L Excoffier

Summary

Affiliation: University of Bern
Country: Switzerland

Publications

  1. pmc Molecular analysis of the beta-globin gene cluster in the Niokholo Mandenka population reveals a recent origin of the beta(S) Senegal mutation
    Mathias Currat
    Genetics and Biometry Laboratory, Department of Anthropology and Ecology, University of Geneva, Geneva, Switzerland
    Am J Hum Genet 70:207-23. 2002
  2. ncbi request reprint Genetic structure and colonization processes in European populations of the common vole, Microtus arvalis
    Gerald Heckel
    Computational and Molecular Population Genetics, Zoological Institute, University of Bern, Baltzerstrasse 6, CH 3012 Bern, Switzerland
    Evolution 59:2231-42. 2005
  3. pmc Mammalian monogamy is not controlled by a single gene
    Sabine Fink
    Computational and Molecular Population Genetics Laboratory, Zoological Institute, University of Bern, Baltzerstrasse 6, CH 3012 Bern, Switzerland
    Proc Natl Acad Sci U S A 103:10956-60. 2006
  4. pmc Modern humans did not admix with Neanderthals during their range expansion into Europe
    Mathias Currat
    Computational and Molecular Population Genetics Lab, Zoological Institute, University of Bern, Switzerland
    PLoS Biol 2:e421. 2004
  5. pmc High variability and non-neutral evolution of the mammalian avpr1a gene
    Sabine Fink
    Computational and Molecular Population Genetics CMPG, Zoological Institute, University of Bern, Baltzerstrasse 6, CH 3012 Bern, Switzerland
    BMC Evol Biol 7:176. 2007
  6. pmc Bayesian analysis of an admixture model with mutations and arbitrarily linked markers
    Laurent Excoffier
    Institut National de la Recherche Agronomique, Centre de Biologie et de Gestion des Populations CBGP, Campus International de Baillarguet, Montferrier sur Lez, France
    Genetics 169:1727-38. 2005
  7. ncbi request reprint Computer programs for population genetics data analysis: a survival guide
    Laurent Excoffier
    Computational and Molecular Population Genetics Laboratory, Zoological Institute, University of Berne, Baltzerstrasse 6, 3012 Berne, Switzerland
    Nat Rev Genet 7:745-58. 2006
  8. doi request reprint Detecting loci under selection in a hierarchically structured population
    L Excoffier
    Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
    Heredity (Edinb) 103:285-98. 2009
  9. doi request reprint Surfing during population expansions promotes genetic revolutions and structuration
    Laurent Excoffier
    Computational and Molecular Population Genetics Lab, Institute of Zoology, University of Berne, Baltzerstrasse 6, Berne, Switzerland
    Trends Ecol Evol 23:347-51. 2008
  10. pmc Gametic phase estimation over large genomic regions using an adaptive window approach
    Laurent Excoffier
    Zoological Institute, University of Bern, Baltzerstrasse 6, CH 3012 Bern, Switzerland
    Hum Genomics 1:7-19. 2003

Collaborators

Detail Information

Publications49

  1. pmc Molecular analysis of the beta-globin gene cluster in the Niokholo Mandenka population reveals a recent origin of the beta(S) Senegal mutation
    Mathias Currat
    Genetics and Biometry Laboratory, Department of Anthropology and Ecology, University of Geneva, Geneva, Switzerland
    Am J Hum Genet 70:207-23. 2002
    ....
  2. ncbi request reprint Genetic structure and colonization processes in European populations of the common vole, Microtus arvalis
    Gerald Heckel
    Computational and Molecular Population Genetics, Zoological Institute, University of Bern, Baltzerstrasse 6, CH 3012 Bern, Switzerland
    Evolution 59:2231-42. 2005
    ..This suggests that some M. arvalis populations persisted during the LGM in suitable habitat further north and that the gradients in genetic diversity may represent traces of a more ancient colonization of Europe by the species...
  3. pmc Mammalian monogamy is not controlled by a single gene
    Sabine Fink
    Computational and Molecular Population Genetics Laboratory, Zoological Institute, University of Bern, Baltzerstrasse 6, CH 3012 Bern, Switzerland
    Proc Natl Acad Sci U S A 103:10956-60. 2006
    ..We thus resolve the contradiction between the claims for an evolutionarily conserved genetic programming of social behavior in mammals and the vast evidence for highly complex and flexible mating systems...
