Recent publications of our students

J. Bergman, A. Betancourt and C. Vogl: Transcription-associated compositional skews in Drosophila genes. Genome Biol Evol doi:10.1093/gbe/evx200 (2017)

T. Taus, A. Futschik and C. Schlötterer: Quantifying selection with Pool-Seq time series data. Mol Biol Evol doi:10.1093/molbev/msx225 (2017)

A.M. Jakšić, R. Kofler and C. Schlötterer: Regulation of transposable elements: interplay between TE-encoded regulatory sequences and host-specific trans-acting factors in Drosophila melanogaster. Mol Ecol doi:10.1111/mec.14259. (2017)

M. Pontz, J. Hofbauer and R. Bürger: Evolutionary dynamics in the two-locus two-allele model with weak selection. J Math Biol doi:10.1007/s00285-017-1140-7 (2017)

N. Barghi, R. Tobler, V. Nolte and C. Schlötterer: Drosophila simulans: A species with improved resolution in Evolve and Resequence studies. G3 7(7):2337-2343 (2017)

A. Durvasula, A. Fulgione, R.M. Gutaker, S.I. Alacakaptan, P.d.J. Flood, C.I. Neto, T. Tsuchimatsu, H.n.A. Burbano, F.X. Pico, C. Alonso-Blanco and A.M. Hancock: African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana. PNAS 114(20):5213-5218 (2017)

F. Balao, E. Trucchi, T. Wolfe, B.H. Hao, M.T. Lorenzo, J. Baar, L. Sedman, C. Kosiol, F. Amman, M.W. Chase, M. Hedren and O. Paun: Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima. Mol Ecol 26(14):3649-3662 (2017)

I. Höllinger and J. Hermisson: Bounds to parapatric speciation: A dobzhansky-muller incompatibility model involving autosomes, X chromosomes and mitochondria. Evolution 71(5):1366-1380 (2017)

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 34(4):957-968 (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 114:88-94 (2017)

B. Horvath and A.T. Kalinka: Effects of larval crowding on quantitative variation for development time and viability in Drosophila melanogaster. Evol Evol 6(23):8460-8473 (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 204(2): 723-735 (2016)

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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