Recent publications of our students

Xiao C, Duarri-Redondo S, Thorhölludottir DAV, Chen Y and Schlötterer C. Non-additive effects between genotypes: Implications for competitive fitness assays. Ecol. Evol. 13(11), e10713. (2023) doi: 10.1002/ece3.10713

Buchner S, Hsu S-K, Nolte V, Otte KA and Schlötterer C. Effects of larval crowding on the transcriptome of Drosophila simulans. Evol. Appl. (2023) in print. doi: 10.1111/eva.13592

Pianezza R, Scarpa A, Narayanan P, Signor S and Kofler R. Spoink, a LTR retrotransposon, invaded D. melanogaster populations in the 1990s. bioRxiv 2023.10.30.564725. (2023) doi: 10.1101/2023.10.30.564725

Wierzbicki F and Kofler R. The composition of piRNA clusters in Drosophila melanogaster deviates from expectations under the trap model. BMC Biol. 21(224). (2023) doi: 10.1101/2023.02.14.528490

Scarpa A and Kofler R. The impact of paramutations on the invasion dynamics of transposable elements. Genetics iyad181, 2023.03.14.532580. (2023) doi: 10.1101/2023.03.14.532580

Signor S, Vedanayagam J, Kim BY, Wierzbicki F, Kofler R and Lai EC. Rapid evolutionary diversification of the flamenco locus across simulans clade Drosophila species. PLoS Genet. 19(8), e1010914. (2023) doi: 10.1371/journal.pgen.1010914

Chen H, Pelizzola M and Futschik A. Haplotype based testing for a better understanding of the selective architecture. BMC Bioinformatics 24(1), 322. (2023) doi: 10.1186/s12859-023-05437-3

Yıldırım B and Vogl C. Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract. J. Evol. Biol. 36(9), 1295–1312. (2023) doi: 10.1111/jeb.14205

Langmüller AM, Nolte V, Dolezal M and Schlötterer C. The genomic distribution of transposable elements is driven by spatially variable purifying selection. Nucleic Acids Res. 51(17), 9203–9213. (2023) doi: 10.1093/nar/gkad635

Szukala A, Bertel C, Frajman B, Schönswetter P and Paun O. Parallel adaptation to lower altitudes is associated with enhanced plasticity in Heliosperma pusillum (Caryophyllaceae). Plant J. early online. (2023) doi: 10.1111/tpj.16342

Scarpa A, Pianezza R, Wierzbicki F and Kofler R. Genomes of historical specimens reveal multiple invasions of LTR retrotransposons in Drosophila melanogaster populations during the 19th century. bioRxiv 2023.06.06.543830. (2023) doi: 10.1101/2023.06.06.543830

Bozlak E, Radovic L, Remer V, Rigler D, Allen L, Brem G, Stalder G, Castaneda C, Cothran G, Raudsepp T, Okuda Y, Moe KK, Moe HH, Kounnavongsa B, Keonouchanh S, Van NH, Vu VH, … Wallner B. Refining the evolutionary tree of the horse Y chromosome. Sci. Rep. 13(1), 8954. (2023) doi: 10.1038/s41598-023-35539-0

Lai W-Y, Otte KA and Schlötterer C. Evolution of metabolome and transcriptome support a hierarchical organization of adaptive traits. Genome Biol. Evol. evad098. (2023) doi: 10.1093/gbe/evad098

Pisupati R, Nizhynska V, Mollá Morales A and Nordborg M. On the causes of gene-body methylation variation in Arabidopsis thaliana. PLoS Genet. 19(5), e1010728. (2023) doi: 10.1371/journal.pgen.1010728

Wölfl B and Hermisson J. A theory of oligogenic adaptation of a quantitative trait. Genetics, iyad139. (2023) doi: 10.1101/2023.04.20.537719

Barghi N and Ramirez-Lanzas C. A high throughput method for egg size measurement in Drosophila. Sci. Rep. 13(1), 3791. (2023) doi: 10.1038/s41598-023-30472-8

Kotari I, Kosiol C and Borges R. The patterns of codon usage between chordates and arthropods are different but co-evolving with mutational biases. bioRxiv 2023.03.30.534958. (2023) doi: 10.1101/2023.03.30.534958

Götsch H and Bürger R. Evolution of quantitative traits under directional selection: Selective sweeps or small allele-frequency changes? bioRxiv 2023.02.23.529647. (2023) doi: 10.1101/2023.02.23.529647

