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Recent publications of our students

Mallard F, Nolte V, Tobler R, Kapun M and Schlötterer C. A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila. Genome Biol. (2018) accepted

Barghi N, Tobler R, Nolte V, Jakšić AM, Mallard F, Otte K, Dolezal M, Taus T, Kofler R and Schlötterer C. Polygenic adaptation fuels genetic redundancy in Drosophila. bioRxiv 332122. (2018) doi: 10.1101/332122

Filiault D, Ballerini E, Mandakova T, Aköz G, Derieg N, Schmutz J, Jenkins J, Grimwood J, Shu S, Hayes R, Hellsten U, Barry K, Yan J, Mihaltcheva S, Karafiatova M, Nizhynska V, Lysak M, … Nordborg M. The Aquilegia genome: adaptive radiation and an extraordinarily polymorphic chromosome with a unique history. bioRxiv 264101. (2018) doi: 10.1101/264101

Bergman J, Betancourt AJ and Vogl C. Transcription-associated compositional skews in Drosophila genes. Genome Biol. Evol. 10(1), 269–275. (2018) doi: 10.1093/gbe/evx200

Bergman J, Schrempf D, Kosiol C and Vogl C. Inference in population genetics using forward and backward, discrete and continuous time processes. J. Theor. Biol. 439, 166–180. (2018) doi: 10.1016/j.jtbi.2017.12.008
Open access embargo

Felkel S, Vogl C, Rigler D, Jagannathan V, Leeb T, Fries R, Neuditschko M, Rieder S, Velie B, Lindgren G, Rubin C-J, Schlötterer C, Rattei T, Brem G and Wallner B. Asian horses deepen the MSY phylogeny. Anim. Genet. 49(1), 90–93. (2018) doi: 10.1111/age.12635
Open access embargo

Gaunitz C, Fages A, Hanghøj K, Albrechtsen A, Khan N, Schubert M, Seguin-Orlando A, Owens IJ, Felkel S, Bignon-Lau O, de Barros Damgaard P, Mittnik A, Mohaseb AF, Davoudi H, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, … Orlando L. Ancient genomes revisit the ancestry of domestic and Przewalski’s horses. Science 360(6384):111-114. (2018)
Open access embargo

Futschik A, Taus T and Zehetmayer S. An omnibus test for the global null hypothesis. Stat. Methods Med. Res. 96228021876832 (2018) doi: 10.1177/0962280218768326

Horváth B and Kalinka AT. The genetics of egg retention and fertilization success in Drosophila: One step closer to understanding the transition from facultative to obligate viviparity. Evolution. 72(2), 318–336. (2018) doi: 10.1111/evo.13411
Open access embargo

Kofler R, Senti K-A, Nolte V, Tobler R and Schlötterer C. Molecular dissection of a natural transposable element invasion. Genome Res. gr.228627.117. (2018) doi: 10.1101/gr.228627.117
Open access embargo

Lirakis M, Dolezal M and Schlötterer C. Redefining reproductive dormancy in Drosophila as a general stress response to cold temperatures. J. Insect Physiol. 107, 175–185. (2018) doi: 10.1016/j.jinsphys.2018.04.006
Open access embargo

Mallard F, Jakšić AM and Schlötterer C. Contesting the evidence for non-adaptive plasticity. Nature 555(7698), E21–E22. (2018) doi: 10.1038/nature25496
Open access embargo

Pontz M, Hofbauer J and Bürger R. Evolutionary dynamics in the two-locus two-allele model with weak selection. J. Math. Biol. 76(1–2), 151–203. (2018) doi: 10.1007/s00285-017-1140-7

Brachi B, Filiault D, Darme P, Mentec M Le, Kerdaffrec E, Rabanal FA, Anastasio A, Box M, Duncan S, Morton T, Novikova P, Perisin M, Tsuchimatsu T, Woolley R, Yu M, Dean C, Nordborg M, … Bergelson J. Plant genes influence microbial hubs that shape beneficial leaf communities. bioRxiv 181198. (2017) doi: 10.1101/181198

