W Stephan

Summary

Affiliation: University of Munich
Country: Germany

Publications

  1. pmc Gene expression variation in African and European populations of Drosophila melanogaster
    Stephan Hutter
    Section of Evolutionary Biology, Department of Biology, University of Munich, Grosshaderner Strasse, Planegg Martinsried 82152, Germany
    Genome Biol 9:R12. 2008
  2. ncbi request reprint The recent demographic and adaptive history of Drosophila melanogaster
    W Stephan
    Section of Evolutionary Biology, Department of Biology II, University of Munich, Planegg Martinsried, Germany
    Heredity (Edinb) 98:65-8. 2007
  3. pmc The hitchhiking effect on linkage disequilibrium between linked neutral loci
    Wolfgang Stephan
    Section of Evolutionary Biology, Biocenter, University of Munich, Planegg Martinsried, Germany
    Genetics 172:2647-63. 2006
  4. ncbi request reprint Using multilocus sequence data to assess population structure, natural selection, and linkage disequilibrium in wild tomatoes
    Uraiwan Arunyawat
    Section of Evolutionary Biology, Department Biologie II, University of Munich LMU, Planegg Martinsried, Germany
    Mol Biol Evol 24:2310-22. 2007
  5. pmc Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations
    Pavlos Pavlidis
    Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg, Germany
    Genetics 185:907-22. 2010
  6. pmc Evidence that strong positive selection drives neofunctionalization in the tandemly duplicated polyhomeotic genes in Drosophila
    Steffen Beisswanger
    Section of Evolutionary Biology, Biocenter, University of Munich, Grosshaderner Strasse 2, 82152 Planegg Martinsried, Germany
    Proc Natl Acad Sci U S A 105:5447-52. 2008
  7. doi request reprint A population genomic approach to map recent positive selection in model species
    P Pavlidis
    Department of Biology, Section of Evolutionary Biology, University of Munich, Grosshaderner Strasse 2, 82152 Planegg Martinsried, Germany
    Mol Ecol 17:3585-98. 2008
  8. pmc Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure
    A Tellier
    Section of Evolutionary Biology, Department Biology II, University of Munich LMU, Planegg Martinsried, Germany
    Heredity (Edinb) 107:189-99. 2011
  9. pmc Inferring the population structure and demography of Drosophila ananassae from multilocus data
    Aparup Das
    Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilians University, 82152 Planegg Martinsried, Germany
    Genetics 168:1975-85. 2004
  10. ncbi request reprint Evidence of gene conversion associated with a selective sweep in Drosophila melanogaster
    Sascha Glinka
    Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilians University, Planegg Martinsried, Germany
    Mol Biol Evol 23:1869-78. 2006

