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opencc-zeroSep 2022View details →

Distinct signals of clinal and seasonal allele frequency change at eQTLs in Drosophila melanogaster

Populations of short-lived organisms can respond to spatial and temporal environmental heterogeneity through local adaptation. However, the comparative signals of local adaptation across space and time remains poorly understood. Here, we examined patterns of allele frequency change across a latitudinal cline and between seasons at previously reported expression quantitative trait loci (eQTLs). We divided eQTLs into groups by utilizing differential expression profiles of fly populations collected across latitudinal clines or exposed to different environmental conditions. In general, we find that eQTLs are enriched for clinally varying polymorphisms, and that these eQTLs change in frequency in concordant ways across the cline and in response to starvation and chill-coma. The enrichment of eQTLs among seasonally varying polymorphisms is more subtle, and the direction of allele frequency change at eQTLs appears to be somewhat idiosyncratic. Taken together, we suggest that clinal adaptation at eQTLs is at least partially distinct from seasonal adaptation.

opencc-by-4.0Aug 2022View details →

Genome-wide selection signatures reveal widespread synergistic effects of two different stressors in Drosophila melanogaster: scripts and files

Pipeline and analysis scripts as well as final data files

opencc-by-4.0Jan 2022View details →

Genome annotations of Drosophila melanogaster and Drosophila simulans wild-type strains from long read sequencing assemblies

Genome assemblies were performed for eight wild-type strains of Drosophila melanogaster and Drosophila simulans from Oxford Nanopore long read sequencing (please refer to Mohamed et al. Cells 2020 (doi:10.3390/cells9081776)). Assemblies were deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB50024 (<a href="https://www.ebi.ac.uk/ena/browser/view/PRJEBxxxx">https://www.ebi.ac.uk/ena/browser/view/</a>PRJEB50024). Transposable Element annotations: we used RepeatMasker 4.1.0 (<a href="http://repeatmasker.org/">http://repeatmasker.org/</a>) -species Drosophila, followed by OneCodeToFindThemAll (Bailly-Bechet et al. 2014) with default parameters. Gene annotations: We retrieved gtf files from FlyBase : <a>ftp.flybase.net/genomes/D</a><a>rosophila_melanogaster/dmel_r6,46_FB2022_03/gft/dmel-all-r6.46.gtf.gz</a> and <a>ftp.flybase.net/genomes/Drosophila_simulans/dsim_r2,02_FB2017_04/gtf/dsim-all-</a><a>r2,02.gtf.gz</a>. The corresponding fasta files were also downloaded from FlyBase: <a>ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6,46_FB2022_03/</a><a>fasta</a><a>/dmel-all-</a><a>chromosome-</a><a>r6.46.</a><a>fasta</a><a>.gz</a> and <a>ftp.flybase.net/genomes/Drosophila_simulans/dsim_r2,02_FB2017_04/</a><a>fasta</a><a>/dsim-all-</a><a>chromosome-</a><a>r2,02.</a><a>fasta</a><a>.gz</a>. We used Liftoff (Shumate and Salzberg, 2020) to lift over gene annotations from the references to our genome assemblies. We used -flank 0.2 and only kept the “gene” and “exon” terms.

opencc-zeroMay 2024View details →

Data from: A social learning primacy trend in mate-copying; an experiment in Drosophila melanogaster

Social learning is learning from the observation of how others interact with the environment. However, in nature, individuals often need to process serial social information and may either favour the most recent information (recency bias), constantly updating knowledge to match the environment, or the information that appeared first in the series (primacy bias), which may slow down adjustment to environmental change. Mate-copying is a widespread form of social learning in a mate choice context related to conformity in mate choice, and where a naïve individual develops a preference for a given mate (or mate phenotype) seen being chosen by conspecifics. Mate-copying is documented in most vertebrate taxa and in the fruit fly Drosophila melanogaster. Here, we tested experimentally whether female fruit flies show a primacy or a recency bias by presenting pictures of a female copulating with one of two contrastingly coloured male phenotypes. We found that after two sequential contradictory demonstrations, females show a tendency to prefer males of the phenotype preferred in the first demonstration, suggesting that mate-copying in D. melanogaster is not based on the most recently observed mating and may be influenced by a form of primacy bias.