Crego CG, Hess J, Yardeni G, Harpe M de La, Beclin F, Cauz-Santos LA, Saadain S, Barbará T, Temsch EM, Weiss-Schneeweiss H, Barfuss MHJ, Till W, Heyduk K, Lexer C, Paun O and Leroy T. Short structural variation fuelled CAM evolution within an explosive bromeliad radiation. bioRxiv 2023.02.01.526631. (2023) doi: 10.1101/2023.02.01.526631

Borges R, Kotari I, Bergman J, Chase MA, Mugal CF and Kosiol C. Traditional phylogenetic models fail to account for variations in the effective population size. bioRxiv 2022.09.26.509598. (2023) doi: 10.1101/2022.09.26.509598

Langmüller AM, Champer J, Lapinska S, Xie L, Metzloff M, Champer SE, Liu J, Xu Y, Du J, Clark AG and Messer PW. Fitness effects of CRISPR endonucleases in Drosophila melanogaster populations. Elife 11, e71809. (2022) doi: 10.7554/eLife.71809

Selvaraju D, Wierzbicki F and Kofler R. P-element invasions in Drosophila erecta shed light on the establishment of host control over a transposable element. bioRxiv 2022.12.22.521571. (2022) doi: 10.1101/2022.12.22.521571

Burny C, Nolte V, Dolezal M and Schlötterer C. Genome-wide selection signatures reveal widespread synergistic effects of two different stressors in Drosophila melanogaster. Proc. R. Soc. B Biol. Sci. 289: 20221857. (2022) doi: 10.1098/rspb.2022.1857

Castaneda C, Radovic L, Felkel S, Juras R, Davis BW, Cothran EG, Wallner B and Raudsepp T. Copy number variation of horse Y chromosome genes in normal equine populations and in horses with abnormal sex development and subfertility: relationship of copy number variations with Y haplogroups. G3 jkac278. (2022) doi: 10.1093/g3journal/jkac278

Radovic L, Remer V, Krcal C, Rigler D, Brem G, Rayane A, Driss K, Benamar M, Machmoum M, Piro M, Krischke D, Butler-Wemken I V and Wallner B. Y chromosome haplotypes enlighten origin, influence, and breeding history of North African Barb horses. Animals. (2022) doi: 10.3390/ani12192579

Eriksson MC, Mandáková T, McCann J, Temsch EM, Chase MW, Hedrén M, Weiss-Schneeweiss H and Paun O. Repeat dynamics across timescales: a perspective from sibling allotetraploid marsh orchids (Dactylorhiza majalis s.l.). Mol. Biol. Evol. msac167. (2022) doi: 10.1093/molbev/msac167

Christodoulaki E, Nolte V, Lai W-Y and Schlötterer C. Natural variation in Drosophila shows weak pleiotropic effects. Genome Biol. 23(1), 116. (2022) doi: 10.1186/s13059-022-02680-4

Yang E, Metzloff M, Langmüller AM, Xu X, Clark AG, Messer PW and Champer J. A homing suppression gene drive with multiplexed gRNAs maintains high drive conversion efficiency and avoids functional resistance alleles. G3 (2022) doi: 10.1093/g3journal/jkac081

Fulgione A, Neto C, Elfarargi AF, Tergemina E, Ansari S, Göktay M, Dinis H, Döring N, Flood PJ, Rodriguez-Pacheco S, Walden N, Koch MA, Roux F, Hermisson J and Hancock AM. Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages. Nat. Commun. (2022) 13(1), 1461. doi: 10.1038/s41467-022-28800-z

Szukala A, Lovegrove-Walsh J, Luqman H, Fior S, Wolfe TM, Frajman B, Schoenswetter P and Paun O. Polygenic routes lead to parallel altitudinal adaptation in Heliosperma pusillum (Caryophyllaceae). Mol. Ecol. (2022) doi: 10.1111/mec.16393

Lirakis M, Nolte V and Schlötterer C. Pool-GWAS on reproductive dormancy in Drosophila simulans suggests a polygenic architecture. G3 jkac027. (2022) doi: 10.1093/g3journal/jkac027

