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1,161 results for “Drosophila melanogaster”
Data from: The organization and evolution of the Responder satellite in species of the Drosophila melanogaster group: dynamic evolution of a target of meiotic drive
Background: Satellite DNA can make up a substantial fraction of eukaryotic genomes and has roles in genome structure and chromosome segregation. The rapid evolution of satellite DNA can contribute to genomic instability and genetic incompatibilities between species. Despite its ubiquity and its contribution to genome evolution, we currently know little about the dynamics of satellite DNA evolution. The Responder (Rsp) satellite DNA family is found in the pericentric heterochromatin of chromosome 2 of Drosophila melanogaster. Rsp is well-known for being the target of Segregation Distorter (SD) an autosomal meiotic drive system in D. melanogaster. I present an evolutionary genetic analysis of the Rsp family of repeats in D. melanogaster and its closely-related species in the melanogaster group (D. simulans, D. sechellia, D. mauritiana, D. erecta, and D. yakuba) using a combination of available BAC sequences, whole genome shotgun Sanger reads, Illumina short read deep sequencing, and fluorescence in situ hybridization. Results: I show that Rsp repeats have euchromatic locations throughout the D. melanogaster genome, that Rsp arrays show evidence for concerted evolution, and that Rsp repeats exist outside of D. melanogaster, in the melanogaster group. The repeats in these species are considerably diverged at the sequence level compared to D. melanogaster, and have a strikingly different genomic distribution, even between closely-related sister taxa. Conclusions: The genomic organization of the Rsp repeat in the D. melanogaster genome is complex--it exists of large blocks of tandem repeats in the heterochromatin and small blocks of tandem repeats in the euchromatin. My discovery of heterochromatic Rsp-like sequences outside of D. melanogaster suggests that SD evolved after its target satellite and that the evolution of the Rsp satellite family is highly dynamic over a short evolutionary time scale (<240,000 years).
Data from: Identification of X-linked quantitative trait loci affecting cold tolerance in Drosophila melanogaster and fine-mapping by selective sweep analysis
Drosophila melanogaster is a cosmopolitan species that colonizes a great variety of environments. One trait that shows abundant evidence for naturally segregating genetic variance in different populations of D. melanogaster is cold tolerance. Previous work has found quantitative trait loci (QTL) exclusively on the second and the third chromosomes. To gain insight into the genetic architecture of cold tolerance on the X chromosome and to compare the results with our analyses of selective sweeps, a mapping population was derived from a cross between substitution lines that solely differed in the origin of their X chromosome: one originates from a European inbred line, the other one from an African inbred line. We found a total of six QTL for cold tolerance factors on the X chromosome of D. melanogaster. Although the composite interval mapping revealed slightly different QTL profiles between sexes, a coherent model suggests that most QTL overlapped between sexes and each explained around 5-14% of the genetic variance (which may be slightly overestimated). The allelic effects were largely additive, but we also detected two significant interactions. Taken together, this provides evidence for multiple QTL that are spread along the entire X chromosome and whose effects range from low to intermediate. One detected transgressive QTL influences cold tolerance in different ways for the two sexes. While females benefit from the European allele increasing their cold tolerance, males tend to do better with the African allele. Finally, using selective sweep mapping the candidate gene CG16700 for cold tolerance co-localizing with a QTL was identified.