opencc-zeroJun 2024View details →

The genetic basis of incipient sexual isolation in Drosophila melanogaster

Speciation is a fundamental evolutionary process, but the genetic changes accompanying speciation are difficult to determine since true species do not produce viable and fertile offspring. Partially reproductively isolated incipient species are useful for assessing genetic changes that occur prior to speciation. Drosophila melanogaster from Zimbabwe, Africa are partially sexually isolated from other D. melanogaster populations whose males have poor mating success with Zimbabwe females. We used the North American D. melanogaster Genetic Reference Panel (DGRP) to show that there is significant genetic variation in the mating success of DGRP males with Zimbabwe females, to map genetic variants and genes associated with variation in mating success, and to determine whether mating success to Zimbabwe females is associated with other quantitative traits previously measured in the DGRP. Incipient sexual isolation is highly polygenic and associated with the common African inversion In(3R)K and the amount of the sex pheromone 5,9-heptacosadiene in DGRP females. We functionally validated the effect of eight candidate genes using RNA interference to provide testable hypotheses for future studies investigating the molecular genetic basis of incipient sexual isolation in D. melanogaster.

opencc-zeroJun 2024View details →

Data for: Altered Circadian Rhythm, Sleep, and Rhodopsin 7-Dependent Shade Preference During Diapause in Drosophila Melanogaster

To survive adverse environments, many animals enter a dormant state such as hibernation, dauer, or diapause. Various Drosophila species undergo adult reproductive diapause in response to cool temperatures and/or short day-length. While it is known that flies are less active during diapause, an in-depth understanding of diapause effects on circadian rhythms and sleep is lacking. Here we show that, in diapause-inducing conditions, Drosophila melanogaster exhibit altered circadian activity profiles, including a severely reduced morning activity peak and an advanced evening activity peak. Consequently, the flies have a single activity peak at a time similar to when non-diapausing flies have a siesta. Temperatures ≤15 °C, rather than short day-length, primarily drive the behavior. At cool temperatures, flies also rapidly enter a deep sleep state that lacks the sleep cycles of flies at higher temperatures and requires particularly high levels of stimulation for arousal. Furthermore, we show that at 18–25 °C, flies prefer to siesta in the shade, a preference that is virtually eliminated at 10 °C. Resting in the shade is driven by an aversion to blue light, sensed by rhodopsin 7 (Rh7) outside of the eyes. Flies at 10 ˚C show neuronal markers of elevated sleep pressure, including increased expression of Bruchpilot and elevated Ca2+ in the R5 ellipsoid body neurons. Therefore, sleep pressure might overcome blue light aversion. Thus at temperatures known to cause reproductive arrest, preserve germline stem cells, and extend lifespan, Drosophila melanogaster are prone to deep sleep and exhibit dramatically altered - yet rhythmic - daily activity patterns.

Fig. 2 in Assessment Of The Influence Of Teratogenic Activity Of Cigarette Smoke On Drosophila Melanogaster

Fig. 2. Frequency of abdominal tergite Fig. 4. Growth of imaginal disks of fruit fly abnormality morphoses in wild type fruit flies (Drosophila melanogaster) in embryonic and (Drosophila melanogaster) depending on postembryonic stages of development the"Elita" cigarette smoke dose and the age of the larvae (hours since the eggs were laid)

Fig. 1 in Assessment Of The Influence Of Teratogenic Activity Of Cigarette Smoke On Drosophila Melanogaster

Fig. 1. Frequency of abdominal tergite Fig. 3. Frequency of abdominal tergite abnormality (morphoses) in w+/w and w+/Y fruit abnormality morphoses in wild type fruit flies flies (Drosophila melanogaster) depending on the (Drosophila melanogaster) depending on "Prima HEBO" cigarette smoke dose and the age the"Elita" cigarette smoke dose and the age of of the larvae (hours since the eggs were laid). the pupae (hours since the eggs were laid)

Fig. 3 in Evaluation Of Teratogenic Activity Of The Smoke Of Burning Combustible Plastic Influencing The Drosophila Melanogaster

Fig. 3. Amount of abdominal tergite anomalies in wild type Drosophila melanogaster depending on the dose of burning plastic (polysterene) smoke and larvae age (hours after eggs are laid)