Balao F, Trucchi E, Wolfe TM, Hao BH, Lorenzo MT, Baar J, Sedman L, Kosiol C, Amman F, Chase MW, Hedrén M and Paun O. 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) doi: 10.1111/mec.14123

Barghi N, Tobler R, Nolte V and Schlötterer C. Drosophila simulans: A species with improved resolution in evolve and resequence studies. G3 7(7), 2337–2343. (2017) doi: 10.1534/g3.117.043349

Bertl J, Ewing G, Kosiol C and Futschik A. Approximate maximum likelihood estimation for population genetic inference. Stat. Appl. Genet. Mol. Biol. 16(5–6), 387–405. (2017) doi: 10.1515/sagmb-2017-0016

Durvasula A*, Fulgione A*, Gutaker RM, Alacakaptan SI, Flood PJ, Neto C, Tsuchimatsu T, Burbano HA, Picó FX, Alonso-Blanco C and Hancock AM. African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana. Proc. Natl. Acad. Sci. 114(20), 5213–5218. (2017), doi: 10.1073/pnas.1616736114 *co-first authors

Fulgione A, Koornneef M, Roux F, Hermisson J and Hancock AM. Madeiran Arabidopsis thaliana reveals ancient long-range colonization and clarifies demography in Eurasia. Mol. Biol. Evol. (2017) doi: 10.1093/molbev/msx300

Gómez-Sánchez D and Schlötterer C. ReadTools : A universal toolkit for handling sequence data from different sequencing platforms. Mol. Ecol. Resour. (2017) doi: 10.1111/1755-0998.12741

Höllinger I and Hermisson J. Bounds to parapatric speciation: A Dobzhansky–Muller incompatibility model involving autosomes, X chromosomes, and mitochondria. Evolution. 71(5), 1366–1380. (2017) doi: 10.1111/evo.13223

Jakšić AM, Kofler R and Schlötterer C. Regulation of transposable elements: Interplay between TE-encoded regulatory sequences and host-specific trans-acting factors in Drosophila melanogaster. Mol. Ecol. 26(19), 5149–5159. (2017) doi: 10.1111/mec.14259

Novikova PY, Tsuchimatsu T, Simon S, Nizhynska V, Voronin V, Burns R, Fedorenko OM, Holm S, Säll T, Prat E, Marande W, Castric V, Nordborg M and Irwin D. Genome sequencing reveals the origin of the allotetraploid Arabidopsis suecica. Mol. Biol. Evol. 34(4), 957–968. (2017) doi: 10.1093/molbev/msw299

Pisupati R, Reichardt I, Seren Ü, Korte P, Nizhynska V, Kerdaffrec E, Uzunova K, Rabanal FA, Filiault DL and Nordborg M. Verification of Arabidopsis stock collections using SNPmatch, a tool for genotyping high-plexed samples. Sci. Data 4, 170184. (2017) doi: 10.1038/sdata.2017.184

Rabanal FA, Nizhynska V, Mandáková T, Novikova PY, Lysak MA, Mott R and Nordborg M. Unstable inheritance of 45S rRNA genes in Arabidopsis thaliana. G3 7(4), 1201–1209. (2017) doi: 10.1534/g3.117.040204

Schrempf D and Hobolth A. 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) doi: 10.1016/j.tpb.2016.12.001

Taus T, Futschik A and Schlötterer C. Quantifying selection with Pool-Seq time series data. Mol. Biol. Evol. 34(11), 3023–3034. (2017) doi: 10.1093/molbev/msx225

Tobler R, Nolte V and Schlötterer C. High rate of translocation-based gene birth on the Drosophila Y chromosome. Proc. Natl. Acad. Sci. 114(44), 11721–11726. (2017) doi: 10.1073/pnas.1706502114