Data from: Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental Drosophila melanogaster populations
Whole genome re-sequencing of experimental populations evolving under a specific selection regime has become a popular approach to determine genotype-phenotype maps and understand adaptation to new environments. Despite its conceptual appeal and success in identifying some causative genes, it has become apparent that many studies suffer from an excess of candidate loci. Several explanations have been proposed for this phenomenon, but it is clear that information about the linkage structure during such experiments is needed. Until now only Pool-Seq data were available, which do not provide sufficient information about the correlation between linked sites. We address this problem in two complementary analyses of three replicate D. melanogaster populations evolving to a new hot temperature environment for almost 70 generations. In the first analysis, we sequenced 58 haploid genomes from the founder population and evolved flies at generation 67. We show that during the experiment LD increased almost uniformly over much greater distances than typically seen in Drosophila. In the second analysis, Pool-Seq time series data of the three replicates were combined with haplotype information from the founder population to follow blocks of initial haplotypes over time. We identified 17 selected haplotype-blocks that started at low frequencies in the base population and increased in frequency during the experiment. The size of these haplotype-blocks ranged from 0.082 to 4.095 Mb. Moreover, between 42-46% of the top candidate SNPs from the comparison of founder and evolved populations fell into the genomic region covered by the haplotype-blocks. We conclude that LD in such rising haplotype-blocks results in long range hitchhiking over multiple kb sized regions. LD in such haplotype-blocks is therefore a major factor contributing to an excess of candidate loci. While modifications of the experimental design may help to reduce the hitchhiking effect and allow for more precise mapping of causative variants, we also note that such haplotype-blocks might be well suited to study the dynamics of selected genomic regions during experimental evolution studies.
Data from: Modulation of social space by dopamine in Drosophila melanogaster, but no effect on the avoidance of the Drosophila stress odorant
Appropriate response to others is necessary for social interactions. Yet little is known about how neurotransmitters regulate attractive and repulsive social cues. Using genetic and pharmacological manipulations in Drosophila melanogaster, we show that dopamine is contributing the response to others in a social group, specifically, social spacing, but not the avoidance of odours released by stressed flies (dSO). Interestingly, this dopamine-mediated behaviour is prominent only in the day-time, and its effect varies depending on tissue, sex and type of manipulation. Furthermore, alteration of dopamine levels has no effect on dSO avoidance regardless of sex, which suggests that a different neurotransmitter regulates this response.
Data from: Nonadditive indirect effects of group genetic diversity on larval viability in Drosophila melanogaster imply key role of maternal decision-making
Genetic variation can have important consequences for populations: high population genetic diversity is typically associated with ecological success. Some mechanisms that account for these benefits assume that local social groups with high genetic diversity are more successful than low-diversity groups. At the same time, active decision-making by individuals can influence group genetic diversity, a behavioral process not generally incorporated into discussions of population-level diversity effects. Here, we examine how maternal decisions that determine group genetic diversity influence the viability of Drosophila melanogaster larvae. Our groups contained wildtype larvae, whose genetic diversity we manipulated; and genetically-marked "tester" larvae, whose genotype and frequency were identical in all trials. We measured wildtype and tester viability for each group. Surprisingly, the viability of wildtype larvae did not depend on group genetic diversity. However, the viability of the tester genotype was substantially depressed in large, high-diversity groups. Further, not all high-diversity groups produced this effect: certain combinations of wildtype genotypes were deleterious to tester viability, while other groups of the same diversity—but containing different wildtype genotypes—were not deleterious. These deleterious combinations of wildtype genotypes could not be predicted by observing the performance of the same tester and wildtype genotypes in low-diversity groups. Taken together, these results suggest that non-additive interactions among genotypes, rather than genetic diversity per se, account for between-group differences in viability in D. melanogaster; and that predicting the consequences of genetic diversity at the population level may not be straightforward.
Data from: Inbreeding reveals mode of past selection on male reproductive characters in Drosophila melanogaster
Directional dominance is a prerequisite of inbreeding depression. Directionality arises when selection drives alleles that increase fitness to fixation and eliminates dominant deleterious alleles, while deleterious recessives are hidden from it and maintained at low frequencies. Traits under directional selection (i.e., fitness traits) are expected to show directional dominance and therefore an increased susceptibility to inbreeding depression. In contrast, traits under stabilizing selection or weakly linked to fitness are predicted to exhibit little-to-no inbreeding depression. Here, we quantify the extent of inbreeding depression in a range of male reproductive characters and then infer the mode of past selection on them. The use of transgenic populations of Drosophila melanogaster with red or green fluorescent-tagged sperm heads permitted in vivo discrimination of sperm from competing males and quantification of characteristics of ejaculate composition, performance, and fate. We found that male attractiveness (mating latency) and competitive fertilization success (P2) both show some inbreeding depression, suggesting they may have been under directional selection, whereas sperm length showed no inbreeding depression suggesting a history of stabilizing selection. However, despite having measured several sperm quality and quantity traits, our data did not allow us to discern the mechanism underlying the lowered competitive fertilization success of inbred (f = 0.50) males.
