Recent publications of our students
Pontz M and Feldman MW. Loss of genetic variation in the two-locus multiallelic haploid model. BioRxiv 981852. (2020) doi: https://doi.org/10.1101/2020.03.07.981852
https://www.biorxiv.org/content/10.1101/2020.03.07.981852v1
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. (2020) doi: 10.1093/gbe/evaa036
https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evaa036/5803073
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
https://elifesciences.org/articles/53237
Spitzer K, Pelizzola M and Futschik A. Modifying the Chi-square and the CMH test for population genetic inference: adapting to over-dispersion. Ann. Appl. Stat. (2020)
https://www.e-publications.org/ims/submission/AOAS/user/submissionFile/39844?confirm=afa966e8
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6883705/
Triqueneaux G, Burny C, Symmons O, Janczarski S, Gruffat H and Yvert G. Cell-to-cell expression dispersion of B-cell surface proteins displays genetic variation among humans. BioRxiv 792606. (2019) doi: 10.1101/792606
https://www.biorxiv.org/content/10.1101/792606v1
Langmüller AM and Schlötterer C. Low concordance of short-term and long-term selection responses in experimental Drosophila populations. bioRxiv 759704. (2019) doi: 10.1101/759704
https://www.biorxiv.org/content/10.1101/759704v1
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
https://genomebiology.biomedcentral.com/articles/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
https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msz183/5545983
Weilguny L, Vlachos C, Selvaraju D and Kofler R. Reconstructing the invasion route of DNA transposons using extant population samples. bioRxiv 729889. (2019) doi: 10.1101/729889
https://www.biorxiv.org/content/10.1101/729889v1
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. bioRxiv 722488. (2019) doi: 10.1101/722488
https://www.biorxiv.org/content/10.1101/722488v1
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
https://www.biorxiv.org/content/10.1101/721340v1
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
https://onlinelibrary.wiley.com/doi/10.1111/eea.12815
Setter D, Mousset S, Cheng X, Nielsen R, DeGiorgio M and Hermisson J. VolcanoFinder: genomic scans for adaptive introgression. bioRxiv 697987. (2019) doi: 10.1101/697987
https://www.biorxiv.org/content/10.1101/697987v1.full
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
https://www.nature.com/articles/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
https://onlinelibrary.wiley.com/doi/abs/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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6537670/
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
https://www.cell.com/cell/fulltext/S0092-8674(19)30384-8
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
https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evz082/5454723
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
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008035
Jakšić AM, Karner J, Nolte V, Hsu S-K, Barghi N, Mallard F, Otte KA, Svečnjak L, Senti KA and Schlötterer C. Neuronal function and dopamine signaling evolve at high temperature in Drosophila. bioRxiv 585422. (2019) doi: 10.1101/585422
https://www.biorxiv.org/content/10.1101/585422v1.full
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
https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msz033/5319976?guestAccessKey=fa3fff8d-08a6-40e9-a3e3-cc25065b22ec
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
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000128
Hsu S-K, Jakšić AM, Nolte V, Barghi N, Mallard F, Otte KA, 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
https://www.mdpi.com/2073-4425/10/2/89
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
http://advances.sciencemag.org/content/5/1/eaau6947
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 genetics.301893.2018. (2019) doi: 10.1534/genetics.118.301893
http://www.genetics.org/content/early/2019/01/24/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
https://onlinelibrary.wiley.com/doi/full/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
https://peerj.com/articles/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
http://journals.plos.org/ploscompbiol/article?id=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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6100727/
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
https://elifesciences.org/articles/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
http://europepmc.org/articles/PMC5786239
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
https://www.sciencedirect.com/science/article/pii/S0022519317305477?via%3Dihub
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
https://onlinelibrary.wiley.com/doi/abs/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, … Orlando L. Ancient genomes revisit the ancestry of domestic and Przewalski’s horses. Science 360(6384):111-114. (2018)
https://science.sciencemag.org/content/360/6384/111.long
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
http://journals.sagepub.com/doi/pdf/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
https://bmcevolbiol.biomedcentral.com/articles/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
https://onlinelibrary.wiley.com/doi/full/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
https://genome.cshlp.org/content/28/6/824
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
https://www.sciencedirect.com/science/article/pii/S0022191017304833?via%3Dihub
Mallard F, Jakšić AM and Schlötterer C. Contesting the evidence for non-adaptive plasticity. Nature 555(7698), E21–E22. (2018) doi: 10.1038/nature25496
https://www.nature.com/articles/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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5754571/
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
https://www.biorxiv.org/content/early/2017/08/29/181198
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5518283/
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
http://europepmc.org/articles/PMC5499140
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
https://www.degruyter.com/view/j/sagmb.2017.16.issue-5-6/sagmb-2017-0016/sagmb-2017-0016.xml
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5441814/
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
http://europepmc.org/articles/PMC5850838
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
https://onlinelibrary.wiley.com/doi/full/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
https://onlinelibrary.wiley.com/doi/abs/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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5012396/
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
https://www.nature.com/articles/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
http://europepmc.org/articles/PMC5400380
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5744633/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386868/
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
https://www.sciencedirect.com/science/article/pii/S004058091630106X?via%3Dihub
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
http://europepmc.org/articles/PMC5850601
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5676891/
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
http://europepmc.org/articles/PMC4949382
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5089930/
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
https://europepmc.org/abstract/MED/27409412
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4794157/
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
https://onlinelibrary.wiley.com/doi/full/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
http://europepmc.org/articles/PMC5082542
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
http://europepmc.org/articles/PMC5012396
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5068858/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5172462/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026257/
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
http://europepmc.org/articles/PMC5100849
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4744716/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114691/
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
https://www.nature.com/articles/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
https://www.sciencedirect.com/science/article/pii/S0022519316302259?via%3Dihub
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
http://www.mdpi.com/2079-3197/4/1/6/htm
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4604832/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405473/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298179/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302420/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4450375/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815507/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4423377/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755034/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443671/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426140/
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
https://www.sciencedirect.com/science/article/pii/S0040580915001045
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045392/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3948587/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048038/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4209139/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4359753/
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
https://onlinelibrary.wiley.com/doi/pdf/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
http://www.nature.com/articles/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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907058/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260678/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605577/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799016/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3563974/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3674992/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3773373/
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
https://onlinelibrary.wiley.com/doi/full/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
https://onlinelibrary.wiley.com/doi/full/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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3755268/
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
https://www.ncbi.nlm.nih.gov/pubmed/23020078
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315028/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3533796/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3482935/
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
https://onlinelibrary.wiley.com/doi/full/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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3360684/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389979/
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
https://onlinelibrary.wiley.com/doi/full/10.1111/j.1558-5646.2011.01423.x
Fabian DK and Flatt T. Life history evolution. Nat. Educ. Knowl. (2012)
http://origin.www.nature.com/scitable/knowledge/library/life-history-evolution-68245673
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3017084/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3257863/
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
https://onlinelibrary.wiley.com/doi/full/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
https://www.sciencedirect.com/science/article/pii/S0531556510002652?via%3Dihub
Fabian DK and Flatt T. The evolution of aging. Nat. Educ. Knowl. (2011)
http://origin.www.nature.com/scitable/knowledge/library/the-evolution-of-aging-23651151
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
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0012421