Fig. 4 in Evaluation Of Teratogenic Activity Of The Smoke Of Burning Combustible Plastic Influencing The Drosophila Melanogaster

Fig. 4. Amount of abdominal tergite anomalies in wild type Drosophila melanogaster depending on the dose of burning plastic (polysterene) smoke and pupae age (hours after eggs are laid)

Fig. 9 in Evaluation Of Teratogenic Activity Of The Smoke Of Burning Combustible Plastic Influencing The Drosophila Melanogaster

Fig. 9. Abdominal tergite anomalies in wild type Drosophila melanogaster in the result of treating pupae with the smoke of burning polysterene; 1 – females, 2 – males

Fig. 2 in Evaluation Of Teratogenic Activity Of The Smoke Of Burning Combustible Plastic Influencing The Drosophila Melanogaster

Fig. 2. Amount of abdominal tergite anomalies in wild type Drosophila melanogaster depending on the dose of burning plastic (polyethyleneterephtalane) smoke and pupae age (hours after eggs are laid)

Fig. 1 in Evaluation Of Teratogenic Activity Of The Smoke Of Burning Combustible Plastic Influencing The Drosophila Melanogaster

Fig. 1. Amount of abdominal tergite anomalies in wild type Drosophila melanogaster depending on the dose of burning plastic (polyethyleneterephtalane) smoke and larvae age (hours after eggs are laid)

opencc-by-4.0Dec 2016View details →

Fig. 3 in Novel aspects of Drosophila suzukii (Diptera: Drosophilidae) biology and an improved method for culturing this invasive species with a modified D. melanogaster diet

Fig. 3. Effect of triethylamine anesthetic exposure on the recovery of Drosophila adults: D. melanogaster (white circles, n = 181 adults), D. suzukii (black circles, n = 175 adults).

opencc-by-4.0Dec 2016View details →

Fig. 2 in Novel aspects of Drosophila suzukii (Diptera: Drosophilidae) biology and an improved method for culturing this invasive species with a modified D. melanogaster diet

Fig. 2. Effects of dietary ethanol (normal environmental ethanol range ≈ 0– 9% ethanol) on Drosophila suzukii survival when compared with D. melanogaster tolerance to ethanol (top graph) and sex-specific sensitivities of D. suzukii adults to ethanol (bottom graph). Summary of probit analyses are provided and statistics with bo = intercept estimate, b1 = estimated slope estimate for each fly species, with b1 = 0 for the baseline control in each graph (D. suzukii [top graph], D. suzukii males [bottom graph]).

opencc-by-4.0Dec 2016View details →

Fig. 1 in Novel aspects of Drosophila suzukii (Diptera: Drosophilidae) biology and an improved method for culturing this invasive species with a modified D. melanogaster diet

Fig. 1. Dietary manipulation of Drosophila suzukii cultures based on the use of 5 berry species (blackberry, strawberry, black cherry, blueberry, and grape) with a no-fruit (No Fruit) control (grey bars), and cultures to which yeast was added (+Y) or omitted (−Y) from 4-24® drosophila media (white bars). Asterisks indicate mean differences from 2 respective baseline controls (B), i.e., Blackberry−Y (14 d) and Blackberry+Y (21 d), according to multiple Wilcoxon 2-sample tests.

opencc-by-4.0May 2015View details →

Figure 4 in The effects of larval diet restriction on developmental time, preadult survival, and wing length in Drosophila melanogaster

Figure 4. Mean wing length (mm) of females and males developed on different diets. The error bars represent standard error of the mean.

opencc-by-4.0May 2015View details →

Figure 3 in The effects of larval diet restriction on developmental time, preadult survival, and wing length in Drosophila melanogaster

Figure 3. Larva-to-pupa, larva-to-adult, and pupa-to-adult viability (number of adults as a proportion of the number of larvae transferred) as a percentage of different diets. The error bars represent standard errors of means.

opencc-by-4.0Jun 2021View details →

Figure 3 in The effect of streptomycin on survival, development, and some biochemical aspects of Drosophila melanogaster

Figure 3. Effects of dietary streptomycin on SOD enzyme activities in 3rd instar larvae, pupae, and adults of D. melanogaster. Bars represent the means of four replicates. Means followed by different letters are significantly different (p <0.05, LSD test).