Research Topics
| L ExcoffierSummaryAffiliation: University of Bern Country: Switzerland Publications
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Detail Information
Publications
Molecular analysis of the beta-globin gene cluster in the Niokholo Mandenka population reveals a recent origin of the beta(S) Senegal mutationMathias Currat
Genetics and Biometry Laboratory, Department of Anthropology and Ecology, University of Geneva, Geneva, Switzerland
Am J Hum Genet 70:207-23. 2002....
Genetic structure and colonization processes in European populations of the common vole, Microtus arvalisGerald 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...- Mammalian monogamy is not controlled by a single geneSabine 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... 
Modern humans did not admix with Neanderthals during their range expansion into EuropeMathias 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...- High variability and non-neutral evolution of the mammalian avpr1a geneSabine 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... - Bayesian analysis of an admixture model with mutations and arbitrarily linked markersLaurent 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... - Computer programs for population genetics data analysis: a survival guideLaurent 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... 
Detecting loci under selection in a hierarchically structured populationL 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...- Surfing during population expansions promotes genetic revolutions and structurationLaurent 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... - Gametic phase estimation over large genomic regions using an adaptive window approachLaurent 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... - Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island modelLaurent 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... - 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 - A statistical evaluation of models for the initial settlement of the american continent emphasizes the importance of gene flow with AsiaN 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... - The fate of mutations surfing on the wave of a range expansionSeraina 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... - Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selectionT 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... - 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.... - Mitochondrial gene diversity in the common vole Microtus arvalis shaped by historical divergence and local adaptationsSabine 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... - Neandertal genetic diversity: a fresh look from old samplesLaurent 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... - Recurrent replacement of mtDNA and cryptic hybridization between two sibling bat species Myotis myotis and Myotis blythiiPierre 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... - 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... - Molecular diversity after a range expansion in heterogeneous environmentsDaniel 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... - ABCtoolbox: a versatile toolkit for approximate Bayesian computationsDaniel 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... - Bayesian inference of the demographic history of chimpanzeesDaniel 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.... - Width of gene expression profile drives alternative splicingDaniel 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... - The hidden side of invasions: massive introgression by local genesMathias 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... - Bayesian estimation of recent migration rates after a spatial expansionGrant 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... - SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex historyGuillaume Laval
Computational and Molecular Population Genetics, Zoological Institute, University of Bern, Baltzerstrasse 6, Bern CH 3012, Switzerland
Bioinformatics 20:2485-7. 2004..AVAILABILITY: http://cmpg.unibe.ch/software/simcoal2/... - Human diversity: our genes tell where we liveLaurent 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... - The effect of the Neolithic expansion on European molecular diversityMathias 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... - Recovering the geographic origin of early modern humans by realistic and spatially explicit simulationsNicolas 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... - Human demographic history: refining the recent African origin modelLaurent 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... - Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populationsGrant 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... - 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.... - Efficient approximate Bayesian computation coupled with Markov chain Monte Carlo without likelihoodDaniel 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... - Estimation of effective population size and detection of a recent population decline coinciding with habitat fragmentation in a ground beetleI 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... - Genomic scans support repetitive continental colonization events during the rapid radiation of voles (Rodentia: Microtus): the utility of AFLPs versus mitochondrial and nuclear sequence markersSabine 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... - Colonization history of the Swiss Rhine basin by the bullhead (Cottus gobio): inference under a Bayesian spatially explicit frameworkSamuel 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... - PGDSpider: an automated data conversion tool for connecting population genetics and genomics programsH 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..AVAILABILITY: PGDSpider is freely available under the BSD 3-Clause license on http://cmpg.unibe.ch/software/PGDSpider/... - Population transcriptomics of life-history variation in the genus SalmoThomas 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... - 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... - A human genome diversity cell line panelHoward M Cann
Science 296:261-2. 2002 - Intra-deme molecular diversity in spatially expanding populationsNicolas 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... - Special issue: analytical methods in phylogeography and genetic structureLaurent Excoffier
Mol Ecol 13:727. 2004 - Statistical evaluation of alternative models of human evolutionNelson 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.... - Genetic variation and population structure in native AmericansSijia 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... - Italy as a major Ice Age refuge area for the bat Myotis myotis (Chiroptera: Vespertilionidae) in EuropeManuel 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... - Geographic patterns of genome admixture in Latin American MestizosSijia 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... - The detection of regions of our genome under selection has increasingly relied on the use of genome scansLaurent Excoffier
Hum Genomics 2:155-7. 2005 - Conserved noncoding sequences are selectively constrained and not mutation cold spotsJared 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...