Recent publications of our students

P.Y. Novikova, T. Tsuchimatsu, S. Simon, V. Nizhynska, V. Voronin, R. Burns, O.M. Fedorenko, S. Holm, T. Säll, E. Prat, W. Marande, V. Castric and M. Nordborg: Genome sequencing reveals the origin of the allotetraploid Arabidopsis suecica. Mol Biol Evol doi: 10.1093/molbev/msw299 (2017)

D. Schrempf and A. Hobolth: An alternative derivation of the stationary distribution of the multivariate neutral Wright-Fisher model for low mutation rates with a view to mutation rate estimation from site frequency data. Theor Popul Biol 29 pii: S0040-5809(16)30106-X. (2016)

B. Horvath and A.T. Kalinka: Effects of larval crowding on quantitative variation for development time and viability in Drosophila melanogaster. Evol Evol DOI: 10.1002/ece3.2552 (2016)

B. Horvath, A.J. Betancourt and A.T. Kalinka: A novel method for quantifying the rate of embryogenesis uncovers considerable genetic variation for the duration of embryonic development in Drosophila melanogaster. BMC Evolutionary Biology 16(1):200 (2016)

R. Kofler, A.M. Langmüller, P. Nouhaud, K.A. Otte and C. Schlötterer: Suitability of Different Mapping Algorithms for Genome-wide Polymorphism Scans with Pool-Seq Data. G3 (Bethesda). pii: g3.116.034488. (2016)

P. Nouhaud, R. Tobler, V. Nolte and C. Schlötterer: Ancestral population reconstitution from isofemale lines as a tool for experimental evolution. Ecol Evol 6: 7169–7175 (2016)

A. Jonas, T. Taus, C. Kosiol, C. Schlötterer and A. Futschik: Estimating the effective population size from temporal allele frequency changes in experimental evolution. Genetics doi: 10.1534/genetics.116.191197

R. Kofler, D. Gomez-Sanchez and C. Schlötterer: PoPoolationTE2: comparative population genomics of transposable elements using Pool-Seq. Mol Biol Evol 33(10):2759-64 (2016)

A.M Jakšić and C. Schlötterer: The interplay of temperature and genotype on patterns of alternative splicing in Drosophila melanogaster. Genetics 204(1):315-25 (2016)

P.Y. Novikova, N. Hohmann, V. Nizhynska, T. Tsuchimatsu, J. Ali, G. Muir, A. Guggisberg, T. Paape, K. Schmid, O.M. Fedorenko, S. Holm, T. Säll, C. Schlötterer, K. Marhold, A. Widmer, J. Sese, K.K. Shimizu, D. Weigel, U. Krämer, M.A. Koch and M. Nordborg: Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nature Genetics 48(9):1077-82 (2016)

D. Schrempf, B.Q. Minh, N. De Maio, A. von Haeseler and C. Kosiol: Reversible Polymorphism-Aware Phylogenetic Models and their Application to Tree Inference. J Theor Biol 407:362-370 (2016)

T. Hill, C. Schlötterer and A.J. Betancourt: Hybrid Dysgenesis in Drosophila simulans Associated with a Rapid Invasion of the P-Element. PLoS Genet 12(5):e1006058. (2016)

K. Gärtner and A. Futschik: Improved Versions of Common Estimators of the Recombination Rate. J Comp Biol 23(9):756-68 (2016)

C. Vogl and J. Bergman: Computation of the Likelihood of Joint Site Frequency Spectra Using Orthogonal Polynomials. Computation 4(1), 6; doi:10.3390/computation4010006 (2016)

A.O. Bergland, R. Tobler, J. González, P. Schmidt and D. Petrov: Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster. Mol Ecol. 25(5):1157-74 (2016)

C. Schlötterer, R. Kofler, E. Versace, R. Tobler and S.U. Franssen: Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation. Heredity 116(2):248 (2015)

C. Vogl and J. Bergman: Inference of directional selection and mutation parameters assuming equilibrium. Theor Popul Biol 106:71-82 (2015)

C. Huber, M. DeGiorgio, I. Hellmann and R. Nielsen: Detecting recent selective sweeps while controlling for mutation rate and background selection. Mol Ecol 25(1):142-56 (2016)

N. De Maio, D. Schrempf and C. Kosiol: PoMo: An allele frequency-based approach for species tree estimation. Syst Biol 64(6):1018-31 (2015)

R. Tobler, J. Hermisson and C. Schlötterer: Parallel trait adaptation across opposing thermal environments in experimental Drosophila melanogaster populations. Evolution 69(7):1745-59 (2015)