Remer V, Bozlak E, Felkel S, Radovic L, Rigler D, Grilz-Seger G, Stefaniuk-Szmukier M, Bugno-Poniewierska M, Brooks S, Miller DC, Antczak DF, Sadeghi R, Cothran G, Juras R, Khanshour AM, Rieder S, Penedo MC, … Wallner B. Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses. Genes. 13(2), 229. (2022) doi: 10.3390/genes13020229

Wierzbicki F, Kofler R and Signor S. Evolutionary dynamics of piRNA clusters in Drosophila. Mol. Ecol. Resour. 1, 102–121. (2022) doi: 10.1101/2021.08.20.457083

Lai W-Y and Schlötterer C. Evolution of phenotypic variance in response to a novel hot environment. Mol. Ecol. 31(3), 934–945. (2022) doi:

Hsu S-K, Lai W-Y, Novak J, Lehner F, Jakšić AM, Versace E and Schlötterer C. Pre- and post-mating reproductive isolation evolve independently during rapid adaptation to high temperature. bioRxiv 2021.11.08.467720. (2021) doi: 10.1101/2021.11.08.467720

Burny C, Nolte V, Dolezal M and Schlötterer C. Genome-wide selection signatures reveal widespread synergistic effects of culture conditions and temperature stress in Drosophila melanogaster. bioRxiv 2021.11.09.467935. (2021) doi: 10.1101/2021.11.09.467935

Wölfl B*, te Rietmole H*, Salvioli M, Kaznatcheev A, Thuijsman F, Brown JS, Burgering B and Staňková K. The contribution of evolutionary game theory to understanding and treating cancer. Dyn. Games Appl. (2021) doi: 10.1007/s13235-021-00397-w
(authors contributed equally)

Burny C, Nolte V, Dolezal M and Schlötterer C. Highly parallel genomic selection response in replicated Drosophila melanogaster populations with reduced genetic variation. Genome Biol. Evol. evab239. (2021) doi: 10.1101/2021.04.06.438598

Yardeni G, Viruel J, Paris M, Hess J, Groot Crego C, de La Harpe M, Rivera N, Barfuss MHJ, Till W, Guzmán-Jacob V, Krömer T, Lexer C, Paun O and Leroy T. Taxon-specific or universal? Using target capture to study the evolutionary history of a rapid radiation. Mol. Ecol. Resour. 00, 1–19. (2021) doi: 10.1101/2021.05.20.444989

Radovic L, Remer V, Reiter S, Bozlak E, Felkel S, Grilz-Seger G, Brem G and Wallner B. 38 Y chromosome genetic variation and deep genealogies provide new insights on Lipizzan sire lines. J. Equine Vet. Sci. 100, 103501. (2021) doi: 10.1016/j.jevs.2021.103501

Wolfe TM, Balao F, Trucchi E, Bachmann G, Gu W, Baar J, Hedren M, Weckwerth W, Leitch AR and Paun O. Recurrent allopolyploidization events diversify eco-physiological traits in marsh orchids. bioRxiv 2021.08.28.458039. (2021) doi: 10.1101/2021.08.28.458039

Shang H, Rendón-Anaya M, Paun O, Field DL, Hess J, Vogl C, Liu J, Ingvarsson PK, Lexer C and Leroy T. Conserved genomic landscapes of differentiation across Populus speciation continuum. bioRxiv 2021.08.26.457771. (2021) doi: 10.1101/2021.08.26.457771

Wierzbicki F*, Schwarz F*, Cannalonga O and Kofler R. Novel quality metrics allow identifying and generating high-quality assemblies of piRNA clusters. Mol. Ecol. Res. (2021) accepted

Johnson KD, Beiglböck M, Eder M, Grass A, Hermisson J, Pammer G, Polechová J, Toneian D and Wölfl B. Disease momentum: Estimating the reproduction number in the presence of superspreading. Infect. Dis. Model. 6, 706–728. (2021) doi: 10.1016/j.idm.2021.03.006 (all authors contributed equally)

Bayle V, Fiche JB, Burny C, Platre MP, Nollmann M, Martinière A and Jaillais Y. Single-particle tracking photoactivated localization microscopy of membrane proteins in living plant tissues. Nat. Protoc. 16(3), 1600–1628. (2021) doi: 10.1038/s41596-020-00471-4

Langmüller AM, Dolezal M and Schlötterer C. Fine mapping without phenotyping: Identification of selection targets in secondary Evolve and Resequence experiments. Genome Biol. Evol. 13(8). (2021) doi: 10.1093/gbe/evab154

