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Prof. Dr. Wolfgang Stephan

Bild des Benutzers wolfgang.stephan

Forschung

Prof. Stephans Forschungsgruppe am Museum für Naturkunde Berlin arbeitet an mathematischen Modellen der schnellen Adaptation. Diese Arbeit wird von der Deutschen Forschungsgemeinschaft als Teil des Schwerpunktprogramms „Rapid evolutionary adaptation: potential and constraints“ unterstützt. Innerhalb dieses Programms bestehen Kooperationen mit dem Max Planck Institut für Evolutionsbiologie in Plön und der Technischen Universität München. Zusammen mit Anja Hörger von der Universität Salzburg hat er das Lehrbuch „Molekulare Populationsgenetik“ geschrieben, das im Jahr 2019 im Springer-Verlag erschienen ist.

Lebenslauf

Ausbildung

Abitur, Humanistisches Gymnasium Hassfurt, 1969
Diplom (M. S.), Physik (Nebenfach: Mathematik), University of Erlangen/Nürnberg, 1977
Dr. rer. nat. (Ph. D.), Theoretische Biophysik, Universität Konstanz, 1981

 

Preise und Ehrungen

DFG Postdoctoral Fellow, 1984
NIH Visiting Associate, 1987-89
NIH Shannon Award, 1991
University of Maryland, Semester Research Award, 1994
University of Barcelona, Distinguished Visiting Research Professor, 1996-97
CNRS, Visiting Scientist, Gif-sur-Yvette, 1998
Bernhard Rensch Lecture, University of Münster, 2006
DFG Research Unit "Natural Selection in Structured Populations", Speaker, 2008-16
DFG Senate Committee "Biodiversity", Panel Member, 2008-16
Center for Advanced Studies (CASLMU), LMU Munich, 2011-
European Research Council (ERC), Panel Member, 2016-

 

Wissenschaftliche Berufungen

Postdoctoral Fellow, Universities of Konstanz and Bremen, 1981-84, and Universities of Sussex and Edinburgh (with J. Maynard Smith and B. Charlesworth), 1984-85
Wissenschaftlicher Assistent, University of Technology Darmstadt, 1985-87
Visiting Associate, NIH, Research Triangle Park (with C.H. Langley), 1987-89
Assistant Professor, Department of Zoology, University of Maryland, College Park, 1989-95
Associate Professor, Department of Zoology, University of Maryland, College Park, 1995-97, and Department of Biology, University of Rochester, 1998-99
Full Professor, Department of Biology, University of Rochester, 1999-2000
Professor and Chair, Department of Biology, University of Munich, 2000-15
Visiting Researcher, Museum für Naturkunde Berlin, 2015-

 

Drittmittel-Förderung

  • NIH Grant, Potential mechanisms of epistatic fitness interactions, 1991-94
  • NSF Grant, Effects of a recent population size bottleneck on genetic variation of whooping cranes (Dissertation Research, Travis Glenn), 1994-96
  • NSF Grant, Effects of natural selection on genetic differentiation, 1994-98
  • NSF Research Training Grant, "Biology of small populations" (University of Maryland), PI, 1996-2001
  • NIH Grant (with S. Tanda, Ohio University), Evolution by mutations with compensatory fitness interactions, 1998-2002
  • DFG Grant, Die Rolle der natürlichen Selektion in der genetischen Differenzierung von Populationen, 2001-06
  • DFG Grant, A population genetic approach to speciation in the genus Lycopersicon, Schwerpunktprogramm "Radiationen - Genese biologischer Diversität", 2002-08
  • DFG Grant (with G. Heubl, LMU Munich), Origin, evolution and adaptive radiation in the genus Micromeria Benth. (Lamiaceae) in Macaronesia, Schwerpunktprogramm "Radiationen - Genese biologischer Diversität", 2002-04
  • DFG Grant, Nachweis der natürlichen Selektion auf dem X-Chromosom von Drosophila melanogaster, 2002-05
  • VolkswagenStiftung Grant (with D. Tautz, U. of Cologne), Detecting adaptive trait loci via selective sweeps, 2003-06
  • DFG Grant (with L. Rose, LMU Munich), Evolution of a pathogen resistance pathway in the tomato genus, 2005-07
  • DFG Grant, Genetics of adaptation: selective sweeps in Drosophila melanogaster, 2007-10
  • DFG Grant, Population genetics of adaptation in wild tomatoes, 2007-10
  • DFG Grant (with U. Gerland, LMU Munich), Adaptation sensu Sewall Wright: evolution over rugged fitness landscapes, 2007-10
  • DFG Research Unit Grant, Selective sweeps in Drosophila melanogaster, 2008-14
  • DFG Grant (with S. Hutter, LMU Munich), Recent selection on immunity genes in Drosophila, Schwerpunktprogramm "Host-parasite coevolution", 2009-12
  • DFG Grant, Species demography and the distribution of fitness effects of new deleterious mutations in wild tomatoes (Solanum section Lycopersicon), 2010-13
  • DFG Grant, Adaptation genomics of wild tomatoes, 2012-15
  • DFG Grant (with S. Hutter, LMU Munich), Evidence for balancing selection at immunity genes in Drosophila, Schwerpunktprogramm "Host-parasite coevolution", 2012-15
  • DFG Grant, Recurrent selective sweeps versus trench warfare in host-parasite coevolution, Schwerpunktprogramm "Probabilistic Structures in Evolution", 2012-15
  • EU Grant, Marie Curie ITN "Intercrossing", Selective sweep data and next-generation-sequence data analysis, 2012-15
  • Center for Advanced Studies CASLMU (with G. Grupe, LMU Munich), Schwerpunktprogramm "Evolutionary Biology", 2014-16
  • DFG Schwerpunktprogramm (with K. Schmid, K. Fischer, E. Stukenbrock, and R. Tiedemann), "Rapid evolutionary adaptation: Potential and constraints", 2015-21
  • DFG Grant, Modeling and inference of genomic signatures of polygenic selection driving fast adaptation, Schwerpunktprogramm "Rapid evolutionary adaptation: Potential and constraints", 2015-21
  • DFG Grant, The role of recombination in rapid adaptive evolution of fungal plant pathogens: a comparative population genomics study (with E. Stukenbrock, MPI für Evolutionsbiologie, Plön), Schwerpunktprogramm "Rapid evolutionary adaptation: Potential and constraints", 2015-21
  • DFG Grant, Recurrent selective sweeps versus trench warfare in host-parasite coevolution: the influence of population size changes (with Aurélien Tellier, TU Munich), Schwerpunktprogramm "Probabilistic Structures in Evolution", 2016-2019
  • Icelandic Research Fund Grant of Excellence (with E. Arnason, K. Halldorsdottir, B. Eldon, and A. Etheridge), “Population genomics of highly fecund codfish“, 2018-21