R. Kofler, T. Hill, V. Nolte, A.J. Betancourt and C. Schlötterer: The recent invasion of natural Drosophila simulans populations by the P-element. Proc Natl Acad Sci U S A 26;112(21):6659-63 (2015)

K.M. Tanaka, C. Hopfen, M.R. Herbert, C. Schlötterer, D.L. Stern, J.P. Masly, A.P. McGregor and M.D. Nunes. Genetic architecture and functional characterization of genes underlying the rapid diversification of male external genitalia between Drosophila simulans and Drosophila mauritiana. Genetics 200(1):357-69 (2015)

D.K. Fabian, J.B. Lack, V. Mathur, C. Schlötterer, P.S. Schmidt, J.E. Pool and T. Flatt: Spatially varying selection shapes life history clines among populations of Drosophila melanogaster from sub‐Saharan Africa. J Evol Biol 28: 826-840 (2015)

H. Topa, A. Jónás, R. Kofler, C. Kosiol and A. Honkela: Gaussian process test for high-throughput sequencing time series: application to experimental evolution. Bioinformatics 31(11):1762-70 (2015)

H. Uecker, D. Setter and J. Hermisson. Adaptive gene introgression after secondary contact. J Math Biol 70(7):1523-80 (2015)

S. Franssen, V. Nolte, R. Tobler and C. Schlötterer: Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental Drosophila melanogaster populations. Mol Biol Evol 32(2):495-509 (2015)

L. Geroldinger and R. Bürger: Clines in quantitative traits: The role of migration patterns and selection scenarios. Theor Popul Biol 99:43-66 (2015)

C. Schlötterer, R. Kofler, E. Versace, R. Tobler and  S.U. Franssen: Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation. Heredity 114(5):431-440 (2014)

C. Huber, M. Nordborg, J. Hermisson and I. Hellmann: Keeping it Local: Evidence for Positive Selection in Swedish Arabidopsis thaliana. Mol Biol and Evol 31(11):3026-39 (2014)

C. Schlötterer, R. Tobler, R. Kofler and V. Nolte: Sequencing pools of individuals - mining genome-wide polymorphism data without big funding. ‎Nat Rev Genet 15(11):749-63 (2014)

E. Versace, V. Nolte, R.V. Pandey, R. Tobler and C. Schlötterer: Experimental evolution reveals habitat-specific fitness dynamics among Wolbachia clades in Drosophila melanogaster. Mol Ecol 23, 802-814 (2014)

R. Tobler, S.U. Franssen, R. Kofler, P. Orozco-terWengel, V. Nolte, J. Hermisson and C. Schlötterer: Massive Habitat-Specific Genomic Response in D. melanogaster Populations during Experimental Evolution in Hot and Cold Environments. Mol Biol Evol 31, 364-375 (2014)

P. Klepsatel, M. Galikova, C.D. Huber and T. Flatt: Similarities and Differences in Altitudinal Versus Latitudinal Variation for Morphological Traits in Drosophila melanogaster. Evolution 68(5):1385-98 (2014)

L. Geroldinger and R. Bürger: A two-locus model of spatially varying stabilizing or directional selection on a quantitative trait. Theor Popul Biol 94, 10-41 (2014)

M. Kapun, H. van Schalkwyk, B. McAllister, T. Flatt and C. Schlötterer. Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations of Drosophila melanogaster. Mol Ecol 23(7):1813-27 (2014)

A. Akerman and R. Bürger: The consequences of gene flow for local adaptation and differentiation: a two-locus two-deme model. J Math Biol 68, 1135-1198 (2014)

A. Akerman and R. Bürger: The consequences of dominance and gene flow for local adaptation and differentiation at two linked loci. Theor Popul Biol 94, 42-62 (2014)

Q. Long, F.A. Rabanal, D.Z. Meng, C.D. Huber, A. Farlow, A. Platzer, Q.R. Zhang, B.J. Vilhjalmsson, A. Korte, V. Nizhynska, V. Voronin, P. Korte, L. Sedman, T. Mandakova, M.A. Lysak, U. Seren, I. Hellmann and M. Nordborg: Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet 45, 884-U218 (2013)

P. Klepsatel, M. Galikova, N. De Maio, S. Ricci, C. Schlötterer and T. Flatt: Reproductive and post-reproductive life history of wild-caught Drosophila melanogaster under laboratory conditions. J Evol Biol 26, 1508-1520 (2013)