Lai W-Y, Nolte V, Jakšić AM and Schlötterer C. Evolution of phenotypic variance provides insights into the genetic basis of adaption. bioRxiv 2021.01.19.427260. (2021) doi: 10.1101/2021.01.19.427260

Hsu SK, Belmouaden C, Nolte V, Schlötterer C (2021) Parallel gene expression evolution in natural and laboratory evolved populations. Mol. Ecol. 30: 884–894. doi: 0.1111/Mec.15649

Pelizzola M, Behr M, Li H, Munk A and Futschik A. Multiple haplotype reconstruction from allele frequency data. Nat. Comput. Sci. 1(4), 262–271. (2021) doi: 10.1038/s43588-021-00056-5

Shang H, Hess J, Pickup M, Field DL, Ingvarsson PK, Liu J and Lexer C. Evolution of strong reproductive isolation in plants: broad-scale patterns and lessons from a perennial model group. Philos. Trans. R. Soc. B Biol. Sci. 375(1806), 20190544. (2020) doi: 10.1098/rstb.2019.0544

Schwarz F, Wierzbicki F, Senti K-A and Kofler R. Tirant stealthily invaded natural Drosophila melanogaster populations during the last century. Mol. Biol. Evol. 38(4), 1482–1497. (2021) doi: 10.1093/molbev/msaa308

Langmüller AM, Nolte V, Galagedara R, Poupardin R, Dolezal M and Schlötterer C. Fitness effects for Ace insecticide resistance mutations are determined by ambient temperature. BMC Biol. 18(1), 157. (2020) doi: 10.1186/s12915-020-00882-5

Jakšić AM, Karner J, Nolte V, Hsu SK, Barghi N, Mallard F, Otte KA, Svečnjak L, Senti KA and Schlötterer C. Neuronal function and dopamine signaling evolve at high temperature in Drosophila. Mol. Biol. Evol. 37(9), 2630–2640. (2020) doi: 10.1093/molbev/msaa116

Weilguny L, Vlachos C, Selvaraju D and Kofler R. Reconstructing the invasion route of the P-element in Drosophila melanogaster using extant population samples. Genome Biol. Evol. 12(11), 2139–2152. (2021) doi: 10.1093/GBE/EVAA190

Gutzat R, Rembart K, Nussbaumer T, Hofmann F, Pisupati R, Bradamante G, Daubel N, Gaidora A, Lettner N, Donà M, Nordborg M, Nodine M and Mittelsten Scheid O. Arabidopsis shoot stem cells display dynamic transcription and DNA methylation patterns. EMBO J. 39(20). (2020) doi: 10.15252/embj.2019103667

Leung K, Ras E, Ferguson KB, Ariëns S, Babendreier D, Bijma P, Bourtzis K, Brodeur J, Bruins MA, Centurión A, Chattington SR, Chinchilla-Ramírez M, Dicke M, Fatouros NE, González-Cabrera J, Groot TVM, Haye T, … Lirakis M, ... Pannebakker BA. Next-generation biological control: the need for integrating genetics and genomics. Biol. Rev. 95(6), 1838–1854. (2020) doi: 10.1111/brv.12641

Langmüller AM and Schlötterer C. Low concordance of short-term and long-term selection responses in experimental Drosophila populations. Mol. Ecol. 29, 3466–3475. (2020) doi: 10.1101/759704

Setter D, Mousset S, Cheng X, Nielsen R, DeGiorgio M and Hermisson J. VolcanoFinder: Genomic scans for adaptive introgression. PLoS Genet. 16(6), e1008867. (2020) doi: 10.1371/journal.pgen.1008867

Triqueneaux G, Burny C, Symmons O, Janczarski S, Gruffat H and Yvert G. Cell-to-cell expression dispersion of B-cell surface proteins is linked to genetic variants in humans. Commun. Biol. 3(1), 346. (2020) doi: 10.1038/s42003-020-1075-1

Eriksson MC, Szukala A, Tian B and Paun O. Current research frontiers in plant epigenetics: an introduction to a Virtual Issue. New Phytol. 226, 285–288. (2020) doi:10.1111/Nph.16493

Mazzucco R, Nolte V, Vijayan T, Schlötterer C. Long-term dynamics among Wolbachia strains during thermal adaptation of their Drosophila melanogaster hosts. Front. Genet. 11, 482. (2020) doi:10.3389/fgene.2020.00482