Detail Information

Publications42

  1. pmc Gene expression variation in African and European populations of Drosophila melanogaster
    Stephan Hutter
    Section of Evolutionary Biology, Department of Biology, University of Munich, Grosshaderner Strasse, Planegg Martinsried 82152, Germany
    Genome Biol 9:R12. 2008
    ..However, previous expression surveys in this species generally focused on a small number of laboratory strains established from derived populations. Thus, these studies were not ideal for population genetic analyses...
  2. ncbi request reprint The recent demographic and adaptive history of Drosophila melanogaster
    W Stephan
    Section of Evolutionary Biology, Department of Biology II, University of Munich, Planegg Martinsried, Germany
    Heredity (Edinb) 98:65-8. 2007
    ..Comparable (but not significantly higher) substitution rates are found in derived populations that colonized new habitats outside Africa, such as in a European population that branched off from the African lineage about 16,000 ya...
  3. pmc The hitchhiking effect on linkage disequilibrium between linked neutral loci
    Wolfgang Stephan
    Section of Evolutionary Biology, Biocenter, University of Munich, Planegg Martinsried, Germany
    Genetics 172:2647-63. 2006
    ..Thus, hitchhiking may have a distinctively patterned LD-reducing effect, in particular near the target of selection...
  4. ncbi request reprint Using multilocus sequence data to assess population structure, natural selection, and linkage disequilibrium in wild tomatoes
    Uraiwan Arunyawat
    Section of Evolutionary Biology, Department Biologie II, University of Munich LMU, Planegg Martinsried, Germany
    Mol Biol Evol 24:2310-22. 2007
    ..The rapid decline of LD seems very promising for future association studies with the purpose of mapping functional variation in wild tomatoes...
  5. pmc Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations
    Pavlos Pavlidis
    Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg, Germany
    Genetics 185:907-22. 2010
    ..We demonstrate that the combination of SFS- and LD-based statistics increases the power to detect recent positive selection in populations that have experienced past demographic changes...
  6. pmc Evidence that strong positive selection drives neofunctionalization in the tandemly duplicated polyhomeotic genes in Drosophila
    Steffen Beisswanger
    Section of Evolutionary Biology, Biocenter, University of Munich, Grosshaderner Strasse 2, 82152 Planegg Martinsried, Germany
    Proc Natl Acad Sci U S A 105:5447-52. 2008
    ..Our results suggest that neofunctionalization has been achieved in the Drosophila ph genes through the action of strong positive selection and the inactivation of gene conversion in part of the gene...
  7. doi request reprint A population genomic approach to map recent positive selection in model species
    P Pavlidis
    Department of Biology, Section of Evolutionary Biology, University of Munich, Grosshaderner Strasse 2, 82152 Planegg Martinsried, Germany
    Mol Ecol 17:3585-98. 2008
    ..In genomic regions of normal recombination rates, the targets of positive selection have been mapped down to the level of individual genes...
  8. pmc Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure
    A Tellier
    Section of Evolutionary Biology, Department Biology II, University of Munich LMU, Planegg Martinsried, Germany
    Heredity (Edinb) 107:189-99. 2011
    ..These results suggest that closely related species with similar genetic backgrounds but experiencing contrasting environments differ in the variance of deleterious fitness effects...
  9. pmc Inferring the population structure and demography of Drosophila ananassae from multilocus data
    Aparup Das
    Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilians University, 82152 Planegg Martinsried, Germany
    Genetics 168:1975-85. 2004
    ..The inferred migration routes of D. ananassae out of Sundaland seem to parallel those of humans in this region. Strong evidence for a population size expansion is seen particularly in the ancestral populations...
  10. ncbi request reprint Evidence of gene conversion associated with a selective sweep in Drosophila melanogaster
    Sascha Glinka
    Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilians University, Planegg Martinsried, Germany
    Mol Biol Evol 23:1869-78. 2006
    ..This region, however, was interrupted by gene conversion events leading to a strong haplotype structure in the center of the valley of reduced variation...
  11. pmc Compensatory evolution of a precursor messenger RNA secondary structure in the Drosophila melanogaster Adh gene
    Ying Chen
    Department of Biology II, University of Munich, 80333 Munich, Germany
    Proc Natl Acad Sci U S A 100:11499-504. 2003
    ..Implications for RNA secondary structure and intron evolution are discussed...
  12. pmc Evidence for a selective sweep in the wapl region of Drosophila melanogaster
    Steffen Beisswanger
    Section of Evolutionary Biology, Department of Biology II, University of Munich, D 82152 Planegg Martinsried, Germany
    Genetics 172:265-74. 2006
    ..Evidence that this sweep may have originated in an ancestral population in Africa is presented...
  13. pmc Inferring the demographic history and rate of adaptive substitution in Drosophila
    Haipeng Li
    Section of Evolutionary Biology, Department of Biology II, University of Munich, Planegg Martinsried, Germany
    PLoS Genet 2:e166. 2006
    ..05% and 0.5%) were fixed in the euchromatic portion of the X in the African population since population size expansion, and about 60 mutations (with s around 0.5%) in the diverging European lineage...
  14. ncbi request reprint Genealogical footprints of speciation processes in wild tomatoes: demography and evidence for historical gene flow