 

Redaktionen

Associate Editor, Evolution, 1993-95
Associate Editor, Molecular Biology and Evolution, 1998-2003
Associate Editor, Genetics, 1998-2003 and 2011-17

 

Doktorandinnen und Doktoranden

T. Wiehe (Dr. rer. nat., 1995; DAAD fellow; now Professor, U. of Cologne)
D. A. Kirby (Ph.D., 1996; now Professor, California State U., San Luis Obispo)
T. C. Glenn (Ph.D., 1997; now Research Scientist, U. of Georgia, SREL)
J. Parsch (Ph.D., 1998; now Professor, LMU Munich)
Y. Kim (Ph.D., 2002; now Professor, Ewha Woman's U., Seoul)
Y. Chen (Ph.D., 2003; Walter-Fitch-Prize 2002; now private sector)
J. F. Baines (Dr. rer. nat., 2004; now Professor, U. of Kiel)
S. Glinka (Dr. rer. nat., 2005; now private sector)
L. Ometto (Dr. rer. nat., 2006; Canestrini Award 2005; now Researcher-tenure track, U. of Pavia)
S. Beisswanger (Dr. rer. nat., 2006; now private sector)
U. Arunyawat (Dr. rer. nat., 2007; DAAD fellow; now Associate Professor, Kasetsart U., Bangkok, Thailand)
S. Hutter (Dr. rer. nat., 2007; now private sector)
N. Svetec (Dr. rer. nat., 2009; now Research Associate, Rockefeller U., New York)
L. Grzeskowiak (Dr. rer. nat., 2009; now private sector)
C. Merino (Dr. rer. nat., 2009; now private sector)
H. Xia (Ph.D., 2010; private sector)
A. Hörger  (Dr. rer. nat., 2011; now Assistant Professor-tenure track, U. of Salzburg)
S. Laurent (Dr. rer. nat., 2011; now Postdoc, MPI für Züchtungsforschung, Köln)
P. Pavlidis (Dr. rer. nat., 2011; Fellow of VW-Foundation; now Researcher-tenure track, Institute of Molecular Biology and Biotechnology (IMBB), Greece)
R. Piskol (Dr. rer. nat., 2011; now private sector)
A. Werzner (Dr. rer. nat., 2011; now DKMS German Bone Marrow Donor Center, Tübingen, Germany)
I. Fischer (Dr. rer. nat., 2012; Fellow of Bavarian Eliteförderung; now private sector)
F. Paparazzo (Dr. rer. nat., 2013; now High School Teacher in Milano)
P. Duchén (Dr. rer. nat., 2014; now Postdoc, University of Fribourg)
R. Wilches (Dr. rer. nat., 2014; Fellow of VW-Foundation; now private sector)
K. Böndel (Dr. rer. nat., 2014; now Group Leader, U. of Hohenheim)
S. Voigt (Dr. rer. nat., 2015; now Postdoc, TU Dresden)
V. Božičević (Dr. rer. nat., 2017; private sector)
K. von Heckel (Dr. rer. nat., 2017; now private sector)
M. Croze  (Dr. rer. nat., 2017; now Postdoc, Ewha Woman's U., Seoul)


Postdocs

J. M. Braverman (1997-98; Sloan fellow; now Jesuit Brother)
C. Kerdelhué (1998-99; now Chargée de recherche, INRA, Orleans)
D. Carlini (1999-2001; now Associate Professor, American U., Washington, DC)
H. Innan (1999-2000; Japan Society for the Promotion of Science fellow; now Professor, Graduate University for Advanced Studies, Hayama, Japan)
E. Baudry (1999-2000; now Maitre de Conference, U. of Paris, Orsay)
A. Das (2000-04; now Director, National Institute of Research in Tribal Health (NIRTH), Jabalpur, India)
S. Mohanty (2000-04; now Associate Professor, Jaypee Institute of Information Technology U., Noida/Delhi)
T. Städler (2001-07; now Wissenschaftlicher Mitarbeiter, ETH Zürich)
H. Stenøien (2001; now Professor, U. of Trondheim)
S. Mousset (2002-04; Marie Curie fellow; now Maitre de Conference, U. of Lyon)
D. Presgraves (2003-04; Alexander von Humboldt fellow; now Professor, U. of Rochester)
H. Li (2003-06; now Group Leader, MPI for Computational Biology, Shanghai)
L. Camus-Kulandaivelu (2007-09; now Chargée de Recherche, CIRAD, Montpellier)
A. Tellier (2007-12; Fellow of VW-Foundation; now Professor, TU Munich)
M. Mboup (2009-12; now private sector)
D. Živković (2009-16, Fellow of VW-Foundation; now private sector)
T. Nosenko (2012-15; now Postdoc, Helmholtz Center, Munich)
A. Wollstein (2012-15, Fellow of VW-Foundation; now private sector)
B. Eldon (since 2015)
S. John (since 2016)