  4. pmc Modern humans did not admix with Neanderthals during their range expansion into Europe
    Mathias Currat
    Computational and Molecular Population Genetics Lab, Zoological Institute, University of Bern, Switzerland
    PLoS Biol 2:e421. 2004
    ..This extremely low number strongly suggests an almost complete sterility between Neanderthal females and modern human males, implying that the two populations were probably distinct biological species...
  5. pmc High variability and non-neutral evolution of the mammalian avpr1a gene
    Sabine Fink
    Computational and Molecular Population Genetics CMPG, Zoological Institute, University of Bern, Baltzerstrasse 6, CH 3012 Bern, Switzerland
    BMC Evol Biol 7:176. 2007
    ..Contrary to previous studies focusing on differences in the promotor region of the gene, we investigate here the level of functional variation in the coding region (exon 1) of this locus...
  6. pmc Bayesian analysis of an admixture model with mutations and arbitrarily linked markers
    Laurent Excoffier
    Institut National de la Recherche Agronomique, Centre de Biologie et de Gestion des Populations CBGP, Campus International de Baillarguet, Montferrier sur Lez, France
    Genetics 169:1727-38. 2005
    ..ligustica populations were completely separated since the last glacial maximum...
  7. ncbi request reprint Computer programs for population genetics data analysis: a survival guide
    Laurent Excoffier
    Computational and Molecular Population Genetics Laboratory, Zoological Institute, University of Berne, Baltzerstrasse 6, 3012 Berne, Switzerland
    Nat Rev Genet 7:745-58. 2006
    ..We describe here the functionalities, special features and assumptions of more than 20 such programs, indicate how they can interoperate, and discuss new directions that could lead to improved software and analyses...
  8. doi request reprint Detecting loci under selection in a hierarchically structured population
    L Excoffier
    Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
    Heredity (Edinb) 103:285-98. 2009
    ..The elimination of false positive loci from genome scans should allow us to better determine on which specific class of genes selection is operating...
  9. doi request reprint Surfing during population expansions promotes genetic revolutions and structuration
    Laurent Excoffier
    Computational and Molecular Population Genetics Lab, Institute of Zoology, University of Berne, Baltzerstrasse 6, Berne, Switzerland
    Trends Ecol Evol 23:347-51. 2008
    ..They also suggest that a single range expansion can create very complex patterns at neutral loci, mimicking adaptive processes and resembling postglacial segregation of clades from distinct refuge areas...
  10. pmc Gametic phase estimation over large genomic regions using an adaptive window approach
    Laurent Excoffier
    Zoological Institute, University of Bern, Baltzerstrasse 6, CH 3012 Bern, Switzerland
    Hum Genomics 1:7-19. 2003
    ..Once again, they found ELB to have consistently better local accuracy than PHASE or HTYPER, while its global accuracy was close to the best...
  11. ncbi request reprint Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model
    Laurent Excoffier
    Computational and Molecular Population Genetics Laboratory, Zoological Institute, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
    Mol Ecol 13:853-64. 2004
    ..I then apply these results to estimate immigration rates in hunter-gather and post-Neolithic human populations from patterns of mitochondrial (mtDNA) diversity. Potential problems with this estimation procedure are also discussed...
  12. ncbi request reprint Comment on "Genetic structure of human populations"
    Laurent Excoffier
    Computational and Molecular Population, Genetics LabZoological Institute, University of Bern, Batzerstrasse 63012, Bern, Switzerland
    Science 300:1877; author reply 1877. 2003
  13. doi request reprint A statistical evaluation of models for the initial settlement of the american continent emphasizes the importance of gene flow with Asia
    N Ray
    Institute of Ecology and Evolution, University of Bern, Switzerland
    Mol Biol Evol 27:337-45. 2010
    ..We estimate that this colonization involved about 100 individuals and occurred some 13,000 years ago, in agreement with well-established archeological data...
