Pesticide Resistance via Transposition-Mediated Adaptive Gene Truncation in
            <i>Drosophila</i>

Aminetzach, Yael T.; Macpherson, J. Michael; Petrov, Dmitri A.

doi:10.1126/science.1112699

Cited by 231 publications

(259 citation statements)

References 16 publications

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“…In the case of divergence, applications of the McDonald-Kreitman test to multiple-gene data sets from Drosophila have concluded that up to 60% of nonsynonymous substitutions and 30% of the substitutions at regulatory sites may be driven by adaptation (Fay et al 2002;Smith and Eyre-Walker 2002;Bierne and Eyre-Walker 2004;Andolfatto 2005;Charlesworth and Eyre-Walker 2006;Welch 2006;Shapiro et al 2007). In the case of polymorphism, the effects of adaptation have also been seen in Drosophila: selective sweeps, which are local reductions in linked neutral polymorphism caused by adaptive substitutions, have been repeatedly detected in Drosophila populations, both in detailed studies of individual loci (e.g., Schlenke and Begun 2004;Aminetzach et al 2005;Beisswanger et al 2006) and in genomic scans (e.g., Glinka et al 2003;Orengo and Aguade 2004;Ometto et al 2005).…”

Section: P Atterns Of Genetic Variation Within and Betweenmentioning

confidence: 99%

Genomewide Spatial Correspondence Between Nonsynonymous Divergence and Neutral Polymorphism Reveals Extensive Adaptation in Drosophila

et al. 2007

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The effect of recurrent selective sweeps is a spatially heterogeneous reduction in neutral polymorphism throughout the genome. The pattern of reduction depends on the selective advantage and recurrence rate of the sweeps. Because many adaptive substitutions responsible for these sweeps also contribute to nonsynonymous divergence, the spatial distribution of nonsynonymous divergence also reflects the distribution of adaptive substitutions. Thus, the spatial correspondence between neutral polymorphism and nonsynonymous divergence may be especially informative about the process of adaptation. Here we study this correspondence using genomewide polymorphism data from Drosophila simulans and the divergence between D. simulans and D. melanogaster. Focusing on highly recombining portions of the autosomes, at a spatial scale appropriate to the study of selective sweeps, we find that neutral polymorphism is both lower and, as measured by a new statistic Q S , less homogeneous where nonsynonymous divergence is higher and that the spatial structure of this correlation is best explained by the action of strong recurrent selective sweeps. We introduce a method to infer, from the spatial correspondence between polymorphism and divergence, the rate and selective strength of adaptation. Our results independently confirm a high rate of adaptive substitution ($1/3000 generations) and newly suggest that many adaptations are of surprisingly great selective effect ($1%), reducing the effective population size by $15% even in highly recombining regions of the genome.

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Section: P Atterns Of Genetic Variation Within and Betweenmentioning

confidence: 99%

Genomewide Spatial Correspondence Between Nonsynonymous Divergence and Neutral Polymorphism Reveals Extensive Adaptation in Drosophila

et al. 2007

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“…Sequences derived from TEs constitute a substantial fraction of genomes of most eukaryotes and the presence or absence of various TE families as well as their distributions among individuals of the same species are well documented in model species such as Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Mus musculus as well as Homo sapiens. Even though researchers have found examples of TE insertions correlated with positive selective sweeps in specific environments (Daborn et al 2002;Aminetzach et al 2005), the great majority of TE insertions have negative impact on host fitness (Mackay 1989;Pasyukova et al 2004) and are widely viewed as 'genomic parasites'. TE insertions in or near genes often change gene expression that result in phenotypic changes of the hosts.…”

Section: Introductionmentioning

confidence: 99%

Transposable elements in natural populations ofDrosophila melanogaster

Lee

Langley

2010

Phil. Trans. R. Soc. B

105

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Transposable elements (TEs) are families of small DNA sequences found in the genomes of virtually all organisms. The sequences typically encode essential components for the replicative transposition sequences of that TE family. Thus, TEs are simply genomic parasites that inflict detrimental mutations on the fitness of their hosts. Several models have been proposed for the containment of TE copy number in outbreeding host populations such as Drosophila. Surveys of the TEs in genomes from natural populations of Drosophila have played a central role in the investigation of TE dynamics. The early surveys indicated that a typical TE insertion is rare in a population, which has been interpreted as evidence that each TE is selected against. The proposed mechanisms of this natural selection are reviewed here. Subsequent and more targeted surveys identify heterogeneity among types of TEs and also highlight the large role of homologous and possibly ectopic crossing over in the dynamics of the Drosophila TEs. The recent discovery of germline-specific RNA interference via the piwi-interacting RNA pathway opens yet another interesting mechanism that may be critical in containing the copy number of TEs in natural populations of Drosophila. The expected flood of Drosophila population genomics is expected to rapidly advance understanding of the dynamics of TEs.

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“…Common examples include insertional inactivation of genes (Greene et al 1994) and DNA rearrangement via ectopic recombination (Kazazian 2004;Bennetzen 2005). Nonetheless, a subset of TE-mediated events is adaptive: in Drosophila, for example, TE insertions have contributed to enhanced insecticide resistance, either by affecting gene expression or by changing gene structure (Schlenke and Begun 2004;Aminetzach et al 2005). Similarly, a ''domesticated'' TE-derived transposase domain contributed directly to two vertebrate proteins, RAG1 and RAG2, that are central to the immune system of jawed vertebrates (Kapitonov and Jurka 2005).…”

Section: Introductionmentioning

confidence: 99%

The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

Lockton

Gaut

2009

J Mol Evol

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The goal of this study was to assess the extent to which transposable elements (TEs) have contributed to protein-coding regions in Arabidopsis thaliana. To do this, we first characterized the extent of chimeric TE-gene constructs. We compared a genome-wide TE database to genomic sequences, annotated coding regions, and EST data. The comparison revealed that 7.8% of expressed genes contained a region with close similarity to a known TE sequence. Some groups of TEs, such as helitrons, were underrepresented in exons relative to their genome-wide distribution; in contrast, Copia-like and En/Spm-like sequences were overrepresented in exons. These 7.8% percent of genes were enriched for some GO-based functions, particularly kinase activity, and lacking in other functions, notably structural molecule activity. We also examined gene family evolution for these genes. Gene family information helped clarify whether the sequence similarity between TE and gene was due to a TE contributing to the gene or, instead, the TE co-opting a portion of the gene. Most (66%) of these genes were not easily assigned to a gene family, and for these we could not infer the direction of the relationship between TE and gene. For the remainder, where appropriate, we built phylogenetic trees to infer the direction of the TE-gene relationship by parsimony. By this method, we verified examples where TEs contributed to expressed proteins. Our results are undoubtedly conservative but suggest that TEs may have contributed small protein segments to as many as 1.2% of all expressed, annotated A. thaliana genes.

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Pesticide Resistance via Transposition-Mediated Adaptive Gene Truncation in Drosophila

Cited by 231 publications

References 16 publications

Genomewide Spatial Correspondence Between Nonsynonymous Divergence and Neutral Polymorphism Reveals Extensive Adaptation in Drosophila

Genomewide Spatial Correspondence Between Nonsynonymous Divergence and Neutral Polymorphism Reveals Extensive Adaptation in Drosophila

Transposable elements in natural populations ofDrosophila melanogaster

The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

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