Data from: Genetic quality affects the rate of male and female reproductive ageing differently in Drosophila melanogaster
Males and females often maximize fitness by pursuing different reproductive strategies, with males commonly assumed to benefit more from increased resource allocation into current reproduction. Such investment should trade-off with somatic maintenance and may explain why males frequently live shorter than females. It also predicts that males should experience faster reproductive ageing. Here we investigate if reproductive ageing and lifespan respond to condition differently in male and female Drosophila melanogaster, as predicted if sexual selection has shaped male and female allocation patterns. We manipulate condition through genetic quality, by comparing individuals inbred or outbred for a major autosome. While genetic quality had a similar effect on condition in both sexes, condition had a much larger general effect on male than female reproductive output, as expected when sexual selection on vigour acts more strongly on males. We find no differences in reproductive ageing between the sexes in low condition, but in high condition reproductive ageing is relatively faster in males. No corresponding sex-specific change was found for lifespan. The sex difference in reproductive ageing appearing in high condition was due specifically to a decreased ageing rate in females, rather than any change in males. Our results suggest that females age slower than males in high condition primarily because sexual selection has favoured sex differences in resource allocation under high condition, with females allocating relatively more towards somatic maintenance than males.
Data from: The role of species-specific sensory cues in male responses to mating rivals in Drosophila melanogaster fruitflies
Complex sets of cues can be important in recognising and responding to conspecific mating competitors and avoiding potentially costly heterospecific competitive interactions. Within Drosophila. melanogaster, males can detect sensory inputs from conspecifics to assess the level of competition. They respond to rivals by significantly extending mating duration and gain significant fitness benefits from doing so. Here, we tested the idea that the multiple sensory cues used by D. melanogaster males to detect conspecifics also function to minimise 'off-target' responses to heterospecific males that they might encounter (D. simulans, D. yakuba. D. pseudoobscura or D. virilis). Focal D. melanogaster males exposed to D. simulans or D. pseudoobscura subsequently increased mating duration, but to a lesser extent than following exposure to conspecific rivals. The magnitude of rivals responses expressed by D. melanogaster males did not align with genetic distance between species and none of the sensory manipulations caused D. melanogaster to respond to males of all other species tested. However, when we removed or provided 'false' sensory cues, D. melanogaster males became more likely to show increased mating duration responses to heterospecific males. We suggest that benefits of avoiding inaccurate assessment of the competitive environment may shape the evolution of recognition cues.
Data from: Local adaptation to developmental density does not lead to higher mating success in Drosophila melanogaster
In this study, we investigate the effect of local adaptation to developmental density on male mating success in laboratory populations of Drosophila melanogaster. Mating success is known to be influenced by body condition which can in turn be influenced by local adaptation. We test the hypothesis that males adapted to a given environment have higher mating success when assayed in that environment. We used males selected for adaptation to high larval density and their controls which are reared at low larval density. We grew assay males in low and high densities while the focal females (raised at low larval density) used for the experiment belonged to the common ancestor of selected and control populations. We considered selected males grown at high density and control males grown at low density as "adapted". Similarly we considered selected males grown at low density and control males grown at high density as "non-adapted". Selected male belonging to a given treatment (larval density) was made to compete with control male of the same treatment for mating with ancestral female. We quantified components of reproductive fitness: mating latency, copulation duration, mating success and number of progeny sired by the "adapted" and "non-adapted" males. The results show that local adaptation does not lead to higher mating success in populations adapted to their own larval rearing environment.
