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Local selective sweeps in Drosophila melanogaster

Abstract
The identification of local selective sweeps by analyzing variability pattern at neutral markers has recently become a very popular approach in population genetics. In D. melanogaster several recent studies identified a number of genomic regions that deviate from neutral expectations and are thus good candidates for a putatively selected region. Nevertheless, is has also become clear that certain demographic events could create a signature that is very similar to a selective sweep. This proposal takes advantage of population structure in non-African populations to identify sweep regions that are specific to local populations/continents. In addition to the analysis of candidate regions in a biogeographic setting, this proposal aims for the characterization of admixture between D. melanogaster populations. Previous work provided some evidence for a chromosome specific admixture pattern. Based on these results, a genome wide survey for chromosome specific admixture in D. melanogaster will be carried out and the driving evolutionary forces will be characterized.
Statistik Austria science classification
106012         Evolutionary research
106013         Genetics
106023         Molecular biology
Lemma
Drosophila melanogaster
Project leader
Schlötterer Christian
Duration
01.10.07-30.09.12
Type of Research
Basic research
Vetmed Research Units
Institute of Population Genetics
Funded by
FWF - Fonds zur Förderung der wissenschaftlichen Forschung, Wien, Austria

Link To Project Finder
21 Publications

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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Martins, NE; Faria, VG; Nolte, V; Schlötterer, C; Teixeira, L; Sucena, É; Magalhães, S (2014): Host adaptation to viruses relies on few genes with different cross-resistance properties. Proc Natl Acad Sci U S A. 2014; 111(16):5938-5943
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Kapun, M; van Schalkwyk, H; McAllister, B; Flatt, T; Schlötterer, C (2014): Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations of Drosophila melanogaster. Mol Ecol. 2014; 23(7):1813-1827
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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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Nunes, MD; Dolezal, M; Schlötterer, C (2013): Extensive paternal mtDNA leakage in natural populations of Drosophila melanogaster. Mol Ecol. 2013; 22(8):2106-2117
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Boitard, S; Kofler, R; Françoise, P; Robelin, D; Schlötterer, C; Futschik, A (2013): Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples. Mol Ecol Resour. 2013; 13(2):337-340
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Nolte, V; Pandey, RV; Kofler, R; Schlötterer, C (2013): Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana. Genome Res. 2013; 23(1):99-110
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Fabian, DK; Kapun, M; Nolte, V; Kofler, R; Schmidt, PS; Schlötterer, C; Flatt, T (2012): Genome-wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America. Mol Ecol. 2012; 21(19):4748-4769
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Orozco-terWengel, P; Kapun, M; Nolte, V; Kofler, R; Flatt, T; Schlötterer, C (2012): Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles. Mol Ecol. 2012; 21(20):4931-4941
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Kofler, R; Schlötterer, C (2012): Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies. Bioinformatics. 2012; 28(15):2084-2085
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Kofler, R; Betancourt, AJ; Schlötterer, C (2012): Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster. PLoS Genet. 2012; 8(1):e1002487
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Esteve-Codina, A; Kofler, R; Palmieri, N; Bussotti, G; Notredame, C; Pérez-Enciso, M (2011): Exploring the gonad transcriptome of two extreme male pigs with RNA-seq. BMC Genomics. 2011; 12:552
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Kofler, R; Pandey, RV; Schlötterer, C (2011): PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics. 2011; 27(24):3435-3436
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Pandey, RV; Nolte, V; Boenigk, J; Schlötterer, C (2011): CANGS DB: a stand-alone web-based database tool for processing, managing and analyzing 454 data in biodiversity studies. BMC Res Notes. 2011; 4:227
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Orozco-terWengel, P; Corander, J; Schlötterer, C (2011): Genealogical lineage sorting leads to significant, but incorrect Bayesian multilocus inference of population structure. Mol Ecol. 2011; 20(6):1108-1121
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Gibert, JM; Karch, F; Schlötterer, C (2011): Segregating variation in the polycomb group gene cramped alters the effect of temperature on multiple traits. PLoS Genet. 2011; 7(1):e1001280
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Kofler, R; Orozco-terWengel, P; De Maio, N; Pandey, RV; Nolte, V; Futschik, A; Kosiol, C; Schlötterer, C (2011): PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals. PLoS One. 2011; 6(1):e15925
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Nunes, MD; Wengel, PO; Kreissl, M; Schlötterer, C (2010): Multiple hybridization events between Drosophila simulans and Drosophila mauritiana are supported by mtDNA introgression. Mol Ecol. 2010; 19(21):4695-4707
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Kapun, M; Nolte, V; Flatt, T; Schlötterer, C (2010): Host range and specificity of the Drosophila C virus. PLoS One. 2010; 5(8):e12421
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Nolte, V; Pandey, RV; Jost, S; Medinger, R; Ottenwälder, B; Boenigk, J; Schlötterer, C (2010): Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity. Mol Ecol. 2010; 19(14):2908-2915
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Nunes, MD; Neumeier, H; Schlötterer, C (2008): Contrasting patterns of natural variation in global Drosophila melanogaster populations. Mol Ecol. 2008; 17(20):4470-4479

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