A Large Panel of Drosophila simulans Reveals an Abundance of Common Variants

Signor, Sarah; New, Felicia N; Nuzhdin, Sergey V.

doi:10.1093/gbe/evx262

Cited by 50 publications

(88 citation statements)

References 118 publications

(145 reference statements)

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“…We obtained all 197 haploid embryo genomes collected from Zambia. Drosophila simulans polymorphism data from 170 inbred individuals from an American population were obtained from Signor et al (2018) 85 . Sequence data for 20 D. yakuba inbred lines are from Rogers et al (2014) 86 .…”

Section: ) Genus Drosophilamentioning

confidence: 99%

Two decades of suspect evidence for adaptive DNA-sequence evolution – Less negative selection misconstrued as positive selection

Chen

Feng

et al. 2020

Preprint

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Evidence for biological adaptation is often obtained by studying DNA sequence evolution. Since the analyses are affected by both positive and negative selection, studies usually assume constant negative selection in the time span of interest. For this reason, hundreds of studies that conclude adaptive evolution might have reported false signals caused by relaxed negative selection. We test this suspicion two ways. First, we analyze the fluctuation in population size, N, during evolution. For example, the evolutionary rate in the primate phylogeny could vary by as much as 2000 fold due to the variation in N alone. Second, we measure the variation in negative selection directly by analyzing the polymorphism data from four taxa (Drosophila, Arabidopsis, primates, and birds, with 64 species in total). The strength of negative selection, as measured by the ratio of nonsynonymous/synonymous polymorphisms, fluctuates strongly and at multiple time scales. The two approaches suggest that the variation in the strength of negative selection may be responsible for the bulk of the reported adaptive genome evolution in the last two decades. This study corroborates the recent report 1 on the inconsistent patterns of adaptive genome evolution. Finally, we discuss the path forward in detecting adaptive sequence evolution.

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Section: ) Genus Drosophilamentioning

confidence: 99%

Two decades of suspect evidence for adaptive DNA-sequence evolution – Less negative selection misconstrued as positive selection

Chen

Feng

et al. 2020

Preprint

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“…Two of the most pronounced of these signals, genome wide, come from insecticide resistance loci Cyp6g1 and Ace . Significant selective signals have also been identified around these loci in other D. melanogaster populations ( Garud and Petrov 2016 ), and related species ( Signor et al 2017 ; D. simulans ), as well as by targeted analyses in D. melanogaster of selection at Ace ( Karasov, Messer and Petrov 2010 ) and Cyp6g1 ( Catania et al 2004 ; Schmidt et al 2010 ).…”

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confidence: 99%

Structural Variants and Selective Sweep Foci Contribute to Insecticide Resistance in theDrosophilaGenetic Reference Panel

Battlay

Leblanc

Green

et al. 2018

G3 Genes|Genomes|Genetics

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Patterns of nucleotide polymorphism within populations of Drosophila melanogaster suggest that insecticides have been the selective agents driving the strongest recent bouts of positive selection. However, there is a need to explicitly link selective sweeps to the particular insecticide phenotypes that could plausibly account for the drastic selective responses that are observed in these non-target insects. Here, we screen the Drosophila Genetic Reference Panel with two common insecticides; malathion (an organophosphate) and permethrin (a pyrethroid). Genome-wide association studies map survival on malathion to two of the largest sweeps in the D. melanogaster genome; Ace and Cyp6g1. Malathion survivorship also correlates with lines which have high levels of Cyp12d1, Jheh1 and Jheh2 transcript abundance. Permethrin phenotypes map to the largest cluster of P450 genes in the Drosophila genome, however in contrast to a selective sweep driven by insecticide use, the derived allele seems to be associated with susceptibility. These results underscore previous findings that highlight the importance of structural variation to insecticide phenotypes: Cyp6g1 exhibits copy number variation and transposable element insertions, Cyp12d1 is tandemly duplicated, the Jheh loci are associated with a Bari1 transposable element insertion, and a Cyp6a17 deletion is associated with susceptibility.

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“…Haplotypes belonging to the most abundant haplotype class (class 1) were highly similar with very few segregating variants ( π = 0.0004). The second haplotype class (class 2) showed normal levels of variation ( π = 0.0082) [ 14 ] and no apparent pattern of linkage disequilibrium (Fig. 1 b).…”

Section: Resultsmentioning

confidence: 99%

Fitness effects for Ace insecticide resistance mutations are determined by ambient temperature

Langmüller¹,

Nolte²,

Galagedara³

et al. 2020

BMC Biol

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Background Insect pest control programs often use periods of insecticide treatment with intermittent breaks, to prevent fixing of mutations conferring insecticide resistance. Such mutations are typically costly in an insecticide-free environment, and their frequency is determined by the balance between insecticide treatment and cost of resistance. Ace, a key gene in neuronal signaling, is a prominent target of many insecticides and across several species, three amino acid replacements (I161V, G265A, and F330Y) provide resistance against several insecticides. Because temperature disturbs neuronal signaling homeostasis, we reasoned that the cost of insecticide resistance could be modulated by ambient temperature. Results Experimental evolution of a natural Drosophila simulans population at hot and cold temperature regimes uncovered a surprisingly strong effect of ambient temperature. In the cold temperature regime, the resistance mutations were strongly counter selected (s = − 0.055), but in a hot environment, the fitness costs of resistance mutations were reduced by almost 50% (s = − 0.031). We attribute this unexpected observation to the advantage of the reduced enzymatic activity of resistance mutations in hot environments. Conclusion We show that fitness costs of insecticide resistance genes are temperature-dependent and suggest that the duration of insecticide-free periods need to be adjusted for different climatic regions to reflect these costs. We suggest that such environment-dependent fitness effects may be more common than previously assumed and pose a major challenge for modeling climate change.

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A Large Panel of Drosophila simulans Reveals an Abundance of Common Variants

Cited by 50 publications

References 118 publications

Two decades of suspect evidence for adaptive DNA-sequence evolution – Less negative selection misconstrued as positive selection

Two decades of suspect evidence for adaptive DNA-sequence evolution – Less negative selection misconstrued as positive selection

Structural Variants and Selective Sweep Foci Contribute to Insecticide Resistance in theDrosophilaGenetic Reference Panel

Fitness effects for Ace insecticide resistance mutations are determined by ambient temperature

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