Data from: Evolution of pre- and post-copulatory traits in male Drosophila melanogaster as a correlated response to selection for resistance to cold stress
Background: In Drosophila melanogaster the fitness of males depends on a broad array of reproductive traits classified as pre- and post-copulatory traits. Exposure to cold stress, can reduce sperm number, male mating ability and courtship behavior. Therefore, it is expected that the adaptation to cold stress will involve changes in pre- and post-copulatory traits. Such evolution of reproductive traits in response to cold stress is not well studied. Methods: We selected replicate populations of D. melanogaster for resistance to cold shock. Over 37–46 generations of selection, we investigated pre- and post-copulatory traits such as mating latency, copulation duration, mating frequency, male fertility, fitness (progeny production) and sperm competitive ability in male flies subjected to cold shock and those not subjected to cold shock. Results: We found that post cold shock, the males from the selected populations had a significantly lower mating latency along with, higher mating frequency, fertility, sperm competitive ability and number of progeny relative to the control populations. Conclusion: While most studies of experimental evolution of cold stress resistance have documented the evolution of survivorship in response to selection, our study clearly shows that adaptation to cold stress involves rapid changes in the pre- and post-copulatory traits. Additionally, improved performances under stressful conditions need not necessarily trade-off with performance under benign conditions.
Data from: Linkage disequilibrium and inversion-typing of the Drosophila melanogaster Genome Reference Panel
We calculated the linkage disequilibrium between all pairs of variants in the Drosophila Genome Reference Panel with minor allele count ≥5. We used r2 ≥ 0.5 as the cutoff for a highly correlated SNP. We make available the list of all highly correlated SNPs for use in association studies. Seventy-six percent of variant SNPs are highly correlated with at least one other SNP, and the mean number of highly correlated SNPs per variant over the whole genome is 83.9. Disequilibrium between distant SNPs is also common when minor allele frequency (MAF) is low: 37% of SNPs with MAF < 0.1 are highly correlated with SNPs more than 100 kb distant. Although SNPs within regions with polymorphic inversions are highly correlated with somewhat larger numbers of SNPs, and these correlated SNPs are on average farther away, the probability that a SNP in such regions is highly correlated with at least one other SNP is very similar to SNPs outside inversions. Previous karyotyping of the DGRP lines has been inconsistent, and we used LD and genotype to investigate these discrepancies. When previous studies agreed on inversion karyotype, our analysis was almost perfectly concordant with those assignments. In discordant cases, and for inversion heterozygotes, our results suggest errors in two previous analyses or discordance between genotype and karyotype. Heterozygosities of chromosome arms are, in many cases, surprisingly highly correlated, suggesting strong epsistatic selection during the inbreeding and maintenance of the DGRP lines.
Data from: Costs and benefits of lifetime exposure to mating rivals in male Drosophila melanogaster
Theory predicts that males should evolve mechanisms to assess competition and allocate resources accordingly. This requires phenotypic plasticity, to accurately match responses to the environment. Plastic responses in males to sexual competition are diverse and widespread. However, our ability to understand and predict how they evolve is limited because their benefits are rarely measured, and costs are, as yet, entirely unquantified. In the fruit fly Drosophila melanogaster, males that anticipate strong competition for matings or fertilisations subsequently mate for longer and transfer more of two key seminal fluid proteins. This results in significantly elevated reproductive output. In this study we examined the fitness effects of male responses to rivals across the entire male lifespan. Males were exposed to rivals or not throughout life whilst controlling mating opportunities. Males showed significant responses to rivals throughout their lifetimes, associated with significant early-life fitness benefits. However, these disappeared after the third mating. There were also significant costs – males exposed to rivals took significantly fewer mating opportunities in later life and had significantly shorter lifespans than controls. The data suggest that there are substantial costs for males of mounting plastic responses to the threat of sexual competition.
