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Botigué, Laura R.; Henn, Brenna M.; Peischl, Stephan; Dupanloup, Isabelle; Lipatov, Mikhail; Maples, Brian K.; Martin, Alicia R.; Yee, M.C.; Cann, Howard; Snyder, Michael P.; Excoffier, Laurent; Kidd, Jeffrey M.; Bustamante, Carlos D. (2015). The Out of Africa expansion affected accumulation of deleterious alleles in human genomes. American Journal of Physical Anthropology, 156(S60), pp. 90-91. Wiley
Excoffier, Laurent (2006). Neandertal genetic diversity: A fresh look from old samples. Current Biology, 16(16), R650-R652. Cambridge, Mass.: Cell Press 10.1016/j.cub.2006.07.035
Oliveira, Sandra; Marchi, Nina; Excoffier, Laurent (2024). Assessing the limits of local ancestry inference from small reference panels. Molecular ecology resources, 24(6), e13981. Wiley 10.1111/1755-0998.13981
Marchi, Nina; Kapopoulou, Adamantia; Excoffier, Laurent (2024). Demogenomic inference from spatially and temporally heterogeneous samples. Molecular ecology resources, 24(1), pp. 1-11. Wiley 10.1111/1755-0998.13877
Meier, Joana; McGee, Matthew D; Marques, David A; Mwaiko, Salome; Kishe, Mary; Wandera, Sylvester; Neumann, Dirk; Mrosso, Hilary; Chapman, Lauren J; Chapman, Colin A; Kaufman, Les; Taabu-Munyaho, Anthony; Wagner, Catherine E; Bruggmann, Rémy; Excoffier, Laurent; Seehausen, Ole (2023). Cycles of fusion and fission enabled rapid parallel adaptive radiations in African cichlids. Science, 381(6665), eade2833. American Association for the Advancement of Science 10.1126/science.ade2833
Schlichta, Flávia; Peischl, Stephan; Excoffier, Laurent (2022). The impact of genetic surfing on neutral genomic diversity. Molecular Biology and Evolution, 39(11) Oxford University Press 10.1093/molbev/msac249
Johri, Parul; Aquadro, Charles F.; Beaumont, Mark; Charlesworth, Brian; Excoffier, Laurent; Eyre-Walker, Adam; Keightley, Peter D.; Lynch, Michael; McVean, Gil; Payseur, Bret A.; Pfeifer, Susanne P.; Stephan, Wolfgang; Jensen, Jeffrey D. (2022). Recommendations for improving statistical inference in population genomics. PLoS biology, 20(5), pp. 1-23. Public Library of Science 10.1371/journal.pbio.3001669
Moinet, Antoine; Schlichta, Flavia; Peischl, Stephan; Excoffier, Laurent (2022). Strong neutral sweeps occurring during a population contraction. Genetics, 220(4) Oxford University Press 10.1093/genetics/iyac021
Marchi, Nina; Winkelbach, Laura; Schulz, Ilektra; Brami, Maxime; Hofmanová, Zuzana; Blöcher, Jens; Reyna-Blanco, Carlos S.; Diekmann, Yoan; Thiéry, Alexandre; Kapopoulou, Adamandia; Link, Vivian; Piuz, Valérie; Kreutzer, Susanne; Figarska, Sylwia M.; Ganiatsou, Elissavet; Pukaj, Albert; Struck, Travis J.; Gutenkunst, Ryan N.; Karul, Necmi; Gerritsen, Fokke; ... (2022). The genomic origins of the world’s first farmers. Cell, 185(11), 1842-1859.e18. Cell Press 10.1016/j.cell.2022.04.008
Moinet, Antoine; Peischl, Stephan; Excoffier, Laurent (25 August 2021). Strong neutral sweeps occurring during a population contraction (bioRxiv). Cold Spring Harbor Laboratory 10.1101/2021.08.25.457712
Foote, Andrew D.; Gilbert, M. Thomas P.; Gopalakrishnan, Shyam; Louis, Marie; Martin, Michael D.; Morin, Phillip A.; Nykänen, Milaja; Scharff-Olsen, Camilla Hjorth; Excoffier, Laurent (21 August 2021). Evidence of long-term purging of mutation load in killer whale genomes (bioRxiv). Cold Spring Harbor Laboratory 10.1101/2021.08.21.457186
Foote, Andrew D.; Hooper, Rebecca; Alexander, Alana; Baird, Robin W.; Baker, Charles Scott; Ballance, Lisa; Barlow, Jay; Brownlow, Andrew; Collins, Tim; Constantine, Rochelle; Dalla Rosa, Luciano; Davison, Nicholas J.; Durban, John W.; Esteban, Ruth; Excoffier, Laurent; Fordyce Martin, Sarah L.; Forney, Karin A.; Gerrodette, Tim; Gilbert, M. Thomas P.; Guinet, Christophe; ... (2021). Runs of homozygosity in killer whale genomes provide a global record of demographic histories. Molecular Ecology, 30(23), pp. 6162-6177. Wiley-Blackwell 10.1111/mec.16137
Currat, Mathias; Quilodrán, Claudio S.; Excoffier, Laurent (2021). Simulations of Human Dispersal and Genetic Diversity. In: Saitou, Naruya (ed.) Evolution of the Human Genome II. Evolutionary Studies (pp. 231-256). Tokyo: Springer Nature 10.1007/978-4-431-56904-6_12
Yilmaz, Bahtiyar; Mooser, Catherine; Keller, Irene; Li, Hai; Zimmermann, Jakob; Bosshard, Lars; Fuhrer, Tobias; Gomez de Agüero, Mercedes; Fernandez Trigo, Nerea; Tschanz-Lischer, Heidi; Limenitakis, Julien P.; Hardt, Wolf-Dietrich; McCoy, Kathleen; Stecher, Bärbel; Excoffier, Laurent; Sauer, Uwe; Ganal-Vonarburg, Stephanie C.; Macpherson, Andrew J. (2021). Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice. Cell host & microbe, 29(4), 650-663.e9. Cell Press 10.1016/j.chom.2021.02.001
