sikora M, Pitulko V, Sousa V, Allentoft ME, Vinner L, Rasmussen S, Margaryan A, de Barros Damgaard P, de la Fuente Castro C, Renaud G, Yang M & et al. (2019) The population history of northeastern Siberia since the Pleistocene. Nature 570: 182-188 [pdf]
  • Gilbert KJ, Peischl S & Excoffier L (2018) Mutation load dynamics during environmentally-driven range shifts. PLoS Genetics 14(9): e1007450 [Abstract and pdf]
  • Pouyet F*, Aeschbacher S*, Thiéry A & Excoffier L (2018) Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences. eLife 7: e36317 [Abstract and pdf]
  • Peischl S, Dupanloup I, Foucal A, Jomphe M, Bruat V, Grenier JC, Gouy A, Gilbert KJ, Gbeha E, Bosshard L, Hip-Ki E, Agbessi M, Hodgkinson A, Vezina H, Awadalla P & Excoffier L (2018) Relaxed Selection During a Recent Human Expansion. Genetics 208: 763-777 [Abstract and pdf]
  • Popadin K, Peischl S, Garieri M, Sailani MR, Letourneau A, Santoni F, Lukowski SW, Bazykin GA, Nikolaev S, Meyer D, Excoffier L, Reymond A & Antonarakis SE (2018) Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection. Genome Research 28: 1-10 [Abstract and pdf]
  • 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 358: 659-662 [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]
  • 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]
  • 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]
  • 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]
  • 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]
  • Slatkin M & Excoffier L (2012) Serial Founder Effects During Range Expansion: A Spatial Analog of Genetic Drift. Genetics 191: 171-181 [Abstract and pdf]
  • Alves I, Sramkova Hanulova A, Foll M & Excoffier L (2012) Genomic data reveals a complex making of humans. PLoS Genetics 8: e1002837 [Abstract and pdf]
  • Arenas M, Ray N, Currat M & Excoffier L (2012) Consequences of Range Contractions and Range Shifts on Molecular Diversity. Molecular Biology and Evolution 29: 207-218 [Abstract and pdf]
  • Moreau C, Bherer C, Vezina H, Jomphe M, Labuda D & Excoffier L (2011) Deep Human Genealogies Reveal a Selective Advantage to Be on an Expanding Wave Front. Science 334: 1148-1150 [Abstract and pdf]
  • Peter BM, Wegmann D & Excoffier L (2010) Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure. Molecular Ecology 19: 4648-4660 [Abstract and pdf]
  • Wegmann D & Excoffier L (2010) Bayesian Inference of the Demographic History of Chimpanzees. Molecular Biology and Evolution 27: 1425-35 [Abstract]
  • Wegmann D, Leuenberger C , Neuenschwander S & Excoffier L (2010) ABCtoolbox: a versatile toolkit for approximate Bayesian computations. BMC Bioinformatics 11: 116 [Abstract and pdf]
  • Excoffier L & Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10: 564-567 [Abstract and pdf]
  • Beaumont MA, Nielsen R, Robert C, Hey J, Gaggiotti O, Knowles L, Estoup A, Panchal M, Corander J, Hickerson M, Sisson SA, Fagundes N, Chikhi L, Beerli P, Vitalis R, Cornuet JM, Huelsenbeck J, Foll M, Yang Z, Rousset F, Balding D & Excoffier L (2010) In defence of model-based inference in phylogeography. Molecular Ecology 19: 436-446 [Abstract]
  • Wegmann D, Leuenberger C & Excoffier L (2009) Efficient Approximate Bayesian Computation Coupled With Markov Chain Monte Carlo Without Likelihood. Genetics 182: 1207-1218 [Abstract and pdf]
  • Excoffier L, Foll M & Petit RJ (2009) Genetic Consequences of Range Expansions. Annual Review in Ecology, Evolution, and Systematics 40: 481-501 [Abstract and pdf]
  • Excoffier L & Ray N (2008) Surfing during population expansions promotes genetic revolutions and structuration. Trends in Ecology and Evolution 23(7): 347-351 [Abstract and pdf]
  • Fagundes N J R, Ray N, Beaumont M, Neuenschwander S, Salzano F M, Bonatto S L & Excoffier L (2007) Statistical evaluation of alternative models of human evolution. Proceedings of the National Academy of Sciences USA 104: 17614-17619 [Abstract]
  • Excoffier L & Heckel G (2006) Computer programs for population genetics data analysis: a survival guide. Nature Reviews Genetics 7: 745-758 [Abstract]
  • Currat M, Excoffier L, Maddison W, Otto SP, Ray N, Whitlock MC & Yeaman S (2006) Comment on 'Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens' and 'Microcephalin, a Gene Regulating Brain Size, Continues to Evolve Adaptively in Humans'. Science 313(5784): 172 [pdf]
  • Ray N, Currat M, Berthier P & Excoffier L (2005) Recovering the geographic origin of early modern humans by realistic and spatially explicit simulations. Genome Research 15(8): 1161-7 [Abstract and pdf]
  • Hamilton G, Stoneking M & Excoffier L (2005) Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populations. Proc. Natl. Acad. Sci. USA 102(21): 7476-80 [Abstract and pdf]
  • Excoffier L (2004) Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model. Molecular Ecology 13(4): 853-64 [Abstract and pdf]
  • Currat M & Excoffier L (2004) Modern humans did not admix with Neanderthals during their range expansion into Europe. PLoS Biology 2(12): 2264-2274 [Abstract and pdf]
  • Excoffier L & Hamilton G (2003) Comment on 'Genetic Structure of Human Populations'. Science 300(5627): 1877b- [pdf]
  • Excoffier L (2003) Human diversity: our genes tell where we live. Current Biology 13(4): R134-6 [Abstract and pdf]
  • Cann H M, de Toma C, Cazes L, Legrand M-F, Morel V, Piouffre L, Bodmer J, Bodmer W F, Bonne-Tamir B, Cambon-Thomsen A, Chen Z & et al. (2002) A Human Genome Diversity Cell Line Panel. Science 296(5566): 261b-262 [Abstract and pdf]
  • Luikart G, Gielly L, Excoffier L, Vigne J D, Bouvet J & Taberlet P (2001) Multiple maternal origins and weak phylogeographic structure in domestic goats. Proc. Natl. Acad. Sci. USA 98(10): 5927-5932
  • Excoffier L & Schneider S (1999) Why hunter-gatherer populations do not show sign of Pleistocene demographic expansions. Proc. Natl. Acad. Sci. USA 96: 10597-10602
  • Aris-Brosou S & Excoffier L (1996) The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism. Mol. Biol. Evol. 13(3): 494-504
  • Excoffier L & Slatkin M (1995) Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol. Biol. Evol. 12(5): 921-927
  • Excoffier L, Smouse P & Quattro J (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 131: 479-491

Full list of publications