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1,161 results for “Drosophila melanogaster”
Data from: The effects of selective history and environmental heterogeneity on inbreeding depression in experimental populations of Drosophila melanogaster
Inbreeding depression varies considerably among populations, but only some aspects of this variation have been thoroughly studied. Because inbreeding depression requires genetic variation, factors that influence the amount of standing variation can affect the magnitude of inbreeding depression. Environmental heterogeneity has long been considered an important contributor to the maintenance of genetic variation, but its effects on inbreeding depression have been largely ignored by empiricists. Here we compare inbreeding depression, measured in two environments, for 20 experimental populations of Drosophila melanogaster that have been maintained under four different selection regimes, including two types of environmentally homogeneous selection and two types environmentally heterogeneous selection. In line with theory, we find considerably higher inbreeding depression in populations from heterogeneous selection regimes. We also use our data set to test whether inbreeding depression is correlated with either stress or the phenotypic coefficient of variation (CV), as suggested by some recent studies. Though both of these factors are significant predictors of inbreeding depression in our study, there is an effect of assay environment on inbreeding depression that cannot be explained by either stress or CV.
Data from: Polymorphism in the neurofibromin gene, Nf1, is associated with antagonistic selection on wing size and development time in Drosophila melanogaster
In many invertebrates, body size shows genetically based clines, with size increasing in colder climates. Large body size is typically associated with prolonged development times. We consider variation in the CNS-specific gene neurofibromin 1 (Nf1) and its association with body size and development time. We identified two major Nf1 haplotypes in natural populations, Nf1-insertion-A and Nf1-deletion-G. These haplotypes are characterized by a 45-base insertion/deletion (INDEL) in Nf1 intron 2 and an A/G synonymous substitution (locus L17277). Linkage disequilibrium (LD) between the INDEL and adjacent sites is high but appears to be restricted within the Nf1 gene interval. In Australia, the frequency of the Nf1-insertion-A haplotype increases with latitude where wing size is larger, independent of the chromosomal inversion In(3R)Payne. Unexpectedly, the Nf1-insertion-A haplotype is negatively associated with wing size. We found that the Nf1-insertion-A haplotype is enriched in females with shorter development time. This suggests that the Nf1 haplotype cline may be driven by selection for development time rather than size; females from southern (higher latitude) D. melanogaster populations maintain a rapid development time despite being relatively larger, and the higher incidence of Nf1-insertion-A in southern Australia may contribute to this pattern whereas the effects of the Nf1 haplotypes on size may be countered by other loci with antagonistic effects on size and development time. Our results point to the potential complexity involved in identifying selection on genetic variants exhibiting pleiotropic effects when studies are based on spatial patterns or association studies.
Data from: Hybridization in the Drosophila melanogaster subgroup: incomplete isolation among the three species of the yakuba complex
In the Drosophila melanogaster subgroup, the yakuba species complex, D. yakuba, D. santomea and D. teissieri have identical mitochondrial genomes in spite of nuclear differentiation. The first two species can be readily hybridized in the laboratory, and produce fertile females and sterile males. They also form hybrids in natural conditions. Nonetheless, the third species, D. teissieri, was thought to be unable to produce hybrids with either D. yakuba or D. santomea. This in turn posed the conundrum of why the three species shared a single mitochondrial genome. In this report we show that D. teissieri can indeed hybridize with both D. yakuba and D. santomea. The resulting female hybrids from both crosses are fertile, while the hybrid males are sterile. We also characterize six isolating mechanisms that might be involved in keeping the three species apart. Our results open the possibility of studying the history of introgression in the yakuba species complex and dissecting the genetic basis of interspecific differences between these three species by genetic mapping.
