DFG FOR 1078 Natural Selection in Structured Populations

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Wang, J., M. Linnenbrink, S. Künzel, R. Fernandes, M.J. Nadeau, P. Rosenstiel, and J.F. Baines (2014)
Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice.
Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):E2703-10. doi: 10.1073/pnas.1402342111. Epub 2014 May 27.

Kemkemer, C., A. Catalán, and J. Parsch (2014)
Escaping the X chromosome leads to increased gene expression in the male germline of Drosophila melanogaster.
Heredity 112: 149-155

Pokalyuk, C., L. Mathew, D. Metzler, and P. Pfaffelhuber
Competing islands limit the rate of adaptation in structured populations.

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

Yin M., S. Giessler, J. Griebel, and J. Wolinska (2014)
Hybridizing Daphnia communities from ten neighbouring quarry lakes: spatio-temporal dynamics, local processes, gene flow and invasiveness.
BMC Evol Biol 14:80

Ma X., A. Petrusek, J. Wolinska, S. Giessler, Y. Zhong, Z. Yang, W. Hu, and M. Yin (2014)
Diversity of the Daphnia longispina species complex in Chinese lakes: a DNA taxonomy approach.
J Plankton Res, doi:10.1093/plankt/fbu091


Duchén, P., D. Zivkovic, S. Hutter, W. Stephan, and S. Laurent (2013)
Demographic Inference Reveals African and European Admixture in the North American Drosophila melanogaster Population.
Genetics, Vol. 193, 291–301

Werzner A., P. Pavlidis, L. Ometto, W. Stephan, and S. Laurent (2013)
Selective Sweep in the Flotillin-2 Region of European Drosophila melanogaster.
PLoS One 8(2): e56629

Glaser-Schmitt, A., A. Catalán, and J. Parsch (2013)
Adaptive divergence of a transcriptional enhancer between populations of Drosophila melanogaster.
Phil. Trans. R. Soc. B 368: 20130024

Linnenbrink, M., J. Wang, E.A. Hardouin, S. Künzel, D. Metzler, and J.F. Baines (2013)
The role of biogeography in shaping diversity of the intestinal microbiota in house mice.
Mol Ecol. 22: 1904-16

Mathew, L. A., P. A. Staab, L. E. Rose, and D. Metzler (2013)
Why to account for finite-sites in population genetic studies and how to do this with Jaatha 2.0.
Ecology and Evolution 3:2647-3662


Müller, L., S. Grath, K. von Heckel, and J. Parsch (2012)
Inter- and intraspecific variation in Drosophila genes with sex-biased expression.
Int. J. Evol. Biol. 2012: 963976

Pokalyuk, C. (2012)
The effect of recurrent mutation on the linkage disequilibrium under a selective sweep.
J. Math. Biol., 64:291--317. 2012

Saminadin-Peter, S. S., C. Kemkemer, P. Pavlidis, and J. Parsch (2012)
Selective sweep of a cis-regulatory sequence in a non-African population of Drosophila melanogaster.
Mol. Biol. Evol. 29 (4): 1167-1174.

Staubach, F., S. Künzel, A.C. Baines, A. Yee, B.M. McGee, F. Bäckhed, J.F. Baines*, and J.M. Johnsen* (2012)
Expression of the blood group-related glycosyltransferase B4galnt2 influences the intestinal microbiota in mice.
The ISME J. 6, 1345–1355
*Equal author contribution

Catalán, A., S. Hutter, and J. Parsch (2012)
Population and sex differences in Drosophila melanogaster brain gene expression.
BMC Genomics 13: 654

Pool, J.E., B. Russell, R.B. Corbett-Detig, R.P. Sugino, K.A. Stevens, C.M. Cardeno, M.W. Crepeau, P. Duchen, J.J. Emerson, P. Saelao, D.J. Begun, and Ch.H. Langley (2012)
Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture.
PLOS Genetics

Pavlidis, P., D. Metzler, and W. Stephan (2012)
Selective sweeps in multi-locus models of quantitative traits.
Genetics 192: 225-239

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 


Ewing, G., J. Hermisson, P. Pfaffelhuber, and J. Rudolf (2011)
Selective sweeps for recessive alleles and for other modes of dominance.
J. Math. Biol. 63:399-431

Laurent, S.J.Y., A. Werzner, L. Excoffier, and W. Stephan (2011)
Approximate Bayesian analysis of Drosophila melanogaster polymorphism data suggest a recent colonization of Southeast Asia.
Mol. Biol. Evol. 28: 2041-2051

Linnenbrink, M., J.M. Johnsen, I. Montero, C.R. Brzezinski, B. Harr, and J.F. Baines (2011)
Long-term balancing selection at the blood group-related gene B4galnt2 in the genus Mus (Rodentia; Muridae).
Mol.Biol. Evol. 28: 2999-3003

Müller, L., S. Hutter, R. Stamboliyska, S. S. Saminadin-Peter, W. Stephan, and J. Parsch (2011)
Population transcriptomics of Drosophila melanogaster females.
BMC Genomics 12: 81

Naduvilezhath, L., L.E. Rose, and D. Metzler (2011)
Jaatha: a fast composite-likelihood approach to estimate demographic parameters.
Molecular Ecology 20(13):2709-23

Pamminger, T., I. Scharf, P. Pennings, and S. Foitzik (2011)
Increased host aggression as an induced defence against slavemaking ants.
Behavioural Ecology, 22: 255-260

Pennings, P., A. Achenbach, and S. Foitzik (2011)
Similar evolutionary potentials in an obligate ant parasite and its two host species.
Journal of Evolutionary Biology, 24: 871–886

Pfaffelhuber, P., and H. Weisshaupt (2011)
Sensitivity analysis of one parameter semigroups exemplified by the Wright-Fisher diffusion.
Intern. J. Funct. Anal., Oper. Th. Appl., 3(2), 109-128

Scharf, I., T. Pamminger, and S. Foitzik (2011)
Differential response of ant colonies to intruders: attack strategies correlate with potential threat.
Ethology, 117: 731–739

Svetec, N., A. Werzner, R. Wilches, P. Pavlidis, J.M. Alvarez-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.
Molecular Ecology 20(3): 530-544

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(5): e18155

Uecker H. and Hermisson J. (2011)
On the fixation process of a beneficial mutation in a variable environment.
Genetics 188: 915-930

Živković, D. and W. Stephan (2011)
Analytical results on the neutral non-equilibrium allele frequency spectrum based on diffusion theory.
Theor. Popul. Biol. 79: 184-191top


Ewing G. and Hermisson J. (2010)
MSMS: A coalescent simulation program including recombination, demographic structure, and selection at a single locus.
Bioinformatics 26: 2064-2065

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

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

Stephan, W. (2010)
Detecting strong positive selection in the genome.
Mol. Ecol. Resources 10: 863-872

Stephan, W. (2010)
Genetic hitchhiking versus background selection: the controversy and its implications.
Phil. Trans.R.Soc B 365: 1245-1253


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