 

Wissenschaftliche Assistentinnen und Assistenten

E. Baake (2000-01; now Professor, U. of Bielefeld)
C. Vogl (2001-02; now Assistant Professor, Vet. med. U. of Vienna)
D. De Lorenzo (2000-06; now Associate Professor, U. Pompeu Fabra, Barcelona)
P. Pfaffelhuber (2004-07; now Professor, U. of Freiburg)
L. Rose (2002-10; now Professor, U. of Düsseldorf)
S. Hutter (2008-15; now private sector)
K. Böndel (2014-15; now Group Leader, U. of Hohenheim)

Publikationen

Prof. Dr. Wolfgang Stephan

a) Lehrbuch

Wolfgang Stephan, Anja C. Hörger (2019):  Molekulare Populationsgenetik – Theoretische Konzepte und empirische Evidenz. Springer-Verlag, Heidelberg

 
b) Begutachtete Fachartikel

  1. Frehland, E. and W. Stephan (1979): Theory of single-file noise. Biochim. Biophys. Acta 553: 326-341
  2. Läuger, P., W. Stephan, and E. Frehland (1980): Fluctuations of barrier structure in ionic channels. Biochim. Biophys. Acta 602: 167-180
  3. Läuger, P., W. Stephan, and E. Frehland (1980): Ion channels and ion pumps. In: Hydrogen Ion Transport in Epithelia (I. Schulz et al., eds.), pp. 3-10, Elsevier/North-Holland Biomedical Press
  4. Frehland, E. and W. Stephan (1983): Rate theory models for ion transport through rigid pores. I. Time-dependent analysis in the case of vanishing interactions. J. theor. Biol. 103: 77-97
  5. Stephan, W. and E. Frehland (1983): Rate theory models for ion transport through rigid pores. II. Time-dependent analysis of the single-file model with special reference to oscillatory behavior. J. theor. Biol. 103: 481-505
  6. Stephan, W., B. Kleutsch, and E. Frehland (1983): Rate theory models for ion transport through rigid pores. III. Continuum vs discrete models in single-file diffusion. J. theor. Biol. 105: 287-310
  7. Stephan, W. (1985): Complex membrane transport systems –  a non-Markovian approach. Biophys. Chem. 21: 41-55
  8. Kreikenbohm, R. and W. Stephan (1985):  Application of a two-compartment model to the wall growth of Pelobacter acidigallici under continuous culture conditions. Biotechnol. Bioeng. 27: 296-301
  9. Stephan, W. (1986): Recombination and the evolution of satellite DNA. Genet. Res. 47: 167-174
  10. Charlesworth, B., C. H. Langley, and W. Stephan (1986): The evolution of restricted recombination and the accumulation of repeated DNA sequences. Genetics 112: 947-962
  11. Stephan, W. (1986): Nonlinear phenomena in the evolution of satellite DNA. Ber. Bunsenges. Phys. Chem. 90: 1029-1034
  12. Stephan, W. (1987): Quantitative variation and chromosomal location of satellite DNAs. Genet. Res. 50: 41-52
  13. Stephan, W. (1989): Tandem-repetitive noncoding DNA: Forms and forces. Mol. Biol. Evol. 6: 198-212
  14. Stephan, W. and C. H. Langley (1989): Molecular genetic variation in the centromeric region of the X chromosome in three Drosophila ananassae populations. I. Contrasts between the vermilion and forked loci. Genetics 121: 89-99
  15. Stephan, W. (1989): Molecular genetic variation in the centromeric region of the X chromosome in three Drosophila ananassae populations. II. The Om(1D) locus. Mol. Biol. Evol. 6: 624-635
  16. Lange, B. W., C. H. Langley, and W. Stephan (1990): Molecular evolution of Drosophila metallothionein genes. Genetics 126: 921-932
  17. Stephan, W., T. H. E. Wiehe, and M. W. Lenz (1992): The effect of strongly selected substitutions on neutral polymorphism: Analytical results based on diffusion theory. Theoret. Popul. Biol. 41: 237-254
  18. Stephan, W. and C. H. Langley (1992): Evolutionary consequences of DNA mismatch inhibited repair opportunity. Genetics 132: 567-574
  19. Stephan, W. and S. J. Mitchell (1992): Reduced levels of DNA polymorphism and fixed between-population differences in the centromeric region of Drosophila ananassae. Genetics 132: 1039-1045
  20. Stephan, W., L. Chao, and J. G. Smale (1993): The advance of Muller's ratchet in a haploid asexual population: Approximate solutions based on diffusion theory. Genet. Res. 61: 225-231
  21. Wiehe, T. H. E. and W. Stephan (1993): Analysis of a genetic hitchhiking model and its application to DNA polymorphism data from Drosophila melanogaster. Mol. Biol. Evol. 10: 842-854
  22. Stephan, W. and D. A. Kirby (1993): RNA folding in Drosophila shows a distance effect for compensatory fitness interactions. Genetics 135: 97-103
  23. Tomimura, Y., M. Matsuda, Y. N.  Tobari, K. L. Cariou, J. L. Da Lage, W. Stephan, and C. H. Langley (1993): Population genetics. In: Drosophila ananassae. Genetical and Biological Aspects (Y. N. Tobari, ed.), pp. 139-198, Japan Scientific Societies Press (Tokyo) and Karger Verlag (Basel)
  24. Stephan, W. (1994): Effects of genetic recombination and population subdivision on nucleotide sequence variation in Drosophila ananassae. In: Non-neutral Evolution: Theories and Molecular Data (B. Golding, ed.), pp. 57-66, Chapman and Hall, New York
  25. Stephan, W. and S. Cho (1994): Possible role of natural selection in the formation of tandem-repetitive noncoding DNA. Genetics 136: 333-341
  26. Charlesworth, B., P. Sniegowski, and W. Stephan (1994): The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371: 215-220