Data from: No apparent cost of evolved immune response in Drosophila melanogaster
Maintenance and deployment of the immune system are costly and are hence predicted to trade-off with other resource demanding traits, such as reproduction. We subjected this long standing idea to test using laboratory experimental evolution approach. In the present study, replicate populations of Drosophila melanogaster were subjected to three selection regimes – I (Infection with Pseudomonas entomophila), S (Sham-infection with MgSO4) and U (Unhandled Control). After 30 generations of selection flies from the I-regime had evolved better survivorship upon infection with P. entomophila compared to flies from U and S regimes. However, contrary to expectations and previous reports, we did not find any evidence of trade-offs between immunity and other life-history related traits, such as longevity, fecundity, egg hatchability or development time. After 45 generations of selection, the selection was relaxed for a set of populations. Even after 15 generations, the post-infection survivorship of populations under relaxed selection regime did not decline. We speculate that either there is a negligible cost to the evolved immune response or that trade-offs occur on traits like reproductive behaviour or other immune mechanisms that we have not investigated in this study. Our research suggests that at least under certain conditions, life-history trade-offs might play little role in maintaining variation in immunity.
Data from: Heritability, evolvability, phenotypic plasticity and temporal variation in sperm-competition success of Drosophila melanogaster
Sperm-competition success (SCS) is seen as centrally important for evolutionary change: superior fathers sire superior sons and thereby inherit the traits that make them superior. Additional hypotheses, that phenotypic plasticity in SCS and sperm ageing explain variation in paternity, are less considered. Even though various alleles have individually been shown to be correlated with variation in SCS, few studies have addressed the heritability, or evolvability, of overall SCS. Those studies that have, found low or no heritability and have not examined evolvability. They have further not excluded phenotypic plasticity, and temporal effects on SCS, despite their known dramatic effects on sperm function. In Drosophila melanogaster, we found that both standard components of sperm competition, sperm defence and sperm offence, showed non-significant or insignificant heritability across several offspring cohorts. Instead, our analysis revealed, for the first time, the existence of phenotypic plasticity in SCS across an extreme environment (5% CO2), and an influence of sperm ageing. Evolvability of SCS was substantial for sperm defence but virtually absent for sperm offence. Our results suggest that the paradigm of explaining evolution by sperm competition is more complex and will benefit from further experimental work on the heritability or evolvability of SCS, measuring phenotypic plasticity, and separating the effects of sperm competition and sperm ageing.
Data from: Developmental plasticity evolved according to specialist–generalist trade-offs in experimental populations of Drosophila melanogaster
We studied the evolution of developmental plasticity in populations of Drosophila melanogaster that evolved at either constant or fluctuating temperatures. Consistent with theory, genotypes that evolved at a constant 16°C or 25°C performed best when raised and tested at that temperature. Genotypes that evolved at fluctuating temperatures performed well at either temperature, but only when raised and tested at the same temperature. Our results confirm evolutionary patterns predicted by theory, including a loss of plasticity and a benefit of specialization in constant environments.
Data from: Covariance among premating, postcopulatory and viability fitness components in Drosophila melanogaster and their influence on paternity measurement
In polyandrous mating systems, male fitness depends on success in premating, postcopulatory, and offspring viability episodes of selection. We tracked male success across all of these episodes simultaneously, using transgenic Drosophila melanogaster with ubiquitously expressed green fluorescent protein (i.e., GFP) in a series of competitive and non-competitive matings. This approach permitted us to track paternity-specific viability over all life stages and to distinguish true competitive fertilization success from differential early offspring viability. Relationships between episodes of selection were generally not present when paternity was measured in eggs, however positive correlations between sperm competitive success and offspring viability became significant when paternity was measured in adult offspring. Additionally, we found a significant male × female interaction on hatching success and a lack of repeatability of offspring viability across a focal male's matings, which may underly the limited number of correlations found between episodes of selection.