Törmä L, Burny C and Schlötterer C. Reversed sex-biased mutation rates for indels and base substitutions in Drosophila melanogaster. bioRxiv 031336. (2020) doi: 10.1101/2020.04.07.029033

Törmä L, Burny C, Nolte V, Senti KA and Schlötterer C. Transcription-coupled repair in Drosophila melanogaster is independent of the mismatch repair pathway. bioRxiv 029033. (2020) doi: 10.1101/2020.04.07.029033

Pontz M and Feldman MW. Loss of genetic variation in the two-locus multiallelic haploid model. Theor. Popul. Biol. 136, 12–21. (2020) doi: 10.1101/2020.03.07.981852

Burny C, Nolte V, Nouhaud P, Dolezal M and Schlötterer C. Secondary evolve and re-sequencing: an experimental confirmation of putative selection targets without phenotyping. Genome Biol. Evol. 12(3), 151–159 (2020) doi: 10.1093/gbe/evaa036

Hsu S-K, Jakšić AM, Nolte V, Lirakis M, Kofler R, Barghi N, Versace E and Schlötterer C. Rapid sex-specific adaptation to high temperature in Drosophila. eLife 9. (2020) doi: 10.7554/eLife.53237

Spitzer K, Pelizzola M and Futschik A. Modifying the chi-square and the cmh test for population genetic inference: Adapting to overdispersion. Ann. Appl. Stat. 14(1), 202–220. (2020) doi: 10.1214/19-AOAS1301

Aköz G and Nordborg M. The Aquilegia genome reveals a hybrid origin of core eudicots. Genome Biol. 20(1), 256. (2019) doi: 10.1186/s13059-019-1888-8

Vlachos C, Burny C, Pelizzola M, Borges R, Futschik A, Kofler R and Schlötterer C. Benchmarking software tools for detecting and quantifying selection in evolve and resequencing studies. Genome Biol. 20(1), 169. (2019) doi: 10.1186/s13059-019-1770-8

Vlachos C and Kofler R. Optimizing the power to identify the genetic basis of complex traits with evolve and resequence studies. Mol. Biol. Evol. 36(12), 2890–2905. (2019) doi: 10.1093/molbev/msz183

Christodoulaki E, Barghi N and Schlötterer C. Distance to trait optimum is a crucial factor determining the genomic signature of polygenic adaptation. bioRxiv 721340. (2019) doi: 10.1101/721340

Lirakis M and Magalhães S. Does experimental evolution produce better biological control agents? A critical review of the evidence. Entomol. Exp. Appl. 167(7), eea.12815. (2019) doi: 10.1111/eea.12815

Felkel S, Vogl C, Rigler D, Dobretsberger V, Chowdhary BP, Distl O, Fries R, Jagannathan V, Janečka JE, Leeb T, Lindgren G, McCue M, Metzger J, Neuditschko M, Rattei T, Raudsepp T, Rieder S, … Wallner B. The horse Y chromosome as an informative marker for tracing sire lines. Sci. Rep. 9(1), 6095. (2019) doi: 10.1038/s41598-019-42640-w

Durmaz E, Rajpurohit S, Betancourt N, Fabian DK, Kapun M, Schmidt P and Flatt T. A clinal polymorphism in the insulin signaling transcription factor foxo contributes to life-history adaptation in Drosophila. Evolution 73(9), 1774–1792. (2019) doi: 10.1111/evo.13759

Felkel S, Wallner B, Chuluunbat B, Yadamsuren A, Faye B, Brem G, Walzer C and Burger PA. A first Y-chromosomal haplotype network to investigate male-driven population dynamics in domestic and wild Bactrian camels. Front. Genet. 10, 423. (2019) doi: 10.3389/fgene.2019.00423

Fages A, … Felkel S, Wallner B, … Orlando L. Tracking five millennia of horse management with extensive ancient genome time series. Cell 177(6), 1419-1435.e31. (2019) doi: 10.1016/j.cell.2019.03.049

Howie JM, Mazzucco R, Taus T, Nolte V and Schlötterer C. DNA motifs are not general predictors of recombination in two Drosophila sister species. Genome Biol. Evol. 11(4), 1345–1357. (2019) doi: 10.1093/gbe/evz082