Choin, Jeremy; Mendoza-Revilla, Javier; Arauna, Lara R.; Cuadros-Espinoza, Sebastian; Cassar, Olivier; Larena, Maximilian; Min-Shan Ko, Albert; Harmant, Christine; Laurent, Romain; Verdu, Paul; Laval, Guillaume; Boland, Anne; Olaso, Robert; Deleuze, Jean-François; Valentin, Frédérique; Ko, Ying-Chin; Jakobsson, Mattias; Gessain, Antoine; Excoffier, Laurent; Stoneking, Mark; ... (2021). Genomic insights into population history and biological adaptation in Oceania. Nature, 592(7855), pp. 583-589. Springer Nature 10.1038/s41586-021-03236-5
Marchi, Nina; Schlichta, Flávia; Excoffier, Laurent (2021). Demographic inference. Current Biology, 31(6), R276-R279. Cell Press 10.1016/j.cub.2021.01.053
Armstrong, Ellie E.; Khan, Anubhab; Taylor, Ryan W.; Gouy, Alexandre; Greenbaum, Gili; Thiéry, Alexandre; Kang, Jonathan T.; Redondo, Sergio A.; Prost, Stefan; Barsh, Gregory; Kaelin, Christopher; Phalke, Sameer; Chugani, Anup; Gilbert, Martin; Miquelle, Dale; Zachariah, Arun; Borthakur, Udayan; Reddy, Anuradha; Louis, Edward; Ryder, Oliver A.; ... (2021). Recent Evolutionary History of Tigers Highlights Contrasting Roles of Genetic Drift and Selection. Molecular Biology and Evolution, 38(6), pp. 2366-2379. Oxford University Press 10.1093/molbev/msab032
Johri, Parul; Riall, Kellen; Becher, Hannes; Excoffier, Laurent; Charlesworth, Brian; Jensen, Jeffrey D. (2021). The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects. Molecular Biology and Evolution, 38(7), pp. 2986-3003. Oxford University Press 10.1093/molbev/msab050
Marques, David A.; Lucek, Kay; Sousa, Vitor C.; Excoffier, Laurent; Seehausen, Ole (2021). Reply to "Re-evaluating the evidence for facilitation of stickleback speciation by admixture in the Lake Constance basin". Nature Communications, 12(1), p. 2807. Springer Nature 10.1038/s41467-021-23096-x
Excoffier, Laurent; Marchi, Nina; Marques, David Alexander; Matthey-Doret, Remi; Gouy, Alexandre; Sousa, Vitor C. (2021). fastsimcoal2 : demographic inference under complex evolutionary scenarios. Bioinformatics, 37(24), pp. 4882-4885. Oxford University Press 10.1093/bioinformatics/btab468
Marchi, Nina; Excoffier, Laurent (2020). Gene flow as a simple cause for an excess of high-frequency-derived alleles. Evolutionary applications, 13(9), pp. 2254-2263. Wiley 10.1111/eva.12998
Bosshard, Lars; Peischl, Stephan; Ackermann, Martin; Excoffier, Laurent (2020). Dissection of the mutation accumulation process during bacterial range expansions. BMC Genomics, 21(1) BioMed Central 10.1186/s12864-020-6676-z
Gouy, Alexandre; Excoffier, Laurent (2020). Polygenic Patterns of Adaptive Introgression in Modern Humans Are Mainly Shaped by Response to Pathogens. Molecular Biology and Evolution, 37(5), pp. 1420-1433. Oxford University Press 10.1093/molbev/msz306
Gilbert, Kimberly J.; Pouyet, Fanny; Excoffier, Laurent; Peischl, Stephan (2020). Transition from Background Selection to Associative Overdominance Promotes Diversity in Regions of Low Recombination. Current Biology, 30(1), pp. 101-107. Cell Press 10.1016/j.cub.2019.11.063
Mc Gee, Matthew D.; Borstein, Samuel R.; Meier, Joana I.; Marques, David A.; Mwaiko, Salome; Taabu, Anthony; Kishe, Mary A.; O’Meara, Brian; Bruggmann, Rémy; Excoffier, Laurent; Seehausen, Ole (2020). The ecological and genomic basis of explosive adaptive radiation. Nature, 586(7827), pp. 75-79. Springer Nature 10.1038/s41586-020-2652-7
Bosshard, Lars; Peischl, Stephan; Ackermann, Martin; Excoffier, Laurent (2019). Mutational and Selective Processes Involved in Evolution during Bacterial Range Expansions. Molecular Biology and Evolution, 36(10), pp. 2313-2327. Oxford University Press 10.1093/molbev/msz148
Sikora, Martin; Pitulko, Vladimir V.; Sousa, Vitor C.; Allentoft, Morten E.; Vinner, Lasse; Rasmussen, Simon; Margaryan, Ashot; de Barros Damgaard, Peter; de la Fuente, Constanza; Renaud, Gabriel; Yang, Melinda A.; Fu, Qiaomei; Dupanloup, Isabelle; Giampoudakis, Konstantinos; Nogués-Bravo, David; Rahbek, Carsten; Kroonen, Guus; Peyrot, Michaël; McColl, Hugh; Vasilyev, Sergey V.; ... (2019). The population history of northeastern Siberia since the Pleistocene. Nature, 570, pp. 182-188. Macmillan Journals Ltd. https://doi.org/10.1038/s41586-019-1279-z
Kuhlwilm, Martin; Han, Sojung; Sousa, Vitor C.; Excoffier, Laurent; Marques-Bonet, Tomas (2019). Ancient admixture from an extinct ape lineage into bonobos. Nature ecology & evolution, 3(6), pp. 957-965. Springer Nature 10.1038/s41559-019-0881-7
Currat, Mathias; Arenas, Miguel; Quilodràn, Claudio S.; Excoffier, Laurent; Ray, Nicolas (2019). SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal. Bioinformatics, 35(21), pp. 4480-4483. Oxford University Press 10.1093/bioinformatics/btz311