Data from: Temperature-size rule is mediated by thermal plasticity of critical size in Drosophila melanogaster
Most ectotherms show an inverse relationship between developmental temperature and body size, a phenomenon known as the temperature size rule (TSR). Several competing hypotheses have been proposed to explain its occurrence. According to one set of views, the TSR results from inevitable biophysical effects of temperature on the rates of growth and differentiation, whereas other views suggest the TSR is an adaptation that can be achieved by a diversity of mechanisms in different taxa. Our data reveal that the fruit fly, Drosophila melanogaster, obeys the TSR using a novel mechanism: reduction of critical size at higher temperatures. In holometabolous insects, attainment of critical size initiates the hormonal cascade that terminates growth, and hence, Drosophila larvae appear to instigate the signal to stop growth at a smaller size at higher temperatures. This is in contrast to findings from another holometabolous insect, Manduca sexta, in which the TSR results from the effect of temperature on the rate and duration of growth. This contrast suggests that there is no single mechanism that accounts for the TSR. Instead, the TSR appears to be an adaptation that is achieved at a proximate level through different mechanisms in different taxa.
Data from: Evidence for complex selection on four-fold degenerate sites in Drosophila melanogaster
We considered genome-wide four-fold degenerate sites from an African Drosophila melanogaster population and compared them to short introns. To include divergence and to polarize the data, we used its close relatives Drosophila simulans, Drosophila sechellia, Drosophila erecta and Drosophila yakuba as outgroups. In D. melanogaster, the GC content at four-fold degenerate sites is higher than in short introns; compared to its relatives, more AT than GC is fixed. The former has been explained by codon usage bias (CUB) favouring GC; the latter by decreased intensity of directional selection or by increased mutation bias towards AT. With a biallelic equilibrium model, evidence for directional selection comes mostly from the GC-rich ancestral base composition. Together with a slight mutation bias, it leads to an asymmetry of the unpolarized allele frequency spectrum, from which directional selection is inferred. Using a quasi-equilibrium model and polarized spectra, however, only purifying and no directional selection is detected. Furthermore, polarized spectra are proportional to those of the presumably unselected short introns. As we have no evidence for a decrease in effective population size, relaxed CUB must be due to a reduction in the selection coefficient. Going beyond the biallelic model and considering all four bases, signs of directional selection are stronger. In contrast to short introns, complementary bases show strand specificity and allele frequency spectra depend on mutation directions. Hence, the traditional biallelic model to describe the evolution of four-fold degenerate sites should be replaced by more complex models assuming only quasi-equilibrium and accounting for all four bases.
Data from: Egg viability, mating frequency and male mating ability evolve in populations of Drosophila melanogaster selected for resistance to cold shock
Background: Ability to resist temperature shock is an important component of fitness of insects and other ectotherms. Increased resistance to temperature shock is known to affect life-history traits. Temperature shock is also known to affect reproductive traits such as mating ability and viability of gametes. Therefore selection for increased temperature shock resistance can affect the evolution of reproductive traits. Methods: We selected replicate populations of Drosophila melanogaster for resistance to cold shock. We then investigated the evolution of reproductive behavior along with other components of fitness- larval survivorship, adult mortality, fecundity, egg viability in these populations. Results: We found that larval survivorship, adult mortality and fecundity post cold shock were not significantly different between selected and control populations. However, compared to the control populations, the selected populations laid significantly higher percentage of fertile eggs (egg viability) 24 hours post cold shock. The selected populations had higher mating frequency both with and without cold shock. After being subjected to cold shock, males from the selected populations successfully mated with significantly more non-virgin females and sired significantly more progeny compared to control males. Conclusions: A number of studies have reported the evolution of survivorship in response to selection for temperature shock resistance. Our results clearly indicate that adaptation to cold shock can involve changes in components of reproductive fitness. Our results have important implications for our understanding of how reproductive behavior can evolve in response to thermal stress.