  14. ncbi request reprint The fate of mutations surfing on the wave of a range expansion
    Seraina Klopfstein
    Computational and Molecular Population Genetics Lab, Institute of Zoology, University of Bern, Bern, Switzerland
    Mol Biol Evol 23:482-90. 2006
    ..By favoring the spread of new mutations, a consequence of the surfing phenomenon is to increase the rate of evolution of spatially expanding populations...
  15. doi request reprint Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection
    T Hofer
    Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
    Ann Hum Genet 73:95-108. 2009
    ..We therefore conclude that most of the observed large allele frequency differences between continents result from demography rather than from positive selection...
  16. doi request reprint Patterns of morphological changes and hybridization between sympatric whitefish morphs (Coregonus spp.) in a Swiss lake: a role for eutrophication?
    D Bittner
    Computational and Molecular Populations Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
    Mol Ecol 19:2152-67. 2010
    ....
  17. ncbi request reprint Mitochondrial gene diversity in the common vole Microtus arvalis shaped by historical divergence and local adaptations
    Sabine Fink
    Computational and Molecular Population Genetics CMPG laboratory, Zoological Institute, University of Bern, Baltzerstrasse 6, CH 3012 Bern, Switzerland
    Mol Ecol 13:3501-14. 2004
    ..We therefore conclude that the molecular diversity of cytb in M. arvalis is overall the result of the demographic history of the populations, but that there have been several episodes of local adaptation to peculiar environments...
  18. ncbi request reprint Neandertal genetic diversity: a fresh look from old samples
    Laurent Excoffier
    Computational and Molecular Population Genetics Lab, Zoological Institute, University of Berne, Baltzerstrasse 6, 3012 Berne, Switzerland
    Curr Biol 16:R650-2. 2006
    ..It suggests that the Neandertal population was extensively subdivided geographically, and that its genetic diversity changed markedly over time...
  19. pmc Recurrent replacement of mtDNA and cryptic hybridization between two sibling bat species Myotis myotis and Myotis blythii
    Pierre Berthier
    Computational and Molecular Population Genetics Laboratory, Zoological Institute, University of Berne, Baltzersrasse 6, 3012 Berne, Switzerland
    Proc Biol Sci 273:3101-9. 2006
    ..blythii from Asia. The sharp contrast obtained from the analysis of mitochondrial and nuclear markers further points to the need to cautiously interpret results based on a single class of genetic markers...
  20. ncbi request reprint Genetic analysis of potential postglacial watershed crossings in Central Europe by the bullhead (Cottus gobio L.)
    P Vonlanthen
    Computational and Molecular Population Genetics lab CMPG, Zoologisches Institut, Universitat Bern, Baltzerstrasse 6, CH 3012 Bern, Switzerland
    Mol Ecol 16:4572-84. 2007
    ..Based on our results on the bullhead, we propose that glacial retreat may have eased the dispersal of numerous European freshwater fish species across several geological boundaries...
  21. pmc Molecular diversity after a range expansion in heterogeneous environments
    Daniel Wegmann
    Computational and Molecular Population Genetics Laboratory, Zoological Institute, University of Bern, Switzerland
    Genetics 174:2009-20. 2006
    ..Overall, temporal heterogeneity and local extinctions are not found to leave any specific signature on molecular diversity that cannot be produced by spatial heterogeneity...
  22. pmc ABCtoolbox: a versatile toolkit for approximate Bayesian computations
    Daniel Wegmann
    Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
    BMC Bioinformatics 11:116. 2010
    ..The situation changed recently with the advent of Approximate Bayesian Computation (ABC) algorithms allowing one to obtain parameter posterior distributions based on simulations not requiring likelihood computations...
  23. doi request reprint Bayesian inference of the demographic history of chimpanzees
    Daniel Wegmann
    Department of Biology, Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
    Mol Biol Evol 27:1425-35. 2010
    ....
  24. pmc Width of gene expression profile drives alternative splicing
    Daniel Wegmann
    Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
    PLoS ONE 3:e3587. 2008
    ..We finally propose that the width of the gene expression profile is an essential factor for the acquisition of new transcript isoforms that could later be maintained by a new form of balancing selection...