Foote, Andrew D.; Martin, Michael D.; Louis, Marie; Pacheco, George; Robertson, Kelly M.; Sinding, Mikkel-Holger S.; Amaral, Ana R.; Baird, Robin W.; Baker, Charles Scott; Ballance, Lisa; Barlow, Jay; Brownlow, Andrew; Collins, Tim; Constantine, Rochelle; Dabin, Willy; Dalla Rosa, Luciano; Davison, Nicholas J.; Durban, John W.; Esteban, Ruth; Ferguson, Steven H.; ... (2019). Killer whale genomes reveal a complex history of recurrent admixture and vicariance. Molecular Ecology, 28(14), pp. 3427-3444. Wiley-Blackwell 10.1111/mec.15099
Marques, David A.; Lucek, Kay; Sousa, Vitor; Excoffier, Laurent; Seehausen, Ole (2019). Admixture between old lineages facilitated contemporary ecological speciation in Lake Constance stickleback. Nature communications, 10(1) Nature Publishing Group 10.1038/s41467-019-12182-w
Gilbert, Kimberly J.; Peischl, Stephan; Excoffier, Laurent (2018). Mutation load dynamics during environmentally-driven range shifts. PLoS genetics, 14(9), pp. 1-18. Public Library of Science 10.1371/journal.pgen.1007450
Pouyet, Fanny; Aeschbacher, Simon; Thiéry, Alexandre Benoit Xavier; Excoffier, Laurent (2018). Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences. eLife, 7, pp. 1-21. eLife Sciences Publications 10.7554/eLife.36317
Pfeifer, Susanne P.; Laurent, Stefan; Martins Conde e Sousa, Vitor; Linnen, Catherine R.; Foll, Matthieu; Excoffier, Laurent; Hoekstra, Hopi E.; Jensen, Jeffrey D. (2018). The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene Flow. Molecular Biology and Evolution, 35(4), pp. 792-806. Oxford University Press 10.1093/molbev/msy004
Meier, Joana; Marques, David Alexander; Wagner, Catherine Elise; Excoffier, Laurent; Seehausen, Ole (2018). Genomics of Parallel Ecological Speciation in Lake Victoria Cichlids. Molecular Biology and Evolution, 35(6), pp. 1489-1506. Oxford University Press 10.1093/molbev/msy051
Popadin, Konstantin; Peischl, Stephan; Garieri, Marco; Sailani, M. Reza; Letourneau, Audrey; Santoni, Federico; Lukowski, Samuel W.; Bazykin, Georgii A.; Nikolaev, Sergey; Meyer, Diogo; Excoffier, Laurent; Reymond, Alexandre; Antonarakis, Stylianos E. (2018). Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection. Genome research, 28(1), pp. 1-10. Cold Spring Harbor, N.Y 10.1101/gr.228411.117
Sikora, Martin; Seguin-Orlando, Andaine; Martins Conde e Sousa, Vitor; 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; ... (2017). Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science, 358(6363), pp. 659-662. American Association for the Advancement of Science 10.1126/science.aao1807
Bosshard, Lars; Dupanloup, Isabelle; Tenaillon, Olivier; Bruggmann, Rémy; Ackermann, Martin; Peischl, Stephan; Excoffier, Laurent (2017). Accumulation of Deleterious Mutations During Bacterial Range Expansions. Genetics, 207(2), pp. 669-684. Genetics Society of America 10.1534/genetics.117.300144
Daub, Joséphine; Moretti, S.; Davydov, I.I.; Excoffier, Laurent; Robinson-Rechavi, M. (2017). Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans. Molecular Biology and Evolution, 34(6), pp. 1391-1402. Oxford University Press 10.1093/molbev/msx083
Meier, Joana; Marques, David Alexander; Mwaiko, Salome; Wagner, Catherine; Excoffier, Laurent; Seehausen, Ole (2017). Ancient hybridization fuels rapid cichlid fish adaptive radiations. Nature communications, 8(14363), p. 14363. Nature Publishing Group 10.1038/ncomms14363
Gouy, Alexandre; Daub, Joséphine T.; Excoffier, Laurent (2017). Detecting gene subnetworks under selection in biological pathways. Nucleic acids research, 45(16), e149. Information Retrieval Ltd. 10.1093/nar/gkx626
Peischl, Stephan; Excoffier, Laurent (2017). EXPANSION LOAD. In: Invasion Genetics: the Bakker and Stebbins legacy (pp. 218-231). Wiley 10.1002/9781119072799.ch13
Amorim, CEG; Hofer, T; Ray, N; Foll, M; Ruiz-Linares, A; Excoffier, Laurent (2017). Long-distance dispersal suppresses introgression of local alleles during range expansions. Heredity, 118(2), pp. 135-142. Oliver and Boyd 10.1038/hdy.2016.68
de Manuel, Marc; Kuhlwilm, Martin; Frandsen, Peter; Martins Conde e Sousa, Vitor; Desai, Tariq; Prado-Martinez, Javier; Hernandez-Rodriguez, Jessica; Duperret, Isabelle; Lao, Oscar; Hallast, Pille; Schmidt, Joshua M.; Herdia-Genestar, José María; Benazzo, Andrea; Barbujani, Guido; Peter, Benjamin M.; Kuderna, Lukas F. K.; Casals, Ferran; Angedakin, Samuel; Arandjelovic, Mimi; Boesch, Christophe; ... (2016). Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science, 354(6311), pp. 477-481. American Association for the Advancement of Science 10.1126/science.aag2602
Foote, Andrew David; Vijay, Nagarjun; Ávila-Arcos, María C.; Baird, Robin W.; Durban, John W.; Fumagalli, Matteo; Gibbs, Richard A.; Hanson, M. Bradley; Korneliussen, Thorfinn S.; Martin, Michael D.; Robertson, Kelly M.; Martins Conde e Sousa, Vitor; Vieira, Filipe G.; Vinar, Tomás; Wade, Paul; Worley, Kim C.; Excoffier, Laurent; Morin, Phillip A.; Gilbert, M. Thomas P. and Wolf, Jochen B.W. (2016). Genome-culture coevolution promotes rapid divergence of killer whale ecotypes. Nature communications, 7(7), p. 11693. Nature Publishing Group 10.1038/ncomms11693