Bertl J and Blum MGB. Can secondary contact following range expansion be distinguished from barriers to gene flow? bioRxiv 43398. (2016) doi: 10.1101/043398

Alonso-Blanco C, Andrade J, Becker C, Bemm F, Bergelson J, Borgwardt KM, Cao J, Chae E, Dezwaan TM, Ding W, Ecker JR, Exposito-Alonso M, Farlow A, Fitz J, Gan X, Grimm DG, Hancock A, ... Novikova PY, ... Nordborg MN, ..., Zhou X. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell 166(2), 481–491. (2016) doi: 10.1016/j.cell.2016.05.063

Bergland AO, Tobler R, González J, Schmidt P and Petrov D. Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster. Mol. Ecol. 25(5), 1157–1174. (2016) doi: 10.1111/mec.13455

Gärtner K and Futschik A. Improved versions of common estimators of the recombination rate. J. Comput. Biol. 23(9), 756–768. (2016) doi: 10.1089/cmb.2016.0039

Hill T, Schlötterer C and Betancourt AJ. Hybrid dysgenesis in Drosophila simulans associated with a rapid invasion of the P-Element. PLoS Genet. 12(3), e1005920. (2016) doi: 10.1371/journal.pgen.1005920

Huber CD, DeGiorgio M, Hellmann I and Nielsen R. Detecting recent selective sweeps while controlling for mutation rate and background selection. Mol. Ecol. 25(1), 142–156. (2016) doi: 10.1111/mec.13351

Jakšić AM and Schlötterer C. The interplay of temperature and genotype on patterns of alternative splicing in Drosophila melanogaster. Genetics 204(1), 315–325. (2016) doi: 10.1534/genetics.116.192310

Jónás Á, Taus T, Kosiol C, Schlötterer C and Futschik A. Estimating the effective population size from temporal allele frequency changes in experimental evolution. Genetics 204(2), 723–735. (2016) doi: 10.1534/genetics.116.191197

Kawakatsu T, Huang SC, Jupe F, Sasaki E, Schmitz RJ, Urich MA, Castanon R, Nery JR, Barragan C, He Y, Chen H, Dubin M, Lee CR, Wang C, Bemm F, Becker C, O’Neil R, ... Novikova PY, ... Ecker JR. Epigenomic diversity in a global collection of Arabidopsis thaliana accessions. Cell 166(2), 492–506. (2016) doi: 10.1016/j.cell.2016.06.044

Kofler R, Gómez-Sánchez D and Schlötterer C. PoPoolationTE2: Comparative population genomics of transposable elements using Pool-Seq. Mol. Biol. Evol. 33(10), 2759–2764. (2016) doi: 10.1093/molbev/msw137

Kofler R*, Langmüller AM*, Nouhaud P, Otte KA and Schlötterer C. Suitability of different mapping algorithms for genome-wide polymorphism scans with Pool-Seq data. G3 6(11), 3507–3515. (2016) doi: 10.1534/g3.116.034488 *co-first authors

Kofler R, Nolte V and Schlötterer C. The impact of library preparation protocols on the consistency of allele frequency estimates in Pool-Seq data. Mol. Ecol. Resour. 16(1), 118–122. (2016) doi: 10.1111/1755-0998.12432

Nouhaud P, Tobler R, Nolte V and Schlötterer C. Ancestral population reconstitution from isofemale lines as a tool for experimental evolution. Ecol. Evol. 6(20), 7169–7175. (2016) doi: 10.1002/ece3.2402

Novikova PY, Hohmann N, Nizhynska V, Tsuchimatsu T, Ali J, Muir G, Guggisberg A, Paape T, Schmid K, Fedorenko OM, Holm S, Säll T, Schlötterer C, Marhold K, Widmer A, Sese J, Shimizu KK, … Nordborg M. Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nat. Genet. 48(9), 1077–1082. (2016) doi: 10.1038/ng.3617