  25. doi request reprint The hidden side of invasions: massive introgression by local genes
    Mathias Currat
    Computational and Molecular Population Genetics Laboratory, Institute of Zoology, University of Bern, Baltzerstrasse 6, 3012 Berne, Switzerland
    Evolution 62:1908-20. 2008
    ..Our results imply that speciation genes can be identified by comparing genomes of interfertile native and invading species pairs...
  26. pmc Bayesian estimation of recent migration rates after a spatial expansion
    Grant Hamilton
    Computational and Molecular Population Genetics Lab, Zoological Institute, University of Bern, Switzerland
    Genetics 170:409-17. 2005
    ..Estimates based on both markers suggest that expansion occurred <10,000 years ago, after the most recent glaciation, and that migration rates are strongly male biased...
  27. ncbi request reprint SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history
    Guillaume Laval
    Computational and Molecular Population Genetics, Zoological Institute, University of Bern, Baltzerstrasse 6, Bern CH 3012, Switzerland
    Bioinformatics 20:2485-7. 2004
    ....
  28. ncbi request reprint Human diversity: our genes tell where we live
    Laurent Excoffier
    Computational and Molecular Population Genetics Lab, Zoological Institute, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
    Curr Biol 13:R134-6. 2003
    ..A detailed genetic analysis of more than a thousand human subjects clusters them into five groups corresponding to major geographical regions. This new study shows that self-reported ancestry is a good predictor of one's genetic make-up...
  29. pmc The effect of the Neolithic expansion on European molecular diversity
    Mathias Currat
    Computational and Molecular Population Genetics Laboratory, Zoological Institute, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
    Proc Biol Sci 272:679-88. 2005
    ..We conclude that the different patterns of molecular diversity observed for Y chromosome and mitochondrial DNA can be at least partly owing to an ascertainment bias when selecting Y chromosome SNPs for studying European populations...
  30. pmc Recovering the geographic origin of early modern humans by realistic and spatially explicit simulations
    Nicolas Ray
    Computational and Molecular Population Genetics Lab, Zoological Institute, University of Bern, 3012 Bern, Switzerland
    Genome Res 15:1161-7. 2005
    ..A new estimation modeling this bias explicitly reveals that East Africa is the most likely place of origin for modern humans...
  31. ncbi request reprint Human demographic history: refining the recent African origin model
    Laurent Excoffier
    Computational and Molecular Population Genetics CMPG Lab, Zoological Institute, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
    Curr Opin Genet Dev 12:675-82. 2002
    ..Under this simple scenario, patterns of molecular diversity suggest that balancing selection could be more prevalent than positive selection in coding regions...
  32. pmc Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populations
    Grant Hamilton
    Computational and Molecular Population Genetics Laboratory, Zoological Institute, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
    Proc Natl Acad Sci U S A 102:7476-80. 2005
    ..This finding is compatible with the hypothesis that men are strictly controlling male immigration and promoting female immigration in patrilocal populations and that immigration is much less regulated in matrilocal populations...
  33. ncbi request reprint Fine-scale genetic structure and dispersal in the common vole (Microtus arvalis)
    Manuel Schweizer
    Computational and Molecular Population Genetics lab CMPG, Zoological Institute, University of Bern, Baltzerstrasse 6, CH 3012 Bern, Switzerland
    Mol Ecol 16:2463-73. 2007
    ....
  34. pmc Efficient approximate Bayesian computation coupled with Markov chain Monte Carlo without likelihood
    Daniel Wegmann
    Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, 3012, Switzerland
    Genetics 182:1207-18. 2009
    ..We then apply our method to a more complex case with the estimation of divergence times and migration rates between three African populations...
  35. ncbi request reprint Estimation of effective population size and detection of a recent population decline coinciding with habitat fragmentation in a ground beetle
    I Keller
    Computational and Molecular Population Genetics Lab, Zoological Institute, University of Bern, Bern, Switzerland
    J Evol Biol 18:90-100. 2005
    ..In the small fragment, N(e) of the local population may be so small that its long-term persistence is endangered...
  36. doi request reprint 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
    Sabine Fink
    Department of Biology, Computational and Molecular Population Genetics CMPG, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH 3012 Bern, Switzerland
    Syst Biol 59:548-72. 2010
    ..More generally, this study supports the suitability of AFLPs as an alternative to sequence markers to resolve the evolutionary history of rapidly radiating taxa...