Alves, Isabel; Arenas Busto, Miguel; Currat, Mathias; Sramkova Hanulova, Anna; Martins Conde e Sousa, Vitor; Ray, Nicolas; Excoffier, Laurent (2016). Long distance dispersal shaped patterns of human genetic diversity in Eurasia. Molecular Biology and Evolution, 33(4), pp. 946-958. Oxford University Press 10.1093/molbev/msv332
Marques, David Alexander; Lucek, Kay Jurka Olaf; Meier, Joana; Mwaiko, Salome; Wagner, Catherine; Excoffier, Laurent; Seehausen, Ole (2016). Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback. PLoS genetics, 12(2), e1005887. Public Library of Science 10.1371/journal.pgen.1005887
Henn, Brenna M.; Botigué, Laura R.; Peischl, Stephan; Duperret, Isabelle; Lipatov, Mikhail; Maples, Brian K.; Martin, Alicia R.; Musharoff, Shaila; Cann, Howard; Snyder, Michael P.; Excoffier, Laurent; Kidd, Jeffrey M.; Bustamante, Carlos D. (2016). Distance from Sub-Saharan Africa Predicts Mutational Load in Diverse Human Genomes. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 113(4), E440-E449. National Academy of Sciences NAS 10.1073/pnas.1510805112
Marques, David Alexander; Lucek, Kay Jurka Olaf; Häsler, Marcel; Feller, Anna Fiona; Meier, Joana; Wagner, Catherine; Excoffier, Laurent; Seehausen, Ole (2016). Genomic landscape of early ecological speciation initiated by selection on nuptial colour. Molecular Ecology, 26(1), pp. 7-24. Wiley-Blackwell 10.1111/mec.13774
Meier, Joana; Martins Conde e Sousa, Vitor; Marques, David Alexander; Selz, Oliver; Wagner, Catherine; Excoffier, Laurent; Seehausen, Ole (2016). Demographic modeling with whole genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization. Molecular Ecology, 26(1), pp. 123-141. Wiley-Blackwell 10.1111/mec.13838
Peischl, Stephan; Dupanloup, Isabelle; Bosshard, Lars; Excoffier, Laurent (2016). Genetic surfing in human populations: from genes to genomes. Current opinion in genetics & development, 41, pp. 53-61. Elsevier 10.1016/j.gde.2016.08.003
Peischl, Stephan; Excoffier, Laurent (2015). Expansion load: recessive mutations and the role of standing genetic variation. Molecular Ecology, 24(9), pp. 2084-2094. Wiley-Blackwell 10.1111/mec.13154
Peischl, Stephan; Kirkpatrick, Mark; Excoffier, Laurent (2015). Expansion Load and the Evolutionary Dynamics of a Species Range. The American naturalist, 185(4), E81-E93. University of Chicago Press 10.1086/680220
Amorim, Carlos Eduardo G.; Daub, Joséphine; Salzano, Francisco M.; Foll, Matthieu; Excoffier, Laurent (2015). Detection of convergent genome-wide signals of adaptation to tropical forests in humans. PLoS ONE, 10(4), pp. 1-19. Public Library of Science 10.1371/journal.pone.0121557
Daub, Joséphine; Duperret, Isabelle; Robinson-Rechavi, Marc; Excoffier, Laurent (2015). Inference of evolutionary forces acting on human biological pathways. Genome biology and evolution, 7(6), pp. 1546-1558. Oxford University Press 10.1093/gbe/evv083
Martins Conde e Sousa, Vitor; Peischl, Stephan; Excoffier, Laurent (2014). Impact of range expansions on current human genomic diversity. Current opinion in genetics & development, 29, pp. 22-30. Elsevier 10.1016/j.gde.2014.07.007
Fischer, Martin; Foll, Matthieu; Heckel, Gerald; Excoffier, Laurent (2014). Continental-Scale Footprint of Balancing and Positive Selection in a Small Rodent (Microtus arvalis). PLoS ONE, 9(11), e112332. Public Library of Science
Foll, Matthieu; Gaggiotti, Oscar; Daub, Joséphine; Vatsiou, Alexandra; Excoffier, Laurent (2014). Widespread Signals of Convergent Adaptation to High Altitude in Asia and America. American journal of human genetics, 95(4), pp. 394-407. Cell Press 10.1016/j.ajhg.2014.09.002
Lischer, Heidi; Excoffier, Laurent; Heckel, Gerald (2014). Ignoring heterozygous sites biases phylogenomic estimates of divergence times: implications for the evolutionary history of Microtus voles. Molecular Biology and Evolution, 31(4), pp. 817-831. Oxford University Press 10.1093/molbev/mst271
Mona, Stefano; Ray, Nicolas; Arenas Busto, Miguel; Excoffier, Laurent (2014). Genetic consequences of habitat fragmentation during a range expansion. Heredity, 112(3), pp. 291-299. Oliver and Boyd 10.1038/hdy.2013.105
Perry, George H.; Foll, Matthieu; Grenier, Jean-Christophe; Patin, Etienne; Nédélec, Yohann; Pacis, Alain; Barakatt, Maxime; Gravel, Simon; Zhou, Xiang; Nsobya, Sam L.; Excoffier, Laurent; Quintana-Murci, Lluis; Dominy, Nathaniel J.; Barreiro, Luis B. (2014). Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 111(35), E3596-E3603. National Academy of Sciences NAS 10.1073/pnas.1402875111