  27. Stephan, W., V. S. Rodriguez, B. Zhou, and J. Parsch (1994): Molecular evolution of the metallothionein gene Mtn in the melanogaster species group: Results from Drosophila ananassae. Genetics 138: 135-143
  28. Braverman, J. M., R. R. Hudson, N. L. Kaplan, C. H. Langley, and W. Stephan (1995): The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics 140: 783-796
  29. Stephan, W. (1995): An improved method for estimating the rate of fixation of favorable mutations based on DNA polymorphism data. Mol. Biol. Evol. 12: 959-962
  30. Kirby, D. A., S. V. Muse, and W. Stephan (1995):  Maintenance of pre-mRNA secondary structure by epistatic selection. Proc. Natl. Acad. Sci. USA 92: 9047-9051
  31. Kirby, D. A. and W. Stephan (1995): Haplotype test reveals departure from neutrality in a segment of the white gene of Drosophila melanogaster. Genetics 141: 1483-1490
  32. Stephan, W. (1995): Perturbation analysis of a two-locus model with directional selection and recombination. J. Math. Biol. 34: 95-109
  33. Glenn, T. C., W. Stephan, H. C. Dessauer, and M. J. Braun (1996): Allelic diversity in alligator microsatellite loci is negatively correlated with GC content of flanking sequences and evolutionary conservation of PCR amplifiability. Mol. Biol. Evol. 13: 1151-1154
  34. Stephan, W. (1996): The rate of compensatory evolution. Genetics 144: 419-426
  35. Kirby, D. A. and W. Stephan (1996): Multi-locus selection and the structure of the white gene of Drosophila melanogaster. Genetics 144: 635-645
  36. Parsch, J., S. Tanda, and W. Stephan (1997): Site-directed mutations reveal long-range compensatory interactions in the Adh gene of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 94: 928-933
  37. Perlitz, M. and W. Stephan (1997): The mean and variance of the number of segregating sites since the last hitchhiking event. J. Math. Biol. 36: 1-23
  38. Glenn, T. C., R. S. Ojerio, W. Stephan, and M. J. Braun (1997): Microsatellite DNA loci for genetic studies of cranes. Proc. North Am. Crane Workshop 7: 36-45
  39. Stephan, W. (1997): Mathematical model of the hitchhiking effect, and its application to DNA polymorphism data. In: Advances in Mathematical Population Dynamics: Molecules, Cells and Man (O. Arino, D. Axelrod, and M. Kimmel, eds.), pp. 29-45, World Scientific, London
  40. Stephan, W. (1997): Tandemly repeated noncoding DNA sequences. In: The Encyclopedia of Molecular Biology and Molecular Medicine, Vol. 6 (R. A. Meyers, ed.), pp. 1-10, Verlagsgesellschaft, Weinheim
  41. Stephan, W., L. Xing, D. A. Kirby, and J. M. Braverman (1998): A test of the background selection hypothesis based on nucleotide data from Drosophila ananassae. Proc. Natl. Acad. Sci. USA 95: 5649-5654
  42. Parsch, J., W. Stephan, and S. Tanda (1998): Long-range base pairing in Drosophila and human mRNA sequences. Mol. Biol. Evol. 15: 820-826
  43. Stephan, W. and Y. Kim (1998): Persistence of microsatellite arrays in finite populations. Mol. Biol. Evol. 15: 1332-1336
  44. Stephan, W. and C. H. Langley (1998): DNA polymorphism in Lycopersicon and crossing-over per physical length. Genetics 150: 1585-1593
  45. Chen, Y., D. B. Carlini, J. F. Baines, J. Parsch, J. M. Braverman, S. Tanda, and W. Stephan (1999): RNA secondary structure and compensatory evolution. Genes and Genetic Systems 74: 271-286
  46. Parsch, J., W. Stephan, and S. Tanda (1999): A highly conserved sequence in the 3' untranslated region of the Drosophila Adh gene plays a functional role in the regulation of Adh expression. Genetics 151: 667-674
  47. Stephan, W., B. Charlesworth, and G. McVean (1999): The effect of background selection at a single locus on weakly selected, partially linked variants. Genet. Res. 73: 133-146
  48. Kim, Y. and W. Stephan (1999): Allele frequency changes of genetic markers in artificial selection experiments – the precision and power of QTL mapping. Genet. Res. 73: 177-184
  49. Glenn, T. C., W. Stephan, and M. J. Braun (1999): Effects of a population bottleneck on whooping crane mitochondrial DNA variation. Cons. Biol. 13: 1097-1107
  50. Begun, D. J., A. J. Betancourt, C. H. Langley, and W. Stephan (1999): Is the Fast/Slow allozyme variation at the Adh locus of Drosophila melanogaster an ancient balanced polymorphism? Mol. Biol. Evol. 16: 1816-1819
  51. Parsch, J., J. M. Braverman, and W. Stephan (2000): Comparative sequence analysis and patterns of covariation in RNA secondary structures. Genetics 154: 909-921
  52. Chen, Y., B. J. Marsh, and W. Stephan (2000): Joint effects of natural selection and recombination on gene flow between Drosophila ananassae populations. Genetics 155: 1185-1194
  53. Kim, Y. and W. Stephan (2000): Joint effects of genetic hitchhiking and background selection on neutral variation. Genetics 155: 1415-1427
  54. Innan, H. and W. Stephan (2000): The coalescent in an exponentially growing metapopulation, and its application to Arabidopsis thaliana. Genetics 155: 2015-2019
  55. Parsch, J., J. Russel, I. Berman, D. L. Hartl, and W. Stephan (2000): Deletion of a conserved regulatory element in the Drosophila Adh gene leads to increased ADH activity but also delays development. Genetics 156: 219-227
  56. Baudry, E., C. Kerdelhué, H. Innan, and W. Stephan (2001): Species and recombination effects on DNA variability in the tomato genus. Genetics 158: 1725-1735