Data from: Cellular basis of morphological variation and temperature-related plasticity in Drosophila melanogaster strains with divergent wing shapes
Organ shape evolves through cross-generational changes in developmental patterns at cellular and/or tissue levels that ultimately alter tissue dimensions and final adult proportions. Here, we investigated the cellular basis of an artificially selected divergence in the outline shape of Drosophila melanogaster wings, by comparing flies with elongated or rounded wing shapes but with remarkably similar wing sizes. We also tested whether cellular plasticity in response to developmental temperature was altered by such selection. Results show that variation in cellular traits is associated with wing shape differences, and that cell number may play an important role in wing shape response to selection. Regarding the effects of developmental temperature, a size-related plastic response was observed, in that flies reared at 16 °C developed larger wings with larger and more numerous cells across all intervein regions relative to flies reared at 25 °C. Nevertheless, no conclusive indication of altered phenotypic plasticity was found between selection strains for any wing or cellular trait. We also described how cell area is distributed across different intervein regions. It follows that cell area tends to decrease along the anterior wing compartment and increase along the posterior one. Remarkably, such pattern was observed not only in the selected strains but also in the natural baseline population, suggesting that it might be canalized during development and was not altered by the intense program of artificial selection for divergent wing shapes.
Data from: HSP90 as a global genetic modifier for male genital morphology in Drosophila melanogaster
The molecular chaperone protein HSP90 has been proposed to modulate genotype-phenotype relationship in a broad range of organisms. To understand the genetic modifier effect of HSP90, genetic variations under the influence of HSP90 need to be identified on a genome-wide scale. Here, we show that HSP90 functions as a genetic modifier of genital morphology in Drosophila melanogaster. We identified a large number of single-nucleotide polymorphisms (SNPs) with an HSP90-dependent effect by using genome wide association analysis. We classified the SNPs into the ones under capacitance effect (smaller allelic effect under HSP90 inhibition) or the ones under potentiation effect (larger allelic effect under HSP90 inhibition). Although the majority of SNPs are under capacitance, there are a large number of SNPs under potentiation. This observation provides support for a model in which Hsp90 is not described exclusively as a 'genetic capacitor', but is described more broadly as a 'genetic modifier'. Because the majority of the candidate genes estimated from SNPs with an HSP90-dependent effect in the current study have never been reported to interact with HSP90 directly, the global genetic modifier effect of HSP90 may be exhibited through epistatic interactions in gene regulatory networks.
Data from: Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the southeastern United States and Caribbean Islands
Drosophila melanogaster is postulated to have colonized North America in the past several 100 years in two waves. Flies from Europe colonized the east coast United States while flies from Africa inhabited the Caribbean, which if true, make the south-east US and Caribbean Islands a secondary contact zone for African and European D. melanogaster. This scenario has been proposed based on phenotypes and limited genetic data. In our study, we have sequenced individual whole genomes of flies from populations in the south-east US and Caribbean Islands and examined these populations in conjunction with population sequences from the west coast US, Africa, and Europe. We find that west coast US populations are closely related to the European population, likely reflecting a rapid westward expansion upon first settlements into North America. We also find genomic evidence of African and European admixture in south-east US and Caribbean populations, with a clinal pattern of decreasing proportions of African ancestry with higher latitude. Our genomic analysis of D. melanogaster populations from the south-east US and Caribbean Islands provides more evidence for the Caribbean Islands as the source of previously reported novel African alleles found in other east coast US populations. We also find the border between the south-east US and the Caribbean island to be the admixture hot zone where distinctly African-like Caribbean flies become genomically more similar to European-like south-east US flies. Our findings have important implications for previous studies examining the generation of east coast US clines via selection.