Schubert, Mikkel; Jónsson, Hákon; Chang, Dan; Der Sarkissian, Clio; Ermini, Luca; Ginolhac, Aurélien; Albrechtsen, Anders; Dupanloup, Isabelle; Foucal, Adrien; Petersen, Bent; Fumagalli, Matteo; Raghavan, Maanasa; Seguin-Orlando, Andaine; Korneliussen, Thorfinn S.; Velazquez, Amhed M. V.; Stenderup, Jesper; Hoover, Cindi A.; Rubin, Carl-Johan; Alfarhan, Ahmed H.; Alquraishi, Saleh A.; ... (2014). Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 111(52), E5661-E5669. National Academy of Sciences NAS 10.1073/pnas.1416991111
Arenas Busto, Miguel; Mona, Stefano; Trochet, Audrey; Sramkova Hanulova, Anna; Currat, Mathias; Ray, Nicolas; Chikhi, Lounes; Rasteiro, Rita; Schmeller, Dirk S.; Excoffier, Laurent (2014). The scaling of genetic diversity in a changing and fragmented world. In: Henle, Klaus; Potts, Simon; Kunin, William; Matsinos, Yiannis; Simila, Jukka; Pantis, John; Grobelnik, Vesna; Penev, Lyubomir; Settele, Josef (eds.) Scaling in Ecology and Biodiversity Conservation. Advanced Books (pp. 55-60). Sofia, Bulgaria: Pensoft Publishers
Excoffier, Laurent; Quilodrán, Claudio; Currat, Mathias (2014). Models of hybridization during range expansions and their application to recent human evolution. In: Derevianko, A.P.; Shunkov, M.V. (eds.) Cultural Developments in the Eurasian Paleolithic and the Origin of Anatomically Modern Humans (pp. 122-137). Novosibirsk: Publishing Department of the Institute of Archaeology and Ethnography SB RAS
Excoffier, Laurent; Dupanloup, Isabelle; Huerta-Sánchez, Emilia; Sousa, Vitor C.; Foll, Matthieu (2013). Robust demographic inference from genomic and SNP data. PLoS genetics, 9(10), e1003905. Public Library of Science 10.1371/journal.pgen.1003905
Martinkova, Natália; Barnett, Ross; Cucchi, Thomas; Struchen, Rahel; Pascal, Marine; Pascal, Michel; Fischer, Martin C.; Higham, Thomas; Brace, Selina; Ho, Simon Y. W.; Quere, Jean-Pierre; O'Higgins, Paul; Excoffier, Laurent; Heckel, Gerald; Hoelzel, A. Rus; Dobney, Keith M.; Searle, Jeremy B. (2013). Divergent evolutionary processes associated with colonization of offshore islands. Molecular Ecology, 22(20), pp. 5205-5220. Wiley-Blackwell 10.1111/mec.12462
Daub, Joséphine; Hofer, Tamara; Cutivet, Emilie; Duperret, Isabelle; Quintana-Murci, L; Robinson-Rechavi, M; Excoffier, Laurent (2013). Evidence for Polygenic Adaptation to Pathogens in the Human Genome. Molecular Biology and Evolution, 30(7), pp. 1544-1558. Oxford University Press 10.1093/molbev/mst080
Arenas, Miguel; François, Olivier; Currat, Mathias; Ray, Nicolas; Excoffier, Laurent (2013). Influence of Admixture and Paleolithic Range Contractions on Current European Diversity Gradients. Molecular Biology and Evolution, 30(1), pp. 57-61. Oxford University Press 10.1093/molbev/mss203
Peischl, Stephan; Duperret, Isabelle; Kirkpatrick, Mark; Excoffier, Laurent (2013). On the accumulation of deleterious mutations during range expansions. Molecular Ecology, 22(24), pp. 5972-5982. Wiley-Blackwell 10.1111/mec.12524
Alves, Isabel; Srámková Hanulová, A.; Foll, Matthieu; Excoffier, Laurent (2012). Genomic Data Reveal a Complex Making of Humans. PLoS genetics, 8(7), e1002837. San Francisco, Calif.: Public Library of Science 10.1371/journal.pgen.1002837
Arenas, M.; Ray, N.; Currat, M.; Excoffier, L. (2012). Consequences of Range Contractions and Range Shifts on Molecular Diversity. Molecular Biology and Evolution, 29(1), pp. 207-218. Oxford: Oxford University Press 10.1093/molbev/msr187
Caetano, S.; Currat, M.; Pennington, R.T.; Prado, D.; Excoffier, L.; Naciri, Y. (2012). Recent colonization of the Galapagos by the tree Geoffroea spinosa Jacq. (Leguminosae). Molecular Ecology, 21(11), pp. 2743-2760. Oxford: Wiley-Blackwell 10.1111/j.1365-294X.2012.05562.x
Hofer, Tamara; Foll, Matthieu; Excoffier, Laurent (2012). Evolutionary forces shaping genomic islands of population differentiation in humans. BMC Genomics, 13(1), p. 107. London: BioMed Central 10.1186/1471-2164-13-107
Kormann, U.; Gugerli, F.; Ray, N.; Excoffier, L.; Bollmann, K. (2012). Parsimony-based pedigree analysis and individual-based landscape genetics suggest topography to restrict dispersal and connectivity in the endangered capercaillie. Biological conservation, 152, pp. 241-252. Barking, UK: Elsevier 10.1016/j.biocon.2012.04.011
Lischer, H.E.L.; Excoffier, L. (2012). PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics, 28(2), pp. 298-299. Oxford: Oxford University Press 10.1093/bioinformatics/btr642
Pimenoff, V.N.; Laval, G.; Comas, D.; Palo, J.U.; Gut, I.; Cann, H.; Excoffier, L.; Sajantila, A. (2012). Similarity in recombination rate and linkage disequilibrium at CYP2C and CYP2D cytochrome P450 gene regions among Europeans indicates signs of selection and no advantage of using tagSNPs in population isolates. Pharmacogenetics and genomics, 22(12), pp. 846-857. London: Lippincott Williams & Wilkins 10.1097/FPC.0b013e32835a3a6d
