Publications

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

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

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

Stephan, W. and D. A. Kirby (1993)
RNA folding in Drosophila shows a distance effect for compensatory fitness interactions. Genetics 135: 97-103

Stephan, W. and C. H. Langley (1993)
Nucleotide sequence variation on the X chromosome. In: Drosophila ananassae. Genetical and Biological Aspects (Y. N. Tobari, ed.), pp. 181-198, Japan Scientific Societies Press (Tokyo) and Karger-Verlag (Basel)

Stephan, W. and S. Cho (1994)
Possible role of natural selection in the formation of tandem-repetitive noncoding DNA. Genetics 136: 333-341

Charlesworth, B., P. Sniegowski, and W. Stephan (1994)
The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371: 215-220

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

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

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

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

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

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

Stephan, W. (1995)
Perturbation analysis of a two-locus model with directional selection and recombination. J. Math. Biol. 34: 95-109

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

Stephan, W. (1996)
The rate of compensatory evolution. Genetics 144: 419-426

Kirby, D. A. and W. Stephan (1996)
Multi-locus selection and the structure of the white gene of Drosophila melanogaster. Genetics 144: 635-645

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

Perlitz, M. and W. Stephan (1997)
The mean and variance of the number of segregating sites since the last hithhiking event. J. Math. Biol. 36: 1-23

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

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

Stephan, W. (1997)
Tandemly repeated non-coding DNA sequences. In: The Encyclopedia of Molecular Biology and Molecular Medicine, Volume 6 (R. A. Meyers, ed.), pp. 1-10, Verlagsgesellschaft, Weinheim

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

Parsch, J., W. Stephan, and S. Tanda (1998)
Long-range base pairing in Drosophila and human mRNA sequences. Mol. Biol. Evol. 15: 820-826

Stephan, W. and Y. Kim (1998)
Persistence of microsatellite arrays in finite populations. Mol. Biol. Evol. 15: 1332-1336

Stephan, W. and C. H. Langley (1998)
DNA polymorphism in Lycopersicon and crossing-over per physical length. Genetics 150: 1585-1593

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

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

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

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

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

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

Parsch, J., J. M. Braverman, and W. Stephan (2000)
Comparative sequence analysis and patterns of covariation in RNA secondary structures. Genetics 154: 909-921

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

Kim, Y. and W. Stephan (2000)
Joint effects of genetic hitchhiking and background selection on neutral variation. Genetics 155: 1415-1427

Innan, H. and W. Stephan (2000)
The coalescent in an exponentially growing metapopulation, and its application to Arabidopsis thaliana . Genetics 155 : 2015-2019

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

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

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

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

Stephan, W. (2002)
Evolution of genome organisation. In: Encyclopedia of Life Sciences , Vol. 6, pp. 673-678, Nature Publishing Group, London

Walsh, J. B. and W. Stephan (2002)
Multigene families: evolution. In: Encyclopedia of Life Sciences , Vol. 12, pp. 406-412, Nature Publishing Group, London

Stephan, W. and J. B. Walsh (2002)
Repetitive DNA: Evolution. In: Encyclopedia of Life Sciences , Vol. 16, pp. 282-288, Nature Publishing Group, London

Kim, Y. and W. Stephan (2002)
Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777

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

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

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

Kim, Y. and W. Stephan (2003)
Selective sweeps in the presence of interference among partially linked loci. Genetics 164: 389-398

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

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

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

Innan, H. and W. Stephan (2003)
Distinguishing the hitchhiking and background selection models. Genetics 165: 2307-2312

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

Das, A., S. Mohanty, and W. Stephan (2004)
Inferring population structure and demography of Drosophila ananassae from multilocus data. Genetics 168: 1975-1985

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

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

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

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, Kluwer Academic/Plenum Publishers

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

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

Glinka, S., W. Stephan, and A. Das (2005)
Homogeneity of common cosmopolitan inversion frequencies in Southeast Asian Drosophila melanogaster. J. Genetics 84: 173-178

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

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

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

Stephan, W. (2005)
Genetic hitchhiking and linkage disequilibrium. In: Mathmatical Population Genetics (E. Baake, W. J. Ewens, and A. Wakolbinger, eds.), pp. 55-57, Mathematisches Forschungsinstitut Oberwolfach, Report No. 40/2005

Chen, Y. and W. Stephan (2006)
Evolution of gene structure. In: Evolutionary Genetics – Concepts and Case Studies (C. W. Fox and J. B. Wolf, eds.), Oxford University Press, Oxford

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

Stephan, W., Y. S. Song, and C. H. Langley (2006)
The hitchhiking effect on linkage disequilibrium between linked loci. Genetics 172: 2647-2663

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

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

Li, H., and W. Stephan (2006)
Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genetics 10: e166

Stephan, W., and H. Li (2007)
The recent demographic and adaptive history of Drosophila melanogaster. Heredity 98: 65-68

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

Varzari, A., W. Stephan, V. Stepanov, 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

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

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. Bio. Evol. 24: 2310-2322

Drosophila 12 Genomes Consortium (2007)
Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218

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

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

Hutter, S., S. S. Saminadin-Peter, W. Stephan and J. Parsch (2008)
Gene expression variation in African and European populations of Drosophila melanogaster. Genome Biology 9: R12

Riebler, A., L. Held, and W. Stephan (2008)
Bayesian variable selection for detecting adaptive genomic differences among populations. Genetics 178: 1817-1829

Beisswanger, S., and W. Stephan (2008)
Evidence that strong positive selection drives neofunctionalization in the tandemly duplicated polyhomeotic genes in Drosophila. Proc. Natl. Acad. Sci. USA 105: 5447-52

Pfaffelhuber, P., A. Lehnert, and W. Stephan (2008)
Linkage disequilibrium under genetic hitchhiking in finite populations. Genetics 179: 527-537

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

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

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

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

Stephan, W. (2008)
Adaptation und Selektion. Biospektrum 14: 255-257

Hutter, S. and W. Stephan (2009)
Reply to Beatriz Vicoso and Brian Charlesworth. Genetics 181: 1703

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

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

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