Schrempf D, Minh BQ, De Maio N, von Haeseler A and Kosiol C. Reversible polymorphism-aware phylogenetic models and their application to tree inference. J. Theor. Biol. 407, 362–370. (2016) doi: 10.1016/j.jtbi.2016.07.042

Vogl C and Bergman J. Computation of the likelihood of joint site frequency spectra using orthogonal polynomials. Computation 4(1), 6. (2016) doi: 10.3390/computation4010006

De Maio N, Schrempf D and Kosiol C. PoMo: An allele frequency-based approach for species tree estimation. Syst. Biol. 64(6), 1018–1031. (2015) doi: 10.1093/sysbio/syv048

Fabian DK, Lack JB, Mathur V, Schlötterer C, Schmidt PS, Pool JE and Flatt T. Spatially varying selection shapes life history clines among populations of Drosophila melanogaster from sub-Saharan Africa. J. Evol. Biol. 28(4), 826–840. (2015) doi: 10.1111/jeb.12607

Franssen SU, Nolte V, Tobler R and Schlötterer C. Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental Drosophila melanogaster populations. Mol. Biol. Evol. 32(2), 495–509. (2015) doi: 10.1093/molbev/msu320

Geroldinger L and Bürger R. Clines in quantitative traits: the role of migration patterns and selection scenarios. Theor. Popul. Biol. 99, 43–66. (2015) doi: S0040-5809(14)00090-2 [pii] 10.1016/j.tpb.2014.10.006

Kofler R, Hill T, Nolte V, Betancourt AJ and Schlötterer C. The recent invasion of natural Drosophila simulans populations by the P-element. Proc. Natl. Acad. Sci. 112(21), 6659–6663. (2015) doi: 10.1073/pnas.1500758112

Schlötterer C, Kofler R, Versace E, Tobler R and Franssen SU. Combining experimental evolution with next-generation sequencing: A powerful tool to study adaptation from standing genetic variation. Heredity. (2015) doi: 10.1038/hdy.2014.86

Tanaka KM, Hopfen C, Herbert MR, Schlötterer C, Stern DL, Masly JP, McGregor AP and Nunes MDS. Genetic architecture and functional characterization of genes underlying the rapid diversification of male external genitalia between Drosophila simulans and Drosophila mauritiana. Genetics 200(1), 357–369. (2015) doi: 10.1534/genetics.114.174045

Tobler R, Hermisson J and Schlötterer C. Parallel trait adaptation across opposing thermal environments in experimental Drosophila melanogaster populations. Evolution. 69(7), 1745–1759. (2015) doi: 10.1111/evo.12705

Topa H*, Jónás Á*, Kofler R, Kosiol C and Honkela A. Gaussian process test for high-throughput sequencing time series: Application to experimental evolution. In Bioinformatics (Vol. 31, pp. 1762–1770). (2015) doi: 10.1093/bioinformatics/btv014 *co-first authors

Uecker H, Setter D and Hermisson J. Adaptive gene introgression after secondary contact. J. Math. Biol. 70(7), 1523–1580. (2015) doi: 10.1007/s00285-014-0802-y

Vogl C and Bergman J. Inference of directional selection and mutation parameters assuming equilibrium. Theor. Popul. Biol. 106, 71–82. (2015) doi: 10.1016/j.tpb.2015.10.003

Akerman A and Bürger R. The consequences of dominance and gene flow for local adaptation and differentiation at two linked loci. Theor. Popul. Biol. 94, 42–62. (2014) doi: S0040-5809(14)00026-4 [pii] 10.1016/j.tpb.2014.04.001

Akerman A and Bürger R. The consequences of gene flow for local adaptation and differentiation: A two-locus two-deme model. J. Math. Biol. 68(5), 1135–1198. (2014) doi: 10.1007/s00285-013-0660-z

Geroldinger L and Bürger R. A two-locus model of spatially varying stabilizing or directional selection on a quantitative trait. Theor. Popul. Biol. 94, 10–41. (2014) doi: S0040-5809(14)00025-2 [pii] 10.1016/j.tpb.2014.03.002

