Genomic signatures of selection at linked sites: unifying the disparity among species

Cutter, Asher D.; Payseur, Bret A.

doi:10.1038/nrg3425

Cited by 453 publications

(653 citation statements)

References 179 publications

(206 reference statements)

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“…Pyrethroid resistance can reduce overall fitness (29) directly through reduced efficiency of the VGSC and associated metabolic costs (30) or indirectly through genetic hitchhiking (31). In addition, under strong selective pressures of pesticide exposure, genetic diversity may become depleted by "genetic erosion," as selection of a few adapted organisms creates genetic bottlenecks (32).…”

Section: Discussion Pyrethroid Resistance Varies Across Species Groupmentioning

confidence: 99%

Multiple origins of pyrethroid insecticide resistance across the species complex of a nontarget aquatic crustacean, Hyalella azteca

Weston

Poynton

Wellborn

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

142

153

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Use of pesticides can have substantial nonlethal impacts on nontarget species, including driving evolutionary change, often with unknown consequences for species, ecosystems, and society. Hyalella azteca, a species complex of North American freshwater amphipods, is widely used for toxicity testing of water and sediment and has frequently shown toxicity due to pyrethroid pesticides. We demonstrate that 10 populations, 3 from laboratory cultures and 7 from California water bodies, differed by at least 550-fold in sensitivity to pyrethroids. The populations sorted into four phylogenetic groups consistent with species-level divergence. By sequencing the primary pyrethroid target site, the voltage-gated sodium channel, we show that point mutations and their spread in natural populations were responsible for differences in pyrethroid sensitivity. At least one population had both mutant and WT alleles, suggesting ongoing evolution of resistance. Although nonresistant H. azteca were susceptible to the typical neurotoxic effects of pyrethroids, gene expression analysis suggests the mode of action in resistant H. azteca was not neurotoxicity but was oxidative stress sustained only at considerably higher pyrethroid concentrations. The finding that a nontarget aquatic species has acquired resistance to pesticides used only on terrestrial pests is troubling evidence of the impact of chronic pesticide transport from land-based applications into aquatic systems. Our findings have farreaching implications for continued uncritical use of H. azteca as a principal species for monitoring and environmental policy decisions.

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Section: Discussion Pyrethroid Resistance Varies Across Species Groupmentioning

confidence: 99%

Multiple origins of pyrethroid insecticide resistance across the species complex of a nontarget aquatic crustacean, Hyalella azteca

Weston

Poynton

Wellborn

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

142

153

View full text Add to dashboard Cite

show abstract

“…), can be found in highly variable habitats, including marine, brackish, and freshwater environments. This diversity allows broad comparative approaches, where genomic insights can provide important information about the molecular basis of adaptation and speciation processes (e.g., Bernardi, 2013;Cutter and Payseur, 2013;Seehausen et al, 2013). Species that occupy heterogeneous environments along their distribution range experience spatially varying selective pressures that can result in local adaptation of ecologically important traits (Kawecki and Ebert, 2004).…”

Section: Marine Fishes As Study Systems For Understanding Evolutionmentioning

confidence: 99%

“…Attaining genome-wide coverage in several species facilitates comparative approaches, for example, related to identifying genes, signaling pathways, or genomic regions involved in adaptive population divergence and speciation (Cutter and Payseur, 2013). Population genetic work applying smaller sets of genetic markers has shown the potential of these methods.…”

Section: Comparative Population Genomicsmentioning

confidence: 99%

Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

Hemmer‐Hansen

Therkildsen

Pujolar

2014

The Biological Bulletin

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“…background selection | selective sweeps | sequence diversity | gene conversion | Drosophila melanogaster A dvances in population genomics are shedding light on the question of the extent to which patterns of DNA sequence variation and evolution are affected by selection at sites that are genetically linked to those under investigation (1)(2)(3). Two main processes have been invoked as causes of such "hitchhiking" effects.…”

mentioning

confidence: 99%

Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion

Campos

Zhao

Charlesworth

2017

Proc. Natl. Acad. Sci. U.S.A.

118

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We used whole-genome resequencing data from a population of Drosophila melanogaster to investigate the causes of the negative correlation between the within-population synonymous nucleotide site diversity (π S ) of a gene and its degree of divergence from related species at nonsynonymous nucleotide sites (K A ). By using the estimated distributions of mutational effects on fitness at nonsynonymous and UTR sites, we predicted the effects of background selection at sites within a gene on π S and found that these could account for only part of the observed correlation between π S and K A . We developed a model of the effects of selective sweeps that included gene conversion as well as crossing over. We used this model to estimate the average strength of selection on positively selected mutations in coding sequences and in UTRs, as well as the proportions of new mutations that are selectively advantageous. Genes with high levels of selective constraint on nonsynonymous sites were found to have lower strengths of positive selection and lower proportions of advantageous mutations than genes with low levels of constraint. Overall, background selection and selective sweeps within a typical gene reduce its synonymous diversity to ∼75% of its value in the absence of selection, with larger reductions for genes with high K A . Gene conversion has a major effect on the estimates of the parameters of positive selection, such that the estimated strength of selection on favorable mutations is greatly reduced if it is ignored. background selection | selective sweeps | sequence diversity | gene conversion | Drosophila melanogaster

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Genomic signatures of selection at linked sites: unifying the disparity among species

Cited by 453 publications

References 179 publications

Multiple origins of pyrethroid insecticide resistance across the species complex of a nontarget aquatic crustacean, Hyalella azteca

Multiple origins of pyrethroid insecticide resistance across the species complex of a nontarget aquatic crustacean, Hyalella azteca

Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion

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