    Thomas Stadler
    Department Biologie II, University of Munich, Grosshaderner Strasse 2, D 82152 Planegg Martinsried, Germany
    Evolution 59:1268-79. 2005
    ....
  15. pmc Distinctly different sex ratios in African and European populations of Drosophila melanogaster inferred from chromosomewide single nucleotide polymorphism data
    Stephan Hutter
    Section of Evolutionary Biology, Biocenter, University of Munich, 82152 Planegg Martinsried, Germany
    Genetics 177:469-80. 2007
    ..The patterns of the frequency spectrum and the levels of linkage disequilibrium observed in Europe suggest that, in addition, positive selection must have acted in the derived population...
  16. ncbi request reprint Inferring the effects of demography and selection on Drosophila melanogaster populations from a chromosome-wide scan of DNA variation
    Lino Ometto
    Section of Evolutionary Biology, Biocenter, University of Munich, Grosshaderner Strasse 2, D 82152 Planegg Martinsried, Germany
    Mol Biol Evol 22:2119-30. 2005
    ..We also found that while this bottleneck can account for most of the reduction in variation observed in the European sample, there is a deficit of polymorphism in some genomic regions that cannot be explained by demography alone...
  17. pmc Maximum-likelihood methods for detecting recent positive selection and localizing the selected site in the genome
    Haipeng Li
    Section of Evolutionary Biology, Department of Biology II, University of Munich, 82152 Planegg Martinsried, Germany
    Genetics 171:377-84. 2005
    ..Evidence of selection was found for both populations (including a selective sweep that was shared between both populations)...
  18. pmc Pleiotropic effect of disrupting a conserved sequence involved in a long-range compensatory interaction in the Drosophila Adh gene
    John F Baines
    Department of Biology II, Section of Evolutionary Biology, University of Munich, 80333 Munich, Germany
    Genetics 166:237-42. 2004
    ..We find that a classical result was not observed due to the pleiotropic effect of changing a nucleotide involved in both long-range base pairing and the negative regulation of gene expression...
  19. ncbi request reprint Homogeneity of common cosmopolitan inversion frequencies in Southeast Asian Drosophila melanogaster
    Sascha Glinka
    Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilians University, Grosshadernerstr 2, 82152 Planegg Martinsried, Germany
    J Genet 84:173-8. 2005
    ..g. balancing selection)...
  20. ncbi request reprint Pervasive adaptive evolution among interactors of the Drosophila hybrid inviability gene, Nup96
    Daven C Presgraves
    Section of Evolutionary Biology, Biocenter, University of Munich, Planegg Martinsried, Germany
    Mol Biol Evol 24:306-14. 2007
    ..We suggest that genetic conflict-driven processes may have contributed to the rapid molecular evolution of Nup107 subcomplex genes...
  21. doi request reprint Analyzing the evolution of RNA secondary structures in vertebrate introns using Kimura's model of compensatory fitness interactions
    Robert Piskol
    Department of Biology II, Section of Evolutionary Biology, Ludwig Maximilians University, Munich, Germany
    Mol Biol Evol 25:2483-92. 2008
    ..Furthermore, we find that wobbles and mismatches are more frequent in the middle of a helix, whereas covariations occur preferentially at the helix ends. The GC content is a major determinant of this pattern...
  22. pmc Insertion/deletion and nucleotide polymorphism data reveal constraints in Drosophila melanogaster introns and intergenic regions
    Lino Ometto
    Section of Evolutionary Biology, Biocenter, University of Munich, Planegg Martinsried, Germany
    Genetics 169:1521-7. 2005
    ....
  23. pmc Detecting a local signature of genetic hitchhiking along a recombining chromosome
    Yuseob Kim
    Department of Evolutionary Biology, University of Munich, 80333 Munich, Germany
    Genetics 160:765-77. 2002
    ..This method also allows us to estimate the strength and the location of directional selection from DNA sequence data...
  24. pmc The role of natural selection in genetic differentiation of worldwide populations of Drosophila ananassae
    John F Baines
    Department of Biology II, Section of Evolutionary Biology, University of Munich, 82152 Planegg Martinsried, Germany
    Genetics 168:1987-98. 2004
    ..Taken together, significant clinal variation and a test against alternative models of natural selection provide evidence of two independent selective sweeps restricted to specific regions of the species range...
  25. pmc Linkage disequilibrium under genetic hitchhiking in finite populations
    P Pfaffelhuber
    Ludwig Maximilians University, Biocenter, 82152 Planegg, Germany
    Genetics 179:527-37. 2008
    ..e., in <0.1N generations-destroyed after the fixation of the beneficial allele for moderately distant neutral loci, where N is the diploid population size...
  26. pmc Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach
    Sascha Glinka
    Section of Evolutionary Biology, Department of Biology II, University of Munich, D 80333 Munich, Germany
    Genetics 165:1269-78. 2003
    ..Our study shows the advantages of a genomic approach (over a locus-specific analysis) in disentangling demographic and selective forces...
  27. pmc Contrasting patterns of sequence divergence and base composition between Drosophila introns and intergenic regions
    Lino Ometto
    Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg Martinsried, Germany
    Biol Lett 2:604-7. 2006
    ..Divergence is positively correlated with recombination rate in intergenic regions, but not in introns. We argue that these differences are due to different selective constraints rather than mutational or recombinational mechanisms...
