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ERC ADG: The architecture of adaptation

Abstract
Objective: One of the central goals in evolutionary biology is to understand adaptation. Experimental evolution represents a highly promising approach to study adaptation. In this proposal, a freshly collected D. simulans population will be allowed to adapt to laboratory conditions under two different temperature regimes: hot (27°C) and cold (18°C). The trajectories of adaptation to these novel environments will be monitored on three levels: 1) genomic, 2) transcriptomic, 3) phenotypic. Allele frequency changes during the experiment will be measured by next generation sequencing of DNA pools (Pool-Seq) to identify targets of selection. RNA-Seq will be used to trace adaptation on the transcriptomic level during three developmental stages. Eight different phenotypes will be scored to measure the phenotypic consequences of adaptation. Combining the adaptive trajectories on these three levels will provide a picture of adaptation for a multi-cellular, out-crossing organism that is far more detailed than any previous results.
Furthermore, the proposal addresses the question of how adaptation on these three levels is reversible if the environment reverts to ancestral conditions. The third aspect of adaptation covered in the proposal is the question of repeatability of adaptation. Again, this question will be addressed on the three levels: genomic, transcriptomic and phenotypic. Using replicates with different degrees of genetic similarity, as well as closely related species, we will test how similar the adaptive response is.
This large-scale study will provide new insights into the importance of standing variation for the adaptation to novel environments. Hence, apart from providing significant evolutionary insights on the trajectories of adaptation, the results we will obtain will have important implications for conservation genetics and commercial breeding.
Kurzbezeichnung
ArchAdapt
Projektleitung
Schlötterer Christian,
Laufzeit
01.07.2012-30.06.2018
Programm
Horizon 2020 - Excellent Science - ERC Advanced Grant (AdG) H2020
Art der Forschung
Grundlagenforschung
Beteiligte Vetmed-Organisationseinheiten
Institut für Populationsgenetik,
Gefördert durch
EU (Kommission der Europäischen Gemeinschaften), Rue de la Loi, Brussels, Europäische Union
36 Publikationen

Barghi, N; Tobler, R; Nolte, V; Jakšić, AM; Mallard, F; Otte, KA; Dolezal, M; Taus, T; Kofler, R; Schlötterer, C (2019): Genetic redundancy fuels polygenic adaptation in Drosophila. PLoS Biol. 2019; 17(2):e3000128
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Hsu, SK; Jakšić, AM; Nolte, V; Barghi, N; Mallard, F; Otte, KA; Schlötterer, C (2019): A 24 h Age Difference Causes Twice as Much Gene Expression Divergence as 100 Generations of Adaptation to a Novel Environment. Genes (Basel). 2019; 10(2): 89.
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Mallard, F; Nolte, V; Tobler, R; Kapun, M; Schlötterer, C (2018): A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila. Genome Biol. 2018; 19(1):119
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Kofler, R; Senti, KA; Nolte, V; Tobler, R; Schlötterer, C (2018): Molecular dissection of a natural transposable element invasion. Genome Res. 2018; 28(6):824-835

Nouhaud, P; Mallard, F; Poupardin, R; Barghi, N; Schlötterer, C (2018): High-throughput fecundity measurements in Drosophila. Sci Rep. 2018; 8(1):4469
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Tobler, R; Nolte, V; Schlötterer, C (2017): High rate of translocation-based gene birth on the Proc Natl Acad Sci U S A. 2017; 114(44):11721-11726
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Taus, T; Futschik, A; Schlötterer, C (2017): Quantifying Selection with Pool-Seq Time Series Data. Mol Biol Evol. 2017; 34(11):3023-3034
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Schou, MF; Loeschcke, V; Bechsgaard, J; Schlötterer, C; Kristensen, TN (2017): Unexpected high genetic diversity in small populations suggests maintenance by associative overdominance. Mol Ecol. 2017; 26(23):6510-6523

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

Wallner, B; Palmieri, N; Vogl, C; Rigler, D; Bozlak, E; Druml, T; Jagannathan, V; Leeb, T; Fries, R; Tetens, J; Thaller, G; Metzger, J; Distl, O; Lindgren, G; Rubin, CJ [and 7 others] (2017): Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions. Curr Biol. 2017; 27(13):2029-2035.e5

Gibert, JM; Blanco, J; Dolezal, M; Nolte, V; Peronnet, F; Schlötterer, C (2017): Strong epistatic and additive effects of linked candidate SNPs for Drosophila pigmentation have implications for analysis of genome-wide association studies results. Genome Biol. 2017; 18(1):126
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Barghi, N; Tobler, R; Nolte, V; Schlötterer, C (2017): Drosophila simulans: A Species with Improved Resolution in Evolve and Resequence Studies. G3 (Bethesda). 2017; 7(7):2337-2343
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Iranmehr, A; Akbari, A; Schlötterer, C; Bafna, V (2017): Clear: Composition of Likelihoods for Evolve and Resequence Experiments. Genetics. 2017; 206(2):1011-1023
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Oppold, AM; Schmidt, H; Rose, M; Hellmann, SL; Dolze, F; Ripp, F; Weich, B; Schmidt-Ott, U; Schmidt, E; Kofler, R; Hankeln, T; Pfenninger, M (2017): Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence. Mol Ecol. 2017; 26(12):3256-3275