  37. doi request reprint Colonization history of the Swiss Rhine basin by the bullhead (Cottus gobio): inference under a Bayesian spatially explicit framework
    Samuel Neuenschwander
    CMPG, Zoological Institute, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
    Mol Ecol 17:757-72. 2008
    ..We discuss the implication of this result, as well as the strengths and limits of the spatially explicit approach coupled to the approximate Bayesian computation framework...
  38. doi request reprint PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs
    H E L Lischer
    Computational and Molecular Population Genetics CMPG laboratory, Institute of Ecology and Evolution, University of Berne, Baltzerstrasse 6, 3012 Berne, Switzerland
    Bioinformatics 28:298-9. 2012
    ..The PGDSpider package includes both an intuitive graphical user interface and a command-line version allowing its integration in complex data analysis pipelines...
  39. doi request reprint Population transcriptomics of life-history variation in the genus Salmo
    Thomas Giger
    CMPG, Zoological Institute, University of Bern, Baltzerstrasse 6, CH 3012 Bern, Switzerland
    Mol Ecol 17:3095-108. 2008
    ..Our findings thus provide new molecular insights into salmonid life-history variation, opening new perspectives in the study of this complex trait...
  40. ncbi request reprint 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"
    Mathias Currat
    Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    Science 313:172; author reply 172. 2006
    ..We show that models of human history that include both population growth and spatial structure can generate the observed patterns without selection...
  41. ncbi request reprint A human genome diversity cell line panel
    Howard M Cann
    Science 296:261-2. 2002
  42. ncbi request reprint Intra-deme molecular diversity in spatially expanding populations
    Nicolas Ray
    Genetics and Biometry Lab, Department of Anthropology and Ecology, University of Geneva, Geneva, Switzerland
    Mol Biol Evol 20:76-86. 2003
    ..The fact that molecular diversity within deme is so dependent on recent levels of gene flow suggests that it should be possible to estimate Nm values from samples drawn from a single deme...
  43. ncbi request reprint Special issue: analytical methods in phylogeography and genetic structure
    Laurent Excoffier
    Mol Ecol 13:727. 2004
  44. pmc Statistical evaluation of alternative models of human evolution
    Nelson J R Fagundes
    Laboratório de Biologia Genômica e Molecular, Faculdade de Biociencias, Pontificia Universidade Catolica do Rio Grande do Sul, 90619 900 Porto Alegre, RS, Brazil
    Proc Natl Acad Sci U S A 104:17614-9. 2007
    ....
  45. pmc Genetic variation and population structure in native Americans
    Sijia Wang
    The Galton Laboratory, Department of Biology, University College London, London, United Kingdom
    PLoS Genet 3:e185. 2007
    ..These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas...
  46. doi request reprint Italy as a major Ice Age refuge area for the bat Myotis myotis (Chiroptera: Vespertilionidae) in Europe
    Manuel Ruedi
    Natural History Museum of Geneva, PO Box, 1211 Genève 6, Switzerland
    Mol Ecol 17:1801-14. 2008
    ..These results underline the conservation value of bats from this region and the need to include the Apennine peninsula in phylogeographical surveys in order to provide a more accurate view of the evolution of bats in Europe...
  47. pmc Geographic patterns of genome admixture in Latin American Mestizos
    Sijia Wang
    The Galton Laboratory, Department of Biology, University College London, London, United Kingdom
    PLoS Genet 4:e1000037. 2008
    ..Our findings agree with available information on the demographic history of Latin America and have a number of implications for the design of association studies in population from the region...
  48. pmc The detection of regions of our genome under selection has increasingly relied on the use of genome scans
    Laurent Excoffier
    Hum Genomics 2:155-7. 2005
  49. ncbi request reprint Conserved noncoding sequences are selectively constrained and not mutation cold spots
    Jared A Drake
    Program in Genomics and Division of Endocrinology, Children s Hospital, Boston, Massachusetts 02115, USA
    Nat Genet 38:223-7. 2006
    ..Thus, conserved noncoding variants are more likely to be functional. Allele frequency distributions highlight selectively constrained genomic regions that should be intensively surveyed for functionally important variation...