Data from: Drosophila melanogaster larvae make nutritional choices that minimize developmental time
Organisms from slime moulds to humans carefully regulate their macronutrient intake to optimize a wide range of life history characters including survival, stress resistance, and reproductive success. However, life history characters often differ in their response to nutrition, forcing organisms to make foraging decisions while balancing the trade-offs between these effects. To date, we have a limited understanding of how the nutritional environment shapes the relationship between life history characters and foraging decisions. To gain insight into the problem, we used a geometric framework for nutrition to assess how the protein and carbohydrate content of the larval diet affected key life history traits in the fruit fly, Drosophila melanogaster. In no-choice assays, survival from egg to pupae, female and male body size, and ovariole number – a proxy for female fecundity – were maximized at the highest protein to carbohydrate (P:C) ratio (1.5:1). In contrast, development time was minimized at intermediate P:C ratios, around 1:2. Next, we subjected larvae to two-choice tests to determine how they regulated their protein and carbohydrate intake in relation to these life history traits. Our results show that larvae targeted their consumption to P:C ratios that minimized development time. Finally, we examined whether adult females also chose to lay their eggs in the P:C ratios that minimized developmental time. Using a three-choice assay, we found that adult females preferentially laid their eggs in food P:C ratios that were suboptimal for all larval life history traits. Our results demonstrate that D. melanogaster larvae make foraging decisions that trade-off developmental time with body size, ovariole number, and survival. In addition, adult females make oviposition decisions that do not appear to benefit the larvae. We propose that these decisions may reflect the living nature of the larval nutritional environment in rotting fruit. These studies illustrate the interaction between the nutritional environment, life history traits, and foraging choices in D. melanogaster, and lend insight into the ecology of their foraging decisions.
Data from: Flexible memory controls sperm competition responses to male Drosophila melanogaster
Males of many species use social cues to predict sperm competition and tailor their reproductive strategies, such as ejaculate or behavioural investment, accordingly. Whilst these plastic strategies are widespread, the underlying mechanisms remain largely unknown. Plastic behaviour requires individuals to learn and memorise cues associated with environmental change before using this experience to modify behaviour. Drosophila melanogaster respond to an increase in sperm competition threat by extending mating duration after exposure to a rival male. This behaviour shows lag times between environmental change and behavioural response suggestive of acquisition and loss of memory. Considering olfaction is important for a male's ability to assess the sperm competition environment, we hypothesised that an olfactory learning and memory pathway may play a key role in controlling this plastic behaviour. We assessed the role of genes and brain structures known to be involved in learning and memory. We show that sperm competition responses depend on anaesthesia sensitive memory, specifically the genes rut and amn. We also show that the γ lobes of the mushroom bodies are integral to the control of plastic mating behaviour. These results reveal the genetic and neural properties required for reacting to changes in the sperm competition environment.
Data from: The effect of deleterious mutations and age on recombination in Drosophila melanogaster
At the population level, recombination mediates the efficiency with which selection can eliminate deleterious mutations. At the individual level, deleterious alleles may influence recombination, which would change the rate at which linkage disequilibrium is eroded and thereby alter the efficiency with which deleterious alleles are purged. Here we test whether the presence of a deleterious allele on one autosome affects recombination on another autosome. We find that deleterious alleles not only alter the rate but also the pattern of recombination. However, there is little support that different deleterious alleles affect recombination in a consistent manner. Because we have detailed information on individual females across their life times, we are able to examine how recombination patterns change with age and find that these patterns are also affected by the presence of deleterious alleles. The differences among genotypes or among age classes is large enough to add substantial noise to genetic mapping experiments that do not consider these sources of variation.
Data from: Plastic and evolutionary responses of cell size and number to larval malnutrition in Drosophila melanogaster
Both development and evolution under chronic malnutrition lead to reduced adult size in Drosophila. We studied the contribution of changes in size vs. number of epidermal cells to plastic and evolutionary reduction of wing size in response to poor larval food. We used flies from six populations selected for tolerance to larval malnutrition and from six unselected control populations, raised either under standard conditions or under larval malnutrition. In the control populations, phenotypic plasticity of wing size was mediated by both cell size and cell number. In contrast, evolutionary change in wing size, which was only observed as a correlated response expressed on standard food, was mediated entirely by reduction in cell number. Plasticity of cell number had been lost in the selected populations, and cell number did not differ between the sexes despite males having smaller wings. Results of this and other experimental evolution studies are consistent with the hypothesis that alleles which increase body size through prolonged growth affect wing size mostly via cell number, whereas alleles which increase size through higher growth rate do so via cell size.