Höllinger I, Pennings PS and Hermisson J. Polygenic adaptation: From sweeps to subtle frequency shifts. PLoS Genet. 15(3), e1008035. (2019) doi: 10.1371/journal.pgen.1008035

Bergman J and Eyre-Walker A. Does adaptive protein evolution proceed by large or small steps at the amino acid level? Mol. Biol. Evol. (2019) doi: 10.1093/molbev/msz033

Barghi N, Tobler R, Nolte V, Jakšić AM, Mallard F, Otte KA, Dolezal M, Taus T, Kofler R and Schlötterer C. Genetic redundancy fuels polygenic adaptation in Drosophila. PLOS Biol. 17(2), e3000128. (2019) doi: 10.1371/journal.pbio.3000128

Hsu S-K, Jakšić AM, Nolte V, Barghi N, Mallard F, Otte KA and Schlötterer C. A 24 h age difference causes twice as much gene expression divergence as 100 generations of adaptation to a novel environment. Genes 10(2), 89. (2019) doi: 10.3390/genes10020089

Rogers J, Raveendran M, Harris RA, Mailund T, Leppälä K, Athanasiadis G, Schierup MH, Cheng J, Munch K, Walker JA, Konkel MK, Jordan V, Steely CJ, Beckstrom TO, Bergey C, Burrell A, Schrempf D, … Consortium BGA. The comparative genomics and complex population history of Papio baboons. Sci. Adv. 5(1), eaau6947. (2019) doi: 10.1126/sciadv.aau6947

Liu J, Champer J, Langmüller AM, Liu C, Chung J, Reeves R, Luthra A, Lee YL, Vaughn AH, Clark AG and Messer PW. Maximum likelihood estimation of fitness components in experimental evolution. Genetics 211(3), 1005–1017. (2019) doi: 10.1534/genetics.118.301893

Fabian DK, Garschall K, Klepsatel P, Santos-Matos G, Sucena É, Kapun M, Lemaitre B, Schlötterer C, Arking R and Flatt T. Evolution of longevity improves immunity in Drosophila. Evol. Lett. (2018) doi: 10.1002/evl3.89

Bertl J, Ringbauer H and Blum MGB. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ 6, e5325. (2018) doi: 10.7717/peerj.5325

Vlachos C and Kofler R. MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies. PLOS Comput. Biol. 14(8), e1006413. (2018) doi: 10.1371/journal.pcbi.1006413

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. 19(1), 119. (2018) doi: 10.1186/s13059-018-1503-4

Filiault DL, Ballerini ES, Mandáková T, Aköz G, Derieg NJ, Schmutz J, Jenkins J, Grimwood J, Shu S, Hayes RD, Hellsten U, Barry K, Yan J, Mihaltcheva S, Karafiátová M, Nizhynska V, Kramer EM, … Nordborg M. The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history. eLife 7. (2018) doi: 10.7554/eLife.36426

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

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

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, …, Wallner B, ..., Orlando L. Ancient genomes revisit the ancestry of domestic and Przewalski’s horses. Science 360(6384):111-114. (2018)

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, Betancourt AJ and Kalinka AT. A novel method for quantifying the rate of embryogenesis uncovers considerable genetic variation for the duration of embryonic development in Drosophila melanogaster. BMC Evol. Biol. 16(1), 1–14. (2016) doi: 10.1186/s12862-016-0776-z

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

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

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

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

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. 35(3), 564–574. (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

Lee CR, Svardal H, Farlow A, Exposito-Alonso M, Ding W, Novikova PY, Alonso-Blanco C, Weigel D and Nordborg M. On the post-glacial spread of human commensal Arabidopsis thaliana. Nat. Commun. 8, 14458. (2017) doi: 10.1038/ncomms14458

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

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

He F, Arce AL, Schmitz G, Koornneef M, Novikova P, Beyer A and de Meaux J. The footprint of polygenic adaptation on stress-responsive cis-regulatory divergence in the Arabidopsis genus. Mol. Biol. Evol. 33(8), 2088–2101. (2016) doi: 10.1093/molbev/msw096

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

Horváth B and Kalinka AT. Effects of larval crowding on quantitative variation for development time and viability in Drosophila melanogaster. Ecol. Evol. 6(23), 8460–8473. (2016) doi: 10.1002/ece3.2552

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. 3(10), 24. (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. 3(10), 9. (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