Reich, D; Patterson, N; Campbell, D; Tandon, A; Mazieres, S; Ray, N; Parra, MV; Rojas, W; Duque, C; Mesa, N; García, LF; Triana, O; Blair, S; Maestre, A; Dib, JC; Bravi, CM; Bailliet, G; Corach, D; Hünemeier, T; Bortolini, MC; ... (2012). Reconstructing Native American population history. Nature, 488(7411), pp. 370-374. London: Macmillan Journals Ltd. 10.1038/nature11258
Slatkin, M.; Excoffier, L. (2012). Serial Founder Effects During Range Expansion: A Spatial Analog of Genetic Drift. Genetics, 191(1), pp. 171-181. Bethesda, Md.: Genetics Society of America 10.1534/genetics.112.139022
Widmer, I.; dal Grande, F.; Excoffier, L.; Holderegger, R.; Keller, C.; Mikryukov, V.S.; Scheidegger, C. (2012). European phylogeography of the epiphytic lichen fungus Lobaria pulmonaria and its green algal symbiont. Molecular Ecology, 21(23), pp. 5827-5844. Oxford: Wiley-Blackwell 10.1111/mec.12051
Currat, Mathias; Excoffier, Laurent (2011). Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 108(37), pp. 15129-15134. Washington, D.C.: National Academy of Sciences NAS 10.1073/pnas.1107450108
Excoffier, Laurent; Foll, Matthieu (2011). fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Bioinformatics, 27(9), pp. 1332-1334. Oxford: Oxford University Press 10.1093/bioinformatics/btr124
Fischer, Martin C.; Foll, Matthieu; Excoffier, Laurent; Heckel, Gerald (2011). Enhanced AFLP genome scans detect local adaptation in high-altitude populations of a small rodent (Microtus arvalis). Molecular Ecology, 20(7), pp. 1450-1462. Oxford: Wiley-Blackwell 10.1111/j.1365-294X.2011.05015.x
Laurent, S.; Werzner, A.; Excoffier, L.; Stephan, W. (2011). Approximate Bayesian analysis of Drosophila melanogaster polymorphism data reveals a recent colonization of Southeast Asia. Molecular Biology and Evolution, 28(7), pp. 2041-2051. Oxford: Oxford University Press 10.1093/molbev/msr031
Moreau, Claudia; Bhérer, Claude; Vézina, Hélène; Jomphe, Michèle; Labuda, Damian; Excoffier, Laurent (2011). Deep Human Genealogies Reveal a Selective Advantage to Be on an Expanding Wave Front. Science, 334(6059), pp. 1148-1150. Washington, D.C.: American Association for the Advancement of Science 10.1126/science.1212880
Bittner, D; Excoffier, L; Largiadèr, C R (2010). Patterns of morphological changes and hybridization between sympatric whitefish morphs (Coregonus spp.) in a Swiss lake: a role for eutrophication? Molecular Ecology, 19(10), pp. 2152-67. Oxford: Wiley-Blackwell 10.1111/j.1365-294X.2010.04623.x
Beaumont, Mark A.; Nielsen, Rasmus; Robert, Christian; Hey, Jody; Gaggiotti, Oscar; Knowles, Lacey; Estoup, Arnaud; Panchal, Mahesh; Corander, Jukka; Hickerson, Mike; Sisso, Scott A.; Fagundes, Nelson; Chikhi, Lounes; Beerli, Peter; Vitalis, Renaud; Cornuet, Jean-Marie; Huelsenbeck, John; Foll, Matthieu; Yang, Ziheng; Rousset, Fraçois; ... (2010). In defence of model-based inference in phylogeography. Molecular Ecology, 19(3), pp. 436-446. Oxford: Wiley-Blackwell 10.1111/j.1365-294X.2009.04515.x
Estoup, Arnaud; Baird, Stuart J.E.; Ray, Nicolas; Currat, Mathias; Cornuet, Jean-Marie; Santos, Filipe; Beaumont, Mark A.; Excoffier, Laurent (2010). Combining genetic, historical and geographical data to reconstruct the dynamics of bioinvasions: application to the cane toad Bufo marinus. Molecular ecology resources, 10(5), pp. 886-901. Oxford: Blackwell Science 10.1111/j.1755-0998.2010.02882.x
Excoffier, Laurent; Lischer, Heidi E.L. (2010). Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular ecology resources, 10(3), pp. 564-567. Oxford: Blackwell Science 10.1111/j.1755-0998.2010.02847.x
Fink, Sabine; Fischer, Martin C.; Excoffier, Laurent; Heckel, Gerald (2010). Genomic scans support repetitive continental colonization events during the rapid radiation of voles (Rodentia: Microtus): the utility of AFLPs versus mitochondrial and nuclear sequence markers. Systematic biology, 59(5), pp. 548-572. Cary, N.C.: Oxford University Press 10.1093/sysbio/syq042
Foll, Matthieu; Fischer, Martin C.; Heckel, Gerald; Excoffier, Laurent (2010). Estimating population structure from AFLP amplification intensity. Molecular Ecology, 19(21), pp. 4638-4647. Oxford: Wiley-Blackwell 10.1111/j.1365-294X.2010.04820.x
Francois, Olivier; Currat, Mathias; Ray, Nicolas; Han, Eunjung; Excoffier, Laurent; Novembre, John (2010). Principal Component Analysis under Population Genetic Models of Range Expansion and Admixture. Molecular Biology and Evolution, 27(6), pp. 1257-1268. Oxford: Oxford University Press 10.1093/molbev/msq010
