Extensive local adaptation within the chemosensory system following Drosophila melanogaster’s global expansion

Arguello, J. Roman; Cardoso-Moreira, Margarida; Grenier, Jennifer K.; Gottipati, Srikanth; Clark, Andrew G.; Benton, Richard

doi:10.1038/ncomms11855

Cited by 52 publications

(61 citation statements)

References 70 publications

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“…In particular, gene targets of positive selection that are responsible for the higher variance are four duplicate Ds GRs (including the three GR59d8, see below) having a ω > 1 (Levene’s test without the four Ds GRs: F = 1.33; df = 1131; and P = 0.251). In cases of dIRs and ORs, whose variance do not differ between D. suzukii and D. biarmipes , the increased rate of amino acid substitutions may be due to pervasive relaxed selection, in accordance with what has been observed at the intra specific level in D. melanogaster (Arguello et al 2016). …”

Section: Discussionsupporting

confidence: 75%

Evolutionary Insights into Taste Perception of the Invasive PestDrosophila suzukii

Crava

Ramasamy

Ometto

et al. 2016

G3 Genes|Genomes|Genetics

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Chemosensory perception allows insects to interact with the environment by perceiving odorant or tastant molecules; genes encoding chemoreceptors are the molecular interface between the environment and the insect, and play a central role in mediating its chemosensory behavior. Here, we explore how the evolution of these genes in the emerging pest Drosophila suzukii correlates with the peculiar ecology of this species. We annotated approximately 130 genes coding for gustatory receptors (GRs) and divergent ionotropic receptors (dIRs) in D. suzukii and in its close relative D. biarmipes. We then analyzed the evolution, in terms of size, of each gene family as well of the molecular evolution of the genes in a 14 Drosophila species phylogenetic framework. We show that the overall evolution of GRs parallels that of dIRs not only in D. suzukii, but also in all other analyzed Drosophila. Our results reveal an unprecedented burst of gene family size in the lineage leading to the suzukii subgroup, as well as genomic changes that characterize D. suzukii, particularly duplications and strong signs of positive selection in the putative bitter-taste receptor GR59d. Expression studies of duplicate genes in D. suzukii support a spatio-temporal subfunctionalization of the duplicate isoforms. Our results suggest that D. suzukii is not characterized by gene loss, as observed in other specialist Drosophila species, but rather by a dramatic acceleration of gene gains, compatible with a highly generalist feeding behavior. Overall, our analyses provide candidate taste receptors specific for D. suzukii that may correlate with its specific behavior, and which may be tested in functional studies to ultimately enhance its control in the field.

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Section: Discussionsupporting

confidence: 75%

Evolutionary Insights into Taste Perception of the Invasive PestDrosophila suzukii

Crava

Ramasamy

Ometto

et al. 2016

G3 Genes|Genomes|Genetics

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“…More advanced methods that rely on the CLR test (e.g., SweepFinder [16], SweepFinder2 [56], and SweeD [17]) or on patterns of LD (e.g., OmegaPlus [18, 57]), perform a window-size optimization approach that provides information on the genomic region affected by a selective sweep at the cost of increased execution times. The aforementioned methods have been widely used to detect recent and strong positive selection in a variety of eukaryotic or prokaryotic organisms, such as human [16, 58, 59], D. melanogaster [60–63], lizards [64], rice [65], butterflies [66], and bacteria [67]. …”

Section: Methods and Toolsmentioning

confidence: 99%

A survey of methods and tools to detect recent and strong positive selection

Pavlidis¹,

Alachiotis²

2017

J of Biol Res-Thessaloniki

111

104

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Positive selection occurs when an allele is favored by natural selection. The frequency of the favored allele increases in the population and due to genetic hitchhiking the neighboring linked variation diminishes, creating so-called selective sweeps. Detecting traces of positive selection in genomes is achieved by searching for signatures introduced by selective sweeps, such as regions of reduced variation, a specific shift of the site frequency spectrum, and particular LD patterns in the region. A variety of methods and tools can be used for detecting sweeps, ranging from simple implementations that compute summary statistics such as Tajima’s D, to more advanced statistical approaches that use combinations of statistics, maximum likelihood, machine learning etc. In this survey, we present and discuss summary statistics and software tools, and classify them based on the selective sweep signature they detect, i.e., SFS-based vs. LD-based, as well as their capacity to analyze whole genomes or just subgenomic regions. Additionally, we summarize the results of comparisons among four open-source software releases (SweeD, SweepFinder, SweepFinder2, and OmegaPlus) regarding sensitivity, specificity, and execution times. In equilibrium neutral models or mild bottlenecks, both SFS- and LD-based methods are able to detect selective sweeps accurately. Methods and tools that rely on LD exhibit higher true positive rates than SFS-based ones under the model of a single sweep or recurrent hitchhiking. However, their false positive rate is elevated when a misspecified demographic model is used to represent the null hypothesis. When the correct (or similar to the correct) demographic model is used instead, the false positive rates are considerably reduced. The accuracy of detecting the true target of selection is decreased in bottleneck scenarios. In terms of execution time, LD-based methods are typically faster than SFS-based methods, due to the nature of required arithmetic.

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“…The olfactory system of Drosophila is conveniently accessible to experimental investigation and current research extends beyond the Or ligand repertoire (Münch and Galizia 2016) to neural circuits underlying odor-mediated behavior (Kohl et al 2013;Auer and Benton 2016;Seki et al 2017), chemical ecology (Depetris-Chauvin et al 2015;Mansourian and Stensmyr 2015) and phylogenetic diversification (Shiao et al 2015;Arguello et al 2016;Ramasamy et al 2016). A future challenge is to extend functional, behavioral, ecological and phylogenetic studies to include vertebrates, towards an understanding of the chemical vocabulary that interconnects us with other living things.…”

Section: Discussionmentioning

confidence: 99%

The Scent of the Fly

et al. 2018

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Abstract(Z)-4-undecenal (Z4-11Al) is the volatile pheromone produced by females of the vinegar fly Drosophila melanogaster. Female flies emit Z4-11Al for species-specific communication and mate-finding. A sensory panel finds that synthetic Z4-11Al has a characteristic flavour, which can be perceived even at the small amounts produced by a single female fly. Since only females produce Z4-11Al, and not males, we can reliably distinguish between single D. melanogaster males and females, according to their scent. Females release Z4-11Al at 2.4 ng/h and we readily sense 1 ng synthetic Z4-11Al in a glass of wine (0.03 nmol/L), while a tenfold concentration is perceived as a loud off-flavour. This corroborates the observation that a glass of wine is spoilt by a single D. melanogaster fly falling into it, which we here show is caused by Z4-11Al. The biological role of Z4-11Al or structurally related aldehydes in humans and the basis for this semiochemical convergence remains yet unclear.

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Extensive local adaptation within the chemosensory system following Drosophila melanogaster’s global expansion

Cited by 52 publications

References 70 publications

Evolutionary Insights into Taste Perception of the Invasive PestDrosophila suzukii

Evolutionary Insights into Taste Perception of the Invasive PestDrosophila suzukii

A survey of methods and tools to detect recent and strong positive selection

The Scent of the Fly

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