P. Klepsatel, M. Galikova, N. De Maio, C.D. Huber, C. Schlötterer and T. Flatt: Variation in Thermal Performance and Reaction Norms among Populations of Drosophila Melanogaster. Evolution 67, 3573-3587 (2013)

M. Kapun, H. van Schalkwyk, B. McAllister, T. Flatt and C. Schlötterer: Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations of Drosophila melanogaster. Mol Ecol 23, 1813–1827 (2013)

N. De Maio, C. Schlötterer and C. Kosiol: Linking Great Apes Genome Evolution across Time Scales Using Polymorphism-Aware Phylogenetic Models. Mol Biol Evol 30, 2249-2262 (2013)

N. De Maio, I. Holmes, C. Schlötterer and C. Kosiol: Estimating Empirical Codon Hidden Markov Models. Mol Biol Evol 30, 725-736 (2013)

H. Bastide, A. Betancourt, V. Nolte, R. Tobler, P. Stobe, A. Futschik and C. Schlötterer: A Genome-Wide, Fine-Scale Map of Natural Pigmentation Variation in Drosophila melanogaster. Plos Genetics 9(6):e1003534 (2013)

S. Arif, S. Murat, I. Almudi, M.D.S. Nunes, D. Bortolamiol-Becet, N.S. McGregor, J.M.S. Currie, H. Hughes, M. Ronshaugen, E. Sucena, E.C. Lai, C. Schlötterer and A.P. McGregor: Evolution of mir-92a Underlies Natural Morphological Variation in Drosophila melanogaster. Curr Biol 23, 523-528 (2013)

S. Arif, M. Hilbrant, C. Hopfen, I. Almudi, M.D.S. Nunes, N. Posnien, L. Kuncheria, K. Tanaka, P. Mitteroecker, C. Schlötterer and A.P. McGregor: Genetic and developmental analysis of differences in eye and face morphology between Drosophila simulans and Drosophila mauritiana. Evol Dev 15, 257-267 (2013)

C. Vogl and F. Clemente: The allele-frequency spectrum in a decoupled Moran model with mutation, drift, and directional selection, assuming small mutation rates. Theor Popul Biol 81, 197-209 (2012)

N. Posnien, C. Hopfen, M. Hilbrant, M. Ramos-Womack, S. Murat, A. Schoenauer, S.L. Herbert, M.D.S. Nunes, S. Arif, C.J. Breuker, C. Schlötterer, P. Mitteroecker and A.P. McGregor: Evolution of Eye Morphology and Rhodopsin Expression in the Drosophila melanogaster Species Subgroup. PLoS One 7(5):e37346 (2012)

P. Orozco-TerWengel, M. Kapun, V. Nolte, R. Kofler, T. Flatt and C. Schlötterer: Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles. Mol Ecol 21, 4931-4941 (2012)

D.K. Fabian, M. Kapun, V. Nolte, R. Kofler, P.S. Schmidt, C. Schlötterer and T. Flatt: Genome-wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America. Mol Ecol 21, 4748-4769 (2012)

D.K. Fabian and T. Flatt: Life History Evolution. Nature Education Knowledge (2012)

F. Clemente and C. Vogl: Evidence for complex selection on four-fold degenerate sites in Drosophila melanogaster. J Evol Biol 25, 2582-2595 (2012)

F. Clemente and C. Vogl: Unconstrained evolution in short introns? - An analysis of genome-wide polymorphism and divergence data from Drosophila. J Evol Biol 25, 1975-1990 (2012)

C. Bank, J. Hermisson and M. Kirkpatrick: Can Reinforcement Complete Speciation? Evolution 66, 229-239 (2012)

C. Bank, R. Bürger and J. Hermisson: The Limits to Parapatric Speciation: Dobzhansky-Muller Incompatibilities in a Continent-Island Model. Genetics 191, 845-U345 (2012)

P. Klepsatel and T. Flatt: The genomic and physiological basis of life history variation in a butterfly metapopulation. Mol Ecol 20, 1795-1798 (2011)

M. Galikova, P. Klepsatel, G. Senti and T. Flatt: Steroid hormone regulation of C. elegans and Drosophila aging and life history. Exp Gerontol 46, 141-147 (2011)

D.K. Fabian and T. Flatt: The evolution of aging. Nature Education Knowledge (2011)

R. Bürger and A. Akerman: The effects of linkage and gene flow on local adaptation: a two-locus continent-island model. Theor Popul Biol 80, 272-288 (2011)

M. Kapun, V. Nolte, T. Flatt and C. Schlötterer: Host range and specificity of the Drosophila C virus. PLoS One 5(8):e12421 (2010)

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