Henle, Klaus; Kunin, William; Schweiger, Oliver; Schmeller, Dirk S.; Grobelnik, Vesna; Matsinos, Yiannis; Pantis, John; Penev, Lyubomir; Potts, Simon G.; Ring, Irene; Similä, Jukka; Tzanopoulos, Joseph; van den Hove, Sybille; Baguette, Michel; Clobert, Jean; Excoffier, Laurent; Framstad, Erik; Grodzińska-Jurczak, Małgorzata; Lengyel, Szabolcs; Marty, Pascal; ... (2010). Securing the Conservation of Biodiversity across Administrative Levels and Spatial, Temporal, and Ecological Scales - Research Needs and Approaches of the SCALES Project. GAIA - ökologische Perspektiven für Wissenschaft und Gesellschaft / ecological perspectives for science and society, 19(3), pp. 187-193. München: Oekom Verlag
Peter, Benjamin P.; Wegmann, Daniel; Excoffier, Laurent (2010). Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure. Molecular Ecology, 19(21), pp. 4648-4660. Oxford: Wiley-Blackwell 10.1111/j.1365-294X.2010.04783.x
Ray, Nicolas; Currat, Mathias; Foll, Matthieu; Excoffier, Laurent (2010). SPLATCHE2: a spatially-explicit simulation framework for complex demography, genetic admixture and recombination. Bioinformatics, 26(23), pp. 2993-2994. Oxford: Oxford University Press 10.1093/bioinformatics/btq579
Ray, Nicolas; Excoffier, Laurent (2010). A first step towards inferring levels of long-distance dispersal during past expansions. Molecular ecology resources, 10(5), pp. 902-914. Oxford: Blackwell Science 10.1111/j.1755-0998.2010.02881.x
Ray, Nicolas; Wegmann, Daniel; Fagundes, Nelson J.R.; Wang, S.; Ruiz-Linares, Andres; Excoffier, Laurent (2010). A statistical evaluation of models for the initial settlement of the American continent emphasizes the importance of gene flow with Asia. Molecular Biology and Evolution, 27(2), pp. 337-345. Oxford: Oxford University Press 10.1093/molbev/msp238
Wegmann, Daniel; Excoffier, Laurent (2010). Bayesian Inference of the Demographic History of Chimpanzees. Molecular Biology and Evolution, 27(6), pp. 1425-1435. Oxford: Oxford University Press 10.1093/molbev/msq028
Wegmann, Daniel; Leuenberger, Christoph; Neuenschwander, Samuel; Excoffier, Laurent (2010). ABCtoolbox: a versatile toolkit for approximate Bayesian computations. BMC bioinformatics, 11(1), p. 116. London: BioMed Central 10.1186/1471-2105-11-116
Yang, Ning Ning; Mazières, Stephane; Bravi, Claudio; Ray, Nicolas; Wang, Sijia; Burley, Mari-Wyn; Bedoya, Gabriel; Rojas, Winston; Parra, Maria V.; Molina, Julio A.; Gallo, Carla; Poletti, Giovanni; Hill, Kim; Hurtado, Ana M.; Petzl-Erler, Maria L.; Tsuneto, Luiza T.; Klitz, William; Barrantes, Ramiro; Llop, Elena; Rothhammer, Francisco; ... (2010). Contrasting Patterns of Nuclear and mtDNA Diversity in Native American Populations. Annals of human genetics, 74(6), pp. 525-538. Oxford: Wiley-Blackwell 10.1111/j.1469-1809.2010.00608.x
Excoffier, Laurent; Foll, Matthieu; Petit, Rémy J. (2009). Genetic Consequences of Range Expansions. Annual review of ecology, evolution, and systematics, 40(1), pp. 481-501. Palo Alto, Calif.: Annual Reviews Inc. 10.1146/annurev.ecolsys.39.110707.173414
Excoffier, Laurent; Hofer, Tamara; Foll, Matthieu (2009). Detecting loci under selection in a hierarchically structured population. Heredity, 103(4), pp. 285-298. London: Oliver and Boyd 10.1038/hdy.2009.74
Hofer, Tamara; Ray, Nicolas; Wegmann, Daniel; Excoffier, Laurent (2009). Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection. Annals of human genetics, 73(Part 1), pp. 95-108. Oxford: Wiley-Blackwell 10.1111/j.1469-1809.2008.00489.x
Makrythanasis, Periklis; Kapranov, Philipp; Bartoloni, Lucia; Reymond, Alexandre; Deutsch, Samuel; Guigo, Roderic; Denoeud, France; Drenkow, Jorg; Rossier, Colette; Ariani, Francesca; Capra, Valeria; Excoffier, Laurent; Renieri, Alessandra; Gingeras, Thomas R.; Antonarakis, Stylianos E. (2009). Variation in Novel Exons (RACEfrags) of the MECP2 Gene in Rett Syndrome Patients and Controls. Human mutation, 30(9), E866 - E879. Hoboken, N.J.: Wiley-Blackwell 10.1002/humu.21073
Petit, Rémy J.; Excoffier, Laurent (2009). Gene flow and species delimitation. Trends in ecology & evolution, 24(7), pp. 386-393. Amsterdam: Elsevier Current Trends 10.1016/j.tree.2009.02.011
Poloni, Estella S.; Naciri, Yamama; Bucho, Rute; Niba, Régine; Kervaire, Barbara; Excoffier, Laurent; Langaney, André; Sanchez-Mazas, Alicia (2009). Genetic Evidence for Complexity in Ethnic Differentiation and History in East Africa. Annals of human genetics, 73(6), pp. 582-600. Oxford: Wiley-Blackwell 10.1111/j.1469-1809.2009.00541.x
Ray, Nicolas; Excoffier, Laurent (2009). Inferring past demography using spatially-explicit population genetic models. Human biology, 81(2-3), pp. 141-157. Detroit, Mich.: Wayne State University Press 10.3378/027.081.0303
Soland-Reckeweg, Gabriele; Heckel, Gerald; Neumann, Peter; Fluri, Peter; Excoffier, Laurent (2009). Gene flow in admixed populations and implications for the conservation of the Western honeybee, Apis mellifera. Journal of insect conservation, 13(3), pp. 317-328. London: Springer Netherlands 10.1007/s10841-008-9175-0