Data from: The effects of male harm vary with female quality and environmental complexity in Drosophila melanogaster
Mate competition provides the opportunity for sexual selection which often acts strongly on males, but also the opportunity for sexual conflict that can alter natural selection on females. Recent attention has focused on the potential of sexual conflict to weaken selection on females if male sexual attention, and hence harm, is disproportionately directed toward high over low quality females, thereby reducing the fitness difference between these females. However, sexual conflict could instead strengthen selection on females if low quality females are more sensitive to male harm than high quality females, thereby magnifying fitness differences between them. We quantify the effects of male exposure on low vs. high quality females in Drosophila melanogaster in each of two environments ("simple" and "complex") that are known to alter behavioural interactions. We show that the effects of male harm are greater for low compared to high quality females in the complex but not the simple environment, consistent with mate competition strengthening selection on females in the former but not in the latter environment.
Combining metabolomics and experimental evolution reveals key mechanisms underlying longevity differences in laboratory evolved Drosophila melanogaster populations
<p>Experimental evolution with Drosophila melanogaster has been used extensively for decades to study aging and longevity. In recent years, the addition of DNA and RNA sequencing to this framework has allowed researchers to leverage the statistical power inherent to experimental evolution to study the genetic basis of longevity itself. Here, we incorporated metabolomic data into to this framework to generate even deeper insights into the physiological and genetic mechanisms underlying longevity differences in three groups of experimentally evolved D. melanogaster populations with different aging and longevity patterns. Our metabolomic analysis found that aging alters mitochondrial metabolism through increased consumption of NAD<sup>+</sup> and increased usage of the TCA cycle. Combining our genomic and metabolomic data produced a list of biologically relevant candidate genes. Among these candidates, we found significant enrichment for genes and pathways associated with neurological development and function, and carbohydrate metabolism. While we do not explicitly find enrichment for aging canonical genes, neurological dysregulation and carbohydrate metabolism are both known to be associated with accelerated aging and reduced longevity. Taken together, our results provide plausible genetic mechanisms for what might be driving longevity differences in this experimental system. More broadly, our findings demonstrate the value of combining multiple types of omic data with experimental evolution when attempting to dissect mechanisms underlying complex and highly polygenic traits such as aging.</p>
Data for "Individual, but not population asymmetries, are modulated by social environment and genotype in Drosophila melanogaster"
<p>Dataset and scripts for the manuscript: "Individual, but not population asymmetries, are modulated by social environment and genotype in <em>Drosophila melanogaster". </em>We upload:</p> <p>1.Data. This directory contains the raw tracking data used for the analysis and the calibration files required by Flytracker for each strain of the Drosophila Genetic Reference Panel (RAL-69, RAL-136, RAL-338, RAL-535, RAL-796).<br> The format of the dataset consists in the output of tracking the (x,y) position and related features (e.g. velocity, distance) of flies in a circular arena using the software Flytracker - http://www.vision.caltech.edu/Tools/FlyTracker/ - For each video we have a trak.mat file and a feat.mat file. For instance, for a video in which we tracked the DGRP line RAL-136 (d338), with a pair of males (mm), trial 3 (t5) we had as outputs d338mmt5joined-feat.mat and d338mmt5joined-track.mat . You can find the description of the output here: http://www.vision.caltech.edu/Tools/FlyTracker/documentation.html</p> <p>2.Load_data _and_circling_scripts. This directory contains a MATLAB file with the instructions on how to load datasets and how to compute the circling index.</p> <p>3.Heatmap. This directory contains the instructions (readme_heatmap.txt) and scripts to (a) fix a bug in the feat files ouput by Flytracker using the calibration files and the script feat_compute_revised.m (b) plot the heatmap of the position and distance between partner flies in a dyad.</p>
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