  57. Innan, H. and W. Stephan (2001): Selection intensity against deleterious mutations in RNA secondary structures and rate of compensatory nucleotide substitutions. Genetics 159: 389-399
  58. Carlini, D. B., Y. Chen, and W. Stephan (2001): The relationship between third codon position nucleotide content, codon bias, mRNA secondary structure, and gene expression in the drosophilid alcohol dehydrogenase genes Adh and Adhr. Genetics 159: 623-633
  59. Kim, Y. and W. Stephan (2002): Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777
  60. Baines, J. F., Y. Chen, A. Das, and W. Stephan (2002): DNA sequence variation at a duplicated gene: Excess of replacement polymorphism and extensive haplotype structure in the Drosophila melanogaster bicoid region. Mol. Biol. Evol. 19: 989-998
  61. Stephan, W. (2002): Evolution of genome organisation. In: Encyclopedia of Life Sciences, Vol. 6, pp. 673- 678, Nature Publishing Group, London
  62. Walsh, J. B. and W. Stephan (2002): Multigene families: evolution. In: Encyclopedia of Life Sciences, Vol. 12, pp. 406-412, Nature Publishing Group, London
  63. Stephan, W. and J. B. Walsh (2002): Repetitive DNA: evolution. In: Encyclopedia of Life Sciences, Vol. 16, pp. 282-288, Nature Publishing Group, London
  64. Stephan, W. and Y. Kim (2002): Recent applications of diffusion theory to population genetics. In: Modern Developments in Theoretical Population Genetics (M. Slatkin and M. Veuille, eds.), pp. 72-93, Oxford University Press, Oxford
  65. Carlini, D. B. and W. Stephan (2003): In vivo introduction of unpreferred synonymous codons into the Drosophila Adh gene results in reduced levels of ADH protein. Genetics 163: 239-243
  66. Kim, Y. and W. Stephan (2003): Selective sweeps in the presence of interference among partially linked loci. Genetics 164: 389-398
  67. Chen, Y. and W. Stephan (2003): Compensatory evolution of a precursor messenger RNA secondary structure in the Drosophila melanogaster Adh gene. Proc. Natl. Acad. Sci. USA 100: 11499-11504
  68. Glinka, S., L. Ometto, S. Mousset, W. Stephan, and D. De Lorenzo (2003): Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multilocus approach. Genetics 165: 1269-1278
  69. Vogl, C., A. Das, M. Beaumont, S. Mohanty, and W. Stephan (2003): Population subdivision and molecular sequence variation: Theory and analysis of Drosophila ananassae data. Genetics 165: 1385-1395
  70. Innan, H. and W. Stephan (2003): Distinguishing the hitchhiking and background selection models. Genetics 165: 2307-2312
  71. Baines, J. F., J. Parsch, and W. Stephan (2004): Pleiotropic effect of disrupting a conserved sequence involved in a long-range compensatory interaction in the Drosophila Adh gene. Genetics 166: 237-242
  72. Das, A., S. Mohanty, and W. Stephan (2004): Inferring population structure and demography of Drosophila ananassae from multilocus data. Genetics 168: 1975-1985
  73. Baines, J. F., A. Das, S. Mousset, and W. Stephan (2004): The role of natural selection in genetic differentiation of worldwide populations of Drosophila ananassae. Genetics 168: 1987-1998
  74. Ometto, L., W. Stephan, and D. De Lorenzo (2005):  Insertion/deletion and nucleotide polymorphism data reveal constraints in Drosophila melanogaster introns and intergenic regions. Genetics 169: 1521-1527
  75. Städler, T., K. Roselius, and W. Stephan (2005): Genealogical footprints of speciation processes in wild tomatoes: Demography and evidence for historical gene flow. Evolution 59: 1268-1279
  76. Stenøien, H. and W. Stephan (2005):  Global mRNA stability is not associated with levels of gene expression in Drosophila melanogaster but shows a negative correlation with codon bias. J. Mol. Evol. 61: 306-314
  77. Glinka, S., W. Stephan, and A. Das (2005): Homogeneity of common cosmopolitan inversion frequencies in Southeast Asian Drosophila melanogaster. J. Genetics 84: 173-178
  78. Li, H. and W. Stephan (2005): Maximum likelihood methods for detecting recent positive selection and localizing the selected site in the genome. Genetics 171: 377-384
  79. Ometto, L., S. Glinka, D. De Lorenzo, and W. Stephan (2005): Inferring the effects of demography and selection on Drosophila melanogaster populations from a chromosome-wide scan of DNA variation. Mol. Biol. Evol. 22: 2119-2130
  80. Roselius, K., W. Stephan, and T. Städler (2005): The relationship of nucleotide polymorphism, recombination rate and selection in wild tomato species. Genetics 171: 753-763
  81. Wiehe, T., K. Schmid, and W. Stephan (2005): Selective sweeps in structured populations – Empirical evidence and theoretical studies. In: Selective Sweep (D. Nurminsky, ed.), pp. 104-117, Molecular Biology Intelligence Unit
  82. Stephan, W. (2005): Noncoding tandemly repeated DNA sequences. In: The Encyclopedia of Molecular Cell Biology and Molecular Medicine, Vol. 9 (R. A. Meyers, ed.), pp. 183-202, Wiley-VCH, Weinheim
  83. Stephan, W. (2005): Genetic hitchhiking and linkage disequilibrium. In: Mathematical Population Genetics (E. Baake, W. J. Ewens, and A. Wakolbinger, eds.), pp. 55-57, Mathematisches Forschungsinstitut Oberwolfach, Report No. 40/2005