Huber CD, Nordborg M, Hermisson J and Hellmann I. Keeping it local: Evidence for positive selection in Swedish Arabidopsis thaliana. Mol. Biol. Evol. 31(11), 3026–3039. (2014) doi: 10.1093/molbev/msu247

Kapun M, Van Schalkwyk H, McAllister BF, Flatt T and Schlötterer C. Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations of Drosophila melanogaster. Mol. Ecol. 23(7), 1813–1827. (2014) doi: 10.1111/mec.12594

Klepsatel P, Gáliková M, Huber CD and Flatt T. Similarities and differences in altitudinal versus latitudinal variation for morphological traits in Drosophila melanogaster. Evolution 68(5), 1385–1398. (2014) doi: 10.1111/evo.12351

Schlötterer C, Tobler R, Kofler R and Nolte V. Sequencing pools of individuals - mining genome-wide polymorphism data without big funding. Nat. Rev. Genet. (2014, November 23) doi: 10.1038/nrg3803

Tobler R, Franssen SU, Kofler R, Orozco-terWengel P, Nolte V, Hermisson J and Schlötterer C. Massive habitat-specific genomic response in D. melanogaster populations during experimental evolution in hot and cold environments. Mol. Biol. Evol. 31(2), 364–375. (2014) doi: 10.1093/molbev/mst205

Versace E, Nolte V, Pandey RV, Tobler R and Schlötterer C. Experimental evolution reveals habitat-specific fitness dynamics among Wolbachia clades in Drosophila melanogaster. Mol. Ecol. 23(4), 802–814. (2014) doi: 10.1111/mec.12643

Arif S, Murat S, Almudi I, Nunes MDS, Bortolamiol-Becet D, McGregor NS, Currie JMS, Hughes H, Ronshaugen M, Sucena É, Lai EC, Schlötterer C and McGregor AP. Evolution of mir-92a underlies natural morphological variation in Drosophila melanogaster. Curr. Biol. 23(6), 523–528. (2013) doi: 10.1016/j.cub.2013.02.018

Arif S, Hilbrant M, Hopfen C, Almudi I, Nunes MDS, Posnien N, Kuncheria L, Tanaka K, Mitteroecker P, Schlötterer C and McGregor AP. Genetic and developmental analysis of differences in eye and face morphology between Drosophila simulans and Drosophila mauritiana. Evol. Dev. 15(4), 257–267. (2013) doi: Doi 10.1111/Ede.12027

De Maio N, Holmes I, Schlötterer C and Kosiol C. Estimating empirical codon hidden markov models. Mol. Biol. Evol. 30(3), 725–736. (2013) doi: 10.1093/molbev/mss266

Bastide H, Betancourt AJ, Nolte V, Tobler R, Stöbe P, Futschik A and Schlötterer C. A genome-wide, fine-scale map of natural pigmentation variation in Drosophila melanogaster. PLoS Genet. 9(6), e1003534. (2013) doi: 10.1371/journal.pgen.1003534

De Maio N, Schlötterer C and Kosiol C. Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models. Mol. Biol. Evol. 30(10), 2249–2262. (2013) doi: 10.1093/molbev/mst131

Klepsatel P, Gáliková M, De Maio N, Ricci S, Schlötterer C and Flatt T. Reproductive and post-reproductive life history of wild-caught Drosophila melanogaster under laboratory conditions. J. Evol. Biol. 26(7), 1508–1520. (2013) doi: 10.1111/jeb.12155

Klepsatel P, Gáliková M, De Maio N, Huber CD, Schlötterer C and Flatt T. Variation in thermal performance and reaction norms among populations of Drosophila melanogaster. Evolution 67(12), 3573–3587. (2013) doi: 10.1111/evo.12221

Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, Platzer A, Zhang Q, Vilhjálmsson BJ, Korte A, Nizhynska V, Voronin V, Korte P, Sedman L, Mandáková T, Lysak MA, Seren Ü, Hellmann I and Nordborg M. Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat. Genet. 45(8), 884–890. (2013) doi: Doi 10.1038/Ng.2678