Otte, KA; Schlötterer, C (2017): Polymorphism-aware protein databases - a prerequisite for an unbiased proteomic analysis of natural populations. Mol Ecol Resour. 2017; 17(6):1148-1155

Franssen, SU; Kofler, R; Schlötterer, C (2017): Uncovering the genetic signature of quantitative trait evolution with replicated time series data. Heredity (Edinb). 2017; 118(1):42-51
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Nouhaud, P; Tobler, R; Nolte, V; Schlötterer, C (2016): Ancestral population reconstitution from isofemale lines as a tool for experimental evolution. Ecol Evol. 2016; 6(20):7169-7175
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Jakšić, AM; Schlötterer, C (2016): The Interplay of Temperature and Genotype on Patterns of Alternative Splicing in Drosophila melanogaster. Genetics. 2016; 204(1):315-325
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Kofler, R; Langmüller, AM; Nouhaud, P; Otte, KA; Schlötterer, C (2016): Suitability of Different Mapping Algorithms for Genome-Wide Polymorphism Scans with Pool-Seq Data. G3 (Bethesda). 2016; 6(11):3507-3515
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Kofler, R; Gómez-Sánchez, D; Schlötterer, C (2016): PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq. Mol Biol Evol. 2016; 33(10):2759-2764
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Jónás, Á; Taus, T; Kosiol, C; Schlötterer, C; Futschik, A (2016): Estimating the Effective Population Size from Temporal Allele Frequency Changes in Experimental Evolution. Genetics. 2016; 204(2):723-735
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Hill, T; Schlötterer, C; Betancourt, AJ (2016): Hybrid Dysgenesis in Drosophila simulans Associated with a Rapid Invasion of the P-Element. PLoS Genet. 2016; 12(3):e1005920
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Bukowicki, M; Franssen, SU; Schlötterer, C (2016): High rates of phasing errors in highly polymorphic species with low levels of linkage disequilibrium. Mol Ecol Resour. 2016; 16(4):874-882
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Endler, L; Betancourt, AJ; Nolte, V; Schlötterer, C (2016): Reconciling Differences in Pool-GWAS Between Populations: A Case Study of Female Abdominal Pigmentation in Drosophila melanogaster. Genetics. 2016; 202(2):843-855
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Kofler, R; Nolte, V; Schlötterer, C (2015): Tempo and Mode of Transposable Element Activity in Drosophila. PLoS Genet. 2015; 11(7):e1005406
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Tobler, R; Hermisson, J; Schlötterer, C (2015): Parallel trait adaptation across opposing thermal environments in experimental Drosophila melanogaster populations. Evolution. 2015; 69(7):1745-1759

Kofler, R; Nolte, V; Schlötterer, C (2016): The impact of library preparation protocols on the consistency of allele frequency estimates in Pool-Seq data. Mol Ecol Resour. 2016; 16(1):118-122
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Kofler, R; Hill, T; Nolte, V; Betancourt, AJ; Schlötterer, C (2015): The recent invasion of natural Drosophila simulans populations by the P-element. Proc Natl Acad Sci U S A. 2015; 112(21):6659-6663
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Terhorst, J; Schlötterer, C; Song, YS (2015): Multi-locus analysis of genomic time series data from experimental evolution. PLoS Genet. 2015; 11(4):e1005069
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Schlötterer, C (2015): Genes from scratch--the evolutionary fate of de novo genes. Trends Genet. 2015; 31(4):215-219
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Topa, H; Jónás, Á; Kofler, R; Kosiol, C; Honkela, A (2015): Gaussian process test for high-throughput sequencing time series: application to experimental evolution. Bioinformatics. 2015; 31(11):1762-1770
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Franssen, SU; Nolte, V; Tobler, R; Schlötterer, C (2015): Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental Drosophila melanogaster populations. Mol Biol Evol. 2015; 32(2):495-509
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Schlötterer, C; Kofler, R; Versace, E; Tobler, R; Franssen, SU (2015): Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation. Heredity (Edinb). 2015; 114(5):431-440
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Kofler, R; Schlötterer, C (2014): A guide for the design of evolve and resequencing studies. Mol Biol Evol. 2014; 31(2):474-483
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Tobler, R; Franssen, SU; Kofler, R; Orozco-Terwengel, P; Nolte, V; Hermisson, J; Schlötterer, C (2014): Massive habitat-specific genomic response in D. melanogaster populations during experimental evolution in hot and cold environments. Mol Biol Evol. 2014; 31(2):364-375
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Pandey, RV; Schlötterer, C (2013): DistMap: a toolkit for distributed short read mapping on a Hadoop cluster. PLoS One. 2013; 8(8):e72614
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