  84. Chen, Y. and W. Stephan (2006): Weak selection on noncoding gene features. In: Evolutionary Genetics – Concepts and Case Studies (C. W. Fox and J. B. Wolf, eds.), pp. 133-143, Oxford University Press, Oxford
  85. Beisswanger, S., W. Stephan, and D. De Lorenzo (2006): Evidence for a selective sweep in the wapl region of Drosophila melanogaster. Genetics 172: 265-274
  86. Stephan, W., Y. S. Song, and C. H. Langley (2006): The hitchhiking effect on linkage disequilibrium between linked neutral loci. Genetics 172: 2647-2663
  87. Glinka, S., D. De Lorenzo, and W. Stephan (2006): Evidence of gene conversion associated with a selective sweep in Drosophila melanogaster. Mol. Biol. Evol. 23: 1869-1878
  88. Ometto, L., D. De Lorenzo, and W. Stephan (2006): Contrasting patterns of sequence divergence and base composition between Drosophila introns and intergenic regions. Biology Letters 2: 604-607
  89. Li, H. and W. Stephan (2006): Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genet. 2: e166
  90. Presgraves, D. C. and W. Stephan (2007): Pervasive adaptive evolution among interactors of the Drosophila hybrid inviability gene, Nup96. Mol. Biol. Evol. 24: 306-314
  91. Varzari, A. W. Stephan, V. Stepanow, F. Raicu, R. Cojocaru, Y. Roschin, C. Glavce, V. Dergachev, M. Spiridonova, H. D. Schmidt, and E. Weiss (2007): Population history of the Dniester-Carpathians: evidence from Alu markers. J. Hum. Genet. 52: 308-316
  92. Hutter, S., H. Li, S. Beisswanger, D. De Lorenzo, and W. Stephan (2007): Distinctly different sex ratios in African and European populations of Drosophila melanogaster inferred from chromosome-wide SNP data. Genetics 177: 469-480
  93. Arunyawat, U., W. Stephan, and T. Städler (2007): Using multilocus sequence data to assess population structure, natural selection and linkage disequilibrium in wild tomatoes. Mol. Biol. Evol. 24: 2310-2322
  94. Ramos-Onsins, S. E., S. Mousset, T. Mitchell-Olds, and W. Stephan (2007): Population genetic inference using a fixed number of segregating sites: a reassessment. Genet. Res. 89: 231-244
  95. Drosophila 12 Genomes Consortium (2007): Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218
  96. Stephan, W. and H. Li (2007): The recent demographic and adaptive history of Drosophila melanogaster. Heredity 98: 65-68
  97. Pavlidis, P., S. Hutter, and W. Stephan (2008): A population genomic approach to map recent positive selection in model species. Mol. Ecol. 17: 3585-3598
  98. Städler, T., U. Arunyawat, and W. Stephan (2008): Population genetics of speciation in two closely related wild tomatoes (Solanum Section Lycopersicon). Genetics 178: 339-350
  99. Riebler, A., L. Held, and W. Stephan (2008): Bayesian variable selection for detecting adaptive genomic differences among populations. Genetics 178: 1817-1829
  100. Pfaffelhuber, P., A. Lehnert, and W. Stephan (2008): Linkage disequilibrium under genetic hitchhiking in finite populations. Genetics 179: 527-537
  101. Hutter, S., S. S. Saminadin-Peter, W. Stephan, and J. Parsch (2008): Gene expression variation in African and European populations of Drosophila melanogaster. Genome Biol. 9: R12
  102. Beisswanger, S. and W. Stephan (2008): Evidence that strong positive selection drives neofunctionalization at the tandemly duplicated polyhomeotic genes in Drosophila. Proc. Natl. Acad. Sci. USA 105: 5447-52
  103. Schug, M. D., J. F. Baines, A. Killon-Atwood, S. Mohanty, A. Das, S. Grath, S. G. Smith, S. Zargham, S. F. McEvey, and W. Stephan (2008): Evolution of mating isolation between populations of Drosophila ananassae. Mol. Ecol. 17: 2706-2721
  104. Eck, S. and W. Stephan (2008): Determining the relationship of gene expression and global mRNA stability in Drosophila melanogaster and Escherichia coli using linear models. Gene 424: 102-107
  105. Piskol, R. and W. Stephan (2008): Analyzing the evolution of RNA secondary structures in vertebrate introns using Kimura’s model of compensatory fitness interactions. Mol. Biol. Evol. 25: 2483-2492
  106. Varzari, A., V. Kharkov, W. Stephan, V. Dergachev, V. Puzyrev, E. Weiss, and V. Stepanov (2009): Searching for the origin of Gagauzes: inferences from Y-chromosome analysis. Am. J. Hum. Biol. 21: 326-336
  107. Hutter, S. and W. Stephan (2009): Recombination rates may affect the ratio of X to autosomal polymorphism in African populations of Drosophila melanogaster: Reply to Beatriz Vicoso and Brian Charlesworth. Genetics 181: 1703
  108. Städler, T., B. Haubold, C. Merino, W. Stephan, and P. Pfaffelhuber (2009): The impact of sampling schemes on the site frequency spectrum in non-equilibrium subdivided populations. Genetics 182: 205-216
  109. Svetec, N., P. Pavlidis, and W. Stephan (2009): Recent strong positive selection on Drosophila melanogaster HDAC6, a gene encoding a stress surveillance factor, as revealed by population genomic analysis. Mol. Biol. Evol. 26: 1549-1556
  110. Hense, W., N. Anderson, S. Hutter, W. Stephan, J. Parsch, and D. B. Carlini (2010): Experimentally increased codon bias in the Drosophila Adh gene leads to an increase in larval, but not adult, alcohol dehydrogenase. Genetics 184: 547-555
  111. Pavlidis, P., S. Laurent, and W. Stephan (2010): msABC: a modification of Hudson’s ms to facilitate multilocus ABC analysis. Mol. Ecol. Resources 10: 723-727