Clemente F and Vogl C. Evidence for complex selection on four-fold degenerate sites in Drosophila melanogaster. J. Evol. Biol. 25(12), 2582–2595. (2012) doi: Doi 10.1111/Jeb.12003

Vogl C and Clemente F. The allele-frequency spectrum in a decoupled Moran model with mutation, drift, and directional selection, assuming small mutation rates. Theor. Popul. Biol. 81(3), 197–209. (2012) doi: Doi 10.1016/J.Tpb.2012.01.001

Orozco-terWengel P, Kapun M, Nolte V, Kofler R, Flatt T and Schlötterer C. Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles. Mol. Ecol. 21(20), 4931–4941. (2012) doi: 10.1111/j.1365-294X.2012.05673.x

Fabian DK, Kapun M, Nolte V, Kofler R, Schmidt PS, Schlötterer C and Flatt T. Genome-wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America. Mol. Ecol. 21(19), 4748–4769. (2012) doi: 10.1111/j.1365-294X.2012.05731.x

Clemente F and Vogl C. Unconstrained evolution in short introns? - An analysis of genome-wide polymorphism and divergence data from Drosophila. J. Evol. Biol. 25(10), 1975–1990. (2012) doi: 10.1111/j.1420-9101.2012.02580.x

Posnien N, Hopfen C, Hilbrant M, Ramos-Womack M, Murat S, Schönauer A, Herbert SL, Nunes MDS, Arif S, Breuker CJ, Schlötterer C, Mitteroecker P and McGregor AP. Evolution of eye morphology and Rhodopsin expression in the Drosophila melanogaster species subgroup. PLoS One 7(5), e37346. (2012) doi: 10.1371/journal.pone.0037346

Bank C, Bürger R and Hermisson J. The limits to parapatric speciation: Dobzhansky-Muller incompatibilities in a continent-Island model. Genetics 191(3), 845–863. (2012) doi: 10.1534/genetics.111.137513

Bank C, Hermisson J and Kirkpatrick M. Can reinforcement complete speciation? Evolution 66(1), 229–239. (2012) doi: 10.1111/j.1558-5646.2011.01423.x

Fabian DK and Flatt T. Life history evolution. Nat. Educ. Knowl. (2012)

Kofler R, Orozco-terWengel P, de Maio N, Pandey RV, Nolte V, Futschik A, Kosiol C and Schlötterer C. Popoolation: A toolbox for population genetic analysis of next generation sequencing data from pooled individuals. PLoS One 6(1), e15925. (2011) doi: 10.1371/journal.pone.0015925

Bürger R and Akerman A. The effects of linkage and gene flow on local adaptation: a two-locus continent-island model. Theor. Popul. Biol. 80(4), 272–288. (2011) doi: S0040-5809(11)00061-X [pii] 10.1016/j.tpb.2011.07.002

Klepsatel P and Flatt T. The genomic and physiological basis of life history variation in a butterfly metapopulation. Mol. Ecol. 20(9), 1795–1798. (2011) doi: 10.1111/j.1365-294X.2011.05078.x

Galikova M, Klepsatel P, Senti G and Flatt T. Steroid hormone regulation of C. elegans and Drosophila aging and life history. Exp. Gerontol. 46(2–3), 141–147. (2011) doi: S0531-5565(10)00265-2 [pii] 10.1016/j.exger.2010.08.021

Fabian DK and Flatt T. The evolution of aging. Nat. Educ. Knowl. (2011)

Kapun M, Nolte V, Flatt T and Schlötterer C. Host range and specificity of the Drosophila C virus. PLoS One 5(8), e12421. (2010) doi: 10.1371/journal.pone.0012421

Fond zur Förderung der wissenschaftlichen Forschung
vetmed uni vienna
Gregor Mendel Institute of Molecular Plant Biology
Universität Wien