  28. doi request reprint msABC: a modification of Hudson's ms to facilitate multi-locus ABC analysis
    P Pavlidis
    Department of Biology II, Section of Evolutionary Biology, University of Munich, Grosshaderner Strasse 2, 82152 Planegg Martinsried, Germany
    Mol Ecol Resour 10:723-7. 2010
    ..The source code of msABC is available at http://bio.lmu.de/~pavlidis/msabc or upon request from the authors...
  29. doi request reprint Recent strong positive selection on Drosophila melanogaster HDAC6, a gene encoding a stress surveillance factor, as revealed by population genomic analysis
    Nicolas Svetec
    Department of Biology, Section of Evolutionary Biology, LMU BioCenter, Planegg Martinsried, Germany
    Mol Biol Evol 26:1549-56. 2009
    ..Its ubiquitin-binding and tubulin-deacetylase activities suggest that HDAC6 is very different from other histone deacetylases. Indeed, recent discoveries have shown that HDAC6 is a key regulator of cytotoxic stress resistance...
  30. pmc Genetic hitchhiking versus background selection: the controversy and its implications
    Wolfgang Stephan
    Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilians University Munich, Grosshaderner Strasse 2, 82152 Planegg, Germany
    Philos Trans R Soc Lond B Biol Sci 365:1245-53. 2010
    ....
  31. pmc In vivo introduction of unpreferred synonymous codons into the Drosophila Adh gene results in reduced levels of ADH protein
    David B Carlini
    Department of Biology, American University, Washington, DC 20016, USA
    Genetics 163:239-43. 2003
    ..The observed differences in protein production appear to be too large to be consistent with current estimates of the strength of selection on synonymous sites in D. melanogaster...
  32. ncbi request reprint DNA sequence variation at a duplicated gene: excess of replacement polymorphism and extensive haplotype structure in the Drosophila melanogaster bicoid region
    John F Baines
    Department Biologie II Evolutionsbiologie, Universitat Munchen, Germany
    Mol Biol Evol 19:989-98. 2002
    ....
  33. doi request reprint Evolution of mating isolation between populations of Drosophila ananassae
    Malcolm D Schug
    Biology Department, University of North Carolina Greensboro, Greensboro, NC 27402, USA
    Mol Ecol 17:2706-21. 2008
    ..Furthermore, both the genetic and behavioral results cast doubt on the status of D. pallidosa as a good species...
  34. pmc The relationship of nucleotide polymorphism, recombination rate and selection in wild tomato species
    Kerstin Roselius
    Department Biologie II, Abteilung Evolutionsbiologie, University of Munich LMU, Planegg Martinsried, Germany
    Genetics 171:753-63. 2005
    ..In addition, we hypothesize that the soil seed bank plays an important role in the maintenance of the large genetic diversity in the SI species (in particular L. peruvianum)...
  35. pmc Distinguishing the hitchhiking and background selection models
    Hideki Innan
    Human Genetics Center, University of Texas Health Science Center, Houston, Texas 77030, USA
    Genetics 165:2307-12. 2003
    ..The method is applied to data from Drosophila melanogaster and two highly selfing tomato species...
  36. pmc Population genetics of speciation in two closely related wild tomatoes (Solanum section Lycopersicon)
    Thomas Stadler
    Department Biologie II, Abteilung Evolutionsbiologie, University of Munich LMU, 82152 Planegg Martinsried, Germany
    Genetics 178:339-50. 2008
    ..55 million years. We discuss possible biases in the demographic parameter estimates due to the current restriction of DPG algorithms to panmictic species...
  37. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  38. pmc Bayesian variable selection for detecting adaptive genomic differences among populations
    Andrea Riebler
    Institute of Social and Preventive Medicine, University of Zurich, Zurich, Switzerland
    Genetics 178:1817-29. 2008
    ..For data sets with small sample sizes, high mutation rates, and/or long sequences, however, methods based on nucleotide statistics should be preferred...
  39. doi request reprint Population genetic inference using a fixed number of segregating sites: a reassessment
    Sebastian E Ramos-Onsins
    Max Planck Institute of Chemical Ecology, Jena, Germany
    Genet Res 89:231-44. 2007
    ..With single-locus data, the FS procedure should not be employed for models other than the standard neutral model...
  40. pmc Population subdivision and molecular sequence variation: theory and analysis of Drosophila ananassae data
    Claus Vogl
    Department Biologie II, Ludwig Maximilians Universitat, D 80333 Munchen, Germany
    Genetics 165:1385-95. 2003
    ..The population as a whole seems to be expanding. A population from Bogor (Java, Indonesia) shows the highest variation and seems closest to the species center...
  41. ncbi request reprint Global mRNA stability is not associated with levels of gene expression in Drosophila melanogaster but shows a negative correlation with codon bias
    Hans K Stenøien
    Plant Ecology Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, SE 752 36, Uppsala, Sweden
    J Mol Evol 61:306-14. 2005
    ..This finding does not support the hypothesis that codon bias has evolved as an indirect consequence of selection favoring thermodynamically stable mRNA molecules...
  42. ncbi request reprint Population history of the Dniester-Carpathians: evidence from Alu markers
    Alexander Varzari
    National Center of Reproductive Health and Medical Genetics, Kishinev, Moldova
    J Hum Genet 52:308-16. 2007
    ..In particular, Gagauzes, a Turkic-speaking population, show closer affinities to their geographical neighbors than to other Turkic populations...