  112. Stephan, W. (2010): Genetic hitchhiking versus background selection: the controversy and its implications. Phil. Trans. R. Soc. B 365: 1245-1253
  113. Pavlidis, P., J. D. Jensen, and W. Stephan (2010): Searching for footprints of positive selection in whole-genome SNP data from non-equilibrium populations. Genetics 185: 907-922
  114. Stephan, W. (2010): Detecting strong positive selection in the genome. Mol. Ecol. Resources 10: 863-872
  115. Xia, H., L. Camus-Kulandaivelu, W. Stephan, A. Tellier, and Z. Zhang (2010): Nucleotide diversity pattern of local adaptation at drought-related candidate genes in wild tomatoes. Mol. Ecol. 19: 4144-4154
  116. Stephan, W. and T. Städler (2010): Population genetics of speciation and demographic inference under population subdivision: insights from studies of wild tomatoes (Solanum Section Lycopersicon). In: Evolution in Action – Case Studies in Adaptive Radiation, Speciation and the Origin of Biodiversity (M. Glaubrecht, ed.), pp. 119-135,  Springer-Verlag, Heidelberg
  117. Svetec, N., A. Werzner, R. Wilches, P. Pavlidis, J. M. Álvarez-Castro, K. W. Broman, D. Metzler, and W. Stephan (2011): Identification of X-linked quantitative trait loci affecting cold tolerance in Drosophila melanogaster and fine-mapping by selective sweep analysis. Mol. Ecol. 20: 530-544
  118. Müller, L., S. Hutter, R. Stamboliyska, S. Saminadin-Peter, W. Stephan, and J. Parsch (2011): Population transcriptomics of Drosophila melanogaster females. BMC Genomics 12: 81
  119. Piskol, R. and W. Stephan (2011): Selective constraints in conserved non-coding RNAs of drosophilid and hominid genomes. Mol. Biol. Evol. 28: 1519-1529
  120. Zivkovic, D. and W. Stephan (2011): Analytical results on the neutral non-equilibrium allele frequency spectrum based on diffusion theory. Theor. Popul. Biol. 79: 184-191
  121. Laurent, S. J., A. Werzner, L. Excoffier, and W. Stephan (2011): Approximate Bayesian analysis of Drosophila melanogaster polymorphism data suggests a recent colonization of Southeast Asia. Mol. Biol. Evol. 28: 2041-2051
  122. Fischer, I., L. Camus-Kulandaivelu, F. Allal, and W. Stephan (2011): Adaptation to drought in two wild tomato species: the evolution of the Asr gene family. New Phytologist 190: 1032-1044
  123. Tellier, A., I. Fischer, C. Merino, H. Xia, L. Camus-Kulandaivelu, T. Städler, and W. Stephan (2011): Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure. Heredity 107: 189-199
  124. Tellier, A., P. Pfaffelhuber, B. Haubold, L. Naduvilezhath, L. E. Rose, T. Städler, W. Stephan, and D. Metzler (2011): Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum. PLoS One 6: e18155
  125. Rose, L. E., L. Grzeskowiak, A. C. Hörger, M. Groth, and W. Stephan (2011): Targets of selection in a disease resistance network in wild tomatoes. Mol. Plant Pathol. 12: 921-927
  126. Piskol, R. and W. Stephan (2011): The role of effective population size in compensatory evolution. Genome Biol. Evol. 3: 528-538
  127. Tellier, A., S. J. Laurent, H. Lainer, P. Pavlidis, and W. Stephan (2011): Inference of seed bank parameters in two wild tomato species using ecological and genetic data. Proc. Natl. Acad. Sci. USA 108: 17052-17057
  128. Pavlidis, P., J. D. Jensen, W. Stephan, and A. Stamatakis (2012): A critical assessment of story-telling: Gene Ontology categories and the importance of genomic scans. Mol. Biol. Evol. 29: 3237-3248
  129. Hörger, A. C., M. Ilyas, W. Stephan, A. Tellier, R. A. L. van der Hoorn, and L. E. Rose (2012): Balancing selection at the tomato RCR3 guardee gene family maintains variation in strength of pathogen defense. PLoS Genet. 8: e1002813
  130. Mboup, M., I. Fischer, H. Lainer, and W. Stephan (2012): Trans-species polymorphism and allele-specific expression in  the CBF gene family of wild tomatoes. Mol. Biol. Evol. 29: 3641-3652
  131. Pavlidis, P., D. Metzler, and W. Stephan (2012): Selective sweeps in multi-locus models of quantitative traits. Genetics 192: 225-239
  132. Duchen, P., D. Zivkovic, S. Hutter, W. Stephan, and S. Laurent (2013): Demographic inference reveals African and European admixture in North American Drosophila melanogaster population. Genetics 193: 291-301
  133. Varzari, A., V. Kharkov, A. G. Nikitin, F. Raicu, K. Simonova, W. Stephan, E. H. Weiss, and V. Stepanow (2013): Paleo-Balkan and Slavic contributions to the genetic pool of Moldavians: insights from the Y chromosome. PLoS One 8: e53731
  134. Werzner, A., P. Pavlidis, L. Ometto, W. Stephan, and S. Laurent (2013): Selective sweep in the Flottilin-2 region of European Drosophila melanogaster. PLoS One 8: e56629
  135. Moreno-Gámez, S., W. Stephan, and A. Tellier (2013): Effects of disease prevalence and spatial heterogeneity on polymorphism maintenance in host-parasite interactions. Plant Pathology 62: 133-141
  136. Fischer, I., K. A. Steige, W. Stephan, and M. Mboup (2013): Sequence evolution and expression regulation of stress-responsive genes in natural populations of wild tomato. PLoS One 8: e78182
  137. Tellier, A., S. Moreno-Gámez, and W. Stephan (2014): Speed of adaptation and genomic footprints of host-parasite coevolution under arms race and trench warfare dynamics. Evolution 68: 2211-2224