Wegmann, Daniel; Leuenberger, Christoph; Excoffier, Laurent (2009). Efficient Approximate Bayesian Computation Coupled With Markov Chain Monte Carlo Without Likelihood. Genetics, 182(4), pp. 1207-1218. Bethesda, Md.: Genetics Society of America 10.1534/genetics.109.102509
Giger, Thomas; Excoffier, Laurent; Amstutz, Ursula; Day, Philip J R; Champigneulle, Alexis; Hansen, Michael M; Kelso, Janet; Largiadèr, Carlo R (2008). Population transcriptomics of life-history variation in the genus Salmo. Molecular Ecology, 17(13), pp. 3095-3108. Oxford: Wiley-Blackwell 10.1111/j.1365-294X.2008.03820.x
Neuenschwander, Samuel; Largiadèr, Carlo R; Ray, Nicolas; Currat, Mathias; Vonlanthen, Pascal; Excoffier, Laurent (2008). Colonization history of the Swiss Rhine basin by the bullhead (Cottus gobio): inference under a Bayesian spatially explicit framework. Molecular Ecology, 17(3), pp. 757-772. Oxford: Wiley-Blackwell 10.1111/j.1365-294X.2007.03621.x
Ruedi, Manuel; Walter, Simon; Fischer, Martin C.; Scaravelli, Dino; Excoffier, Laurent; Heckel, Gerald (2008). Italy as a major Ice Age refuge area for the bat Myotis myotis (Chiroptera: Vespertilionidae) in Europe. Molecular Ecology, 17(7), pp. 1801-1814. Oxford: Wiley-Blackwell 10.1111/j.1365-294X.2008.03702.x
Wang, Sijia; Ray, Nicolas; Rojas, Winston; Parra, Maria V.; Bedoya, Gabriel; Gallo, Carla; Poletti, Giovanni; Mazzotti, Guido; Hill, Kim; Hurtado, Ana M.; Camrena, Beatriz; Nicolini, Humberto; Klitz, William; Barrantes, Ramiro; Molina, Julio A.; Freimer, Nelson B.; Bortolini, Maria Cátira; Salzano, Francisco M.; Petzl-Erler, Maria L.; Tsuneto, Luiza T.; ... (2008). Geographic Patterns of Genome Admixture in Latin American Mestizos. PLoS genetics, 4(3), e1000037. San Francisco, Calif.: Public Library of Science 10.1371/journal.pgen.1000037
Wegmann, Daniel; Dupanloup, Isabelle; Excoffier, Laurent (2008). Width of Gene Expression Profile Drives Alternative Splicing. PLoS ONE, 3(10), e3587. Lawrence, Kans.: Public Library of Science 10.1371/journal.pone.0003587
Vonlanthen, Pascal; Excoffier, Laurent; Bittner, David; Persat, H; Neuenschwander, S; Largiadèr, Carlo (2007). Genetic analysis of potential postglacial watershed crossings in central Europe by the bullhead (Cottus gobio L). Molecular Ecology, 16(21), pp. 4572-4584. Oxford: Wiley-Blackwell 10.1111/j.1365-294X.2007.03531.x
Fink, Sabine; Excoffier, Laurent; Heckel, Gerhard (2007). High variability and non-neutral evolution of the mammalian avpr1a gene. BMC evolutionary biology, 7(1), p. 176. London: BioMed Central 10.1186/1471-2148-7-176
Pawlowski, Jan; Fahrni, José; Lecroq, B; Longet, David; Cornelius, N; Excoffier, Laurent; Cedhagen, Tomas; Gooday, Andrew (2007). Bipolar gene flow in deep-sea benthic foraminifera. Molecular Ecology, 16(19), pp. 4089-4096. Oxford: Wiley-Blackwell 10.1111/j.1365-294X.2007.03465.x
Schweizer, Manuel; Excoffier, Laurent; Heckel, Gerald (2007). Fine-scale genetic structure and dispersal in the common vole (Microtus arvalis). Molecular Ecology, 16(12), pp. 2463-2473. Oxford: Wiley-Blackwell 10.1111/j.1365-294X.2007.03284.x
Wang, Sijia; Lewis, Cecil; Jakobsson, Mattias; Ramachandran, Sohini; Ray, Nicolas; Bedoya, Gabriel; Rojas, Winston; Parra, Maria; Molina, Julio; Gallo, Carla; Mazzotti, Guido; Poletti, Giovanni; Hill, Kim; Hurtado, Ana; Labuda, Damian; Klitz, William; Barrantes, Ramiro; Bortolini, Maria; Salzano, Francisco; Petzl-Erler, Maria; ... (2007). Genetic Variation and Population Structure in Native Americans. PLoS genetics, 3(11), e185. San Francisco, Calif.: Public Library of Science 10.1371/journal.pgen.0030185
Giger, Thomas; Excoffier, Laurent; Day, Philip J R; Champigneulle, Alexis; Hansen, Michael M; Powell, Richard; Largiadèr, Carlo R (2006). Life history shapes gene expression in salmonids. Current Biology, 16(8), R281-R282. Cambridge, Mass.: Cell Press 10.1016/j.cub.2006.03.053
Excoffier, Laurent; Heckel, Gerald (2006). Computer programs for population genetics data analysis: a survival guide. Nature Reviews. Genetics, 7(10), pp. 745-758. London: Natue Publishing Group 10.1038/nrg1904
Klopfstein, Seraina; Currat, Mathias; Excoffier, Laurent (2006). The fate of mutations surfing on the wave of a range expansion. Molecular Biology and Evolution, 23(3), pp. 482-490. Oxford: Oxford University Press 10.1093/molbev/msj057
Currat, Mathias; Excoffier, Laurent (2004). Modern Humans Did Not Admix with Neanderthals during Their Range Expansion into Europe. PLoS biology, 2(12), e421. Public Library of Science 10.1371/journal.pbio.0020421
Laval, Guillaume; Excoffier, Laurent (2004). SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics, 20(15), pp. 2485-2487. Oxford University Press 10.1093/bioinformatics/bth264