  138. Wilches, R., S. Voigt, P. Duchen, S. Laurent, and W. Stephan (2014): Fine-mapping and selective sweep analysis of QTL for cold tolerance in Drosophila melanogaster. G3-Genes Genomes Genetics 4: 1635-1645
  139. Grzeskowiak, L., W. Stephan, and L. E. Rose (2014): Epistatic selection and coadaptation in the Prf resistance complex of wild tomato. Infection, Genetics and Evolution 27: 456-471
  140. Wollstein, A. and W. Stephan (2014): Adaptive fixation in two-locus models of stabilizing selection and genetic drift. Genetics 198: 685-697
  141. Wollstein, A. and W. Stephan (2015): Inferring positive selection in humans from genomic data. Investigative Genet. 6: 5
  142. Jain, K. and W. Stephan (2015): Response of polygenic traits under stabilizing selection and mutation when loci have unequal effects. G3-Genes Genomes Genetics 5: 1065-1074
  143. Voigt, S., S. Laurent, M. Litovchenko, and W. Stephan (2015): Positive selection at the polyhomeotic locus leads to reduced thermosensitivity of gene expression in temperate Drosophila melanogaster. Genetics 200: 591-599
  144. Zivkovic, D., M. Steinrücken, Y. S. Song, and W. Stephan (2015): Transition densities and sample frequency spectra of diffusion processes with selection and variable population size. Genetics 200: 601-617
  145. Paparazzo, F., A. Tellier, W. Stephan, and S. Hutter (2015): Survival rate and transcriptional response upon infection with the generalist parasite Beauveria bassiana in a world-wide sample of Drosophila melanogaster. PloS One 10: e0132129
  146. Böndel, K. B., H. Lainer, T. Nosenko, M. Mboup, A. Tellier, and W. Stephan (2015): North-south colonization associated with local adaptation of wild tomato species Solanum chilense. Mol. Biol. Evol. 32: 2932-2943
  147. Stephan, W. (2016): Signatures of positive selection: from selective sweeps at individual loci to subtle allele frequency changes in polygenic adaptation. Mol. Ecol. 25: 79-88
  148. Kusumi, J., M. Ichinose, M. Takefu, R. Piskol, W. Stephan, and M. Iizuka (2016): A model of compensatory molecular evolution involving multiple sites in RNA molecules. J. theor. Biol. 388: 96-107
  149. Bozicevic, V., S. Hutter, W. Stephan, and A. Wollstein (2016): Population genetic evidence for cold adaptation in European Drosophila melanogaster populations. Mol. Ecol. 25: 1175-1191
  150. Croze, M., D. Zivkovic, W. Stephan, and S. Hutter (2016): Balancing selection at immunity genes: review of the current literature and new analysis in Drosophila melanogaster. Zoology 119: 322-329
  151. Nosenko, T., K. B. Böndel, G. Kumpfmüller, and W. Stephan (2016): Adaptation to low temperatures in the wild tomato species Solanum chilense. Mol. Ecol. 25: 2853-2869
  152. von Heckel, K., W. Stephan, and S. Hutter (2016): Canalization of gene expression is a major signature of regulatory cold adaptation in temperate Drosophila melanogaster. BMC Genomics 17: 574
  153. Croze, M., A. Wollstein, V. Bozicevic, D. Zivkovic, W. Stephan, and S. Hutter (2017): A genome-wide scan for genes under balancing selection in Drosophila melanogaster. BMC Evolutionary Biology 17: 15
  154. Jain, K. and W. Stephan (2017): Rapid adaptation of a polygenic trait after a sudden environmental shift. Genetics 206: 389-406
  155. Jain, K. and W. Stephan (2017): Modes of rapid polygenic adaptation. Mol. Biol. Evol. 34: 3169-3175
  156. Eldon, B. and W. Stephan (2018): Evolution of highly fecund haploid populations. Theoret. Popul. Biol. 119: 48-56
  157. Böndel, K. B., T. Nosenko, and W. Stephan (2018): Signatures of natural selection in abiotic stress-responsive genes of Solanum chilense. R. Soc. Open Sci. 5: 171198
  158. Stephan, W. (2019): Selective sweeps. Genetics 211: 5-13
  159. Jensen, J. D., B. A. Payseur, W. Stephan, C. F. Aquadro, M. Lynch, D. Charlesworth, and B. Charlesworth (2019): The importance of the Neutral Theory in 1968 and 50 years on: a reply to Kern and Hahn 2018. Evolution 73: 111-114
  160. Voigt, S., A. C. Erpf, and W. Stephan (2019): Decreased temperature sensitivity of vestigial gene expression in temperate populations of Drosophila melanogaster. Genes 10: 498
  161. Feurtey, A., D. Stevens, W. Stephan, and E. H. Stukenbrock (2019): Interspecific gene exchange introduces high genetic variability in crop pathogen. Genome Biol. Evol. 11: 3095-3105
  162. Stam, R., T. Nosenko, A. C. Hörger, W. Stephan, M. Seidel, J. Kuhn, G. Haberer, and A. Tellier (2019): The de novo reference genome and transcriptome of the wild tomato species S. chilense confirm birth and death of NLR genes in tomato. G3-Genes Genomes Genetics 9: 3933-3941
  163. Zivkovic, D., S. John, M. Verin, W. Stephan, and A. Tellier (2019): Neutral genomic signatures of host-parasite coevolution. BMC Evolutionary Biology 19: 230
  164. John, S. and W. Stephan (2020): Important role of genetic drift in rapid polygenic adaptation. Ecology and Evolution, in press
  165. Stephan, W. and A. Tellier (2020): Stochastic processes and host-parasite coevolution: linking coevolutionary dynamics and DNA polymorphism data. In: Probabilistic Structures in Evolution (E. Baake and A. Wakolbinger, eds.), European Mathematical Society Series of Congress Reports, in press