Data from: The genetic architecture of defence as resistance to and tolerance of bacterial infection in Drosophila melanogaster
Defence against pathogenic infection can take two forms: resistance and tolerance. Resistance is the ability of the host to limit a pathogen burden, whereas tolerance is the ability to limit the negative consequences of infection at a given level of infection intensity. Evolutionarily, a tolerance strategy that is independent of resistance could allow the host to avoid mounting a costly immune response and, theoretically, to avoid a co-evolutionary arms race between pathogen virulence and host resistance. Biomedically, understanding the mechanisms of tolerance and how they relate to resistance could potentially yield treatment strategies that focus on health improvement instead of pathogen elimination. To understand the impact of tolerance on host defence and identify genetic variants that determine host tolerance, we defined genetic variation in tolerance as the residual deviation from a binomial regression of fitness under infection against infection intensity. We then performed a genomewide association study to map the genetic basis of variation in resistance to and tolerance of infection by the bacterium Providencia rettgeri. We found a positive genetic correlation between resistance and tolerance, and we demonstrated that the level of resistance is highly predictive of tolerance. We identified 30 loci that predict tolerance, many of which are in genes involved in the regulation of immunity and metabolism. We used RNAi to confirm that a subset of mapped genes have a role in defence, including putative wound repair genes grainy head and debris buster. Our results indicate that tolerance is not an independent strategy from resistance, but that defence arises from a collection of physiological processes intertwined with canonical immunity and resistance.
Data from: Variation in thermal performance and reaction norms among populations of Drosophila melanogaster
The major goal of evolutionary thermal biology is to understand how variation in temperature shapes phenotypic evolution. Comparing thermal reaction norms among populations from different thermal environments allows us to gain insights into the evolutionary mechanisms underlying thermal adaptation. Here, we have examined thermal adaptation in six wild populations of the fruit fly (Drosophila melanogaster) from markedly different natural environments by analyzing thermal reaction norms for fecundity, thorax length, wing area and ovariole number under ecologically realistic fluctuating temperature regimes in the laboratory. Contrary to expectation, we found only minor differences in the thermal optima for fecundity among populations. Differentiation among populations was mainly due to differences in absolute (and partly also relative) thermal fecundity performance. Despite significant variation among populations in the absolute values of morphological traits, we observed only minor differentiation in their reaction norms. Overall, the thermal reaction norms for all traits examined were remarkably similar among different populations. Our results therefore suggest that thermal adaptation in D. melanogaster predominantly involves evolutionary changes in absolute trait values rather than in aspects of thermal reaction norms.
Data from: Measuring the fitness benefits of male mate choice in Drosophila melanogaster
It is increasingly realised that the potential for male mate choice is widespread across many taxa. However, measurements of the relative magnitude of the fitness benefits that such choice can confer are lacking. Here we directly measured, in a comprehensive set of tests that manipulated key variables, the fitness benefits of male mate choice in Drosophila melanogaster, by measuring egg production in females that were chosen or rejected by males. The results provided significant evidence for male mate choice. In absolute terms, the observed degree of choice increased male fitness by an average of only 1.59 eggs. However, using a novel technique we show that this benefit of choice represented 14.5% of the maximum potential fitness benefit of choice. The magnitude of mate choice was not significantly altered by variation in (i) mate compatibility, (ii) phenotypic plasticity in male mate choice, or (iii) whether choosing males were preferred or non-preferred by females. Overall, we show that male mate choice represents a subtle but significant opportunity for sexual selection, and we offer a novel and widely applicable method for quantifying mate choice.
Data from: Does phenotypic plasticity for adult size versus food level in Drosophila melanogaster evolve in response to adaptation to different rearing densities?
Recent studies using inbred lines of Drosophila have suggested that there is extensive genetic variability for phenotypic plasticity of body size versus food level. If true, we expect that the outcome of evolution at very different food levels should yield genotypes whose adult sizes show different patterns of phenotypic plasticity. We have tested this prediction with six independent populations of Drosophila melanogaster kept at extreme (low vs. high) densities for 125 generations. We found that the phenotypic plasticity of body size versus food level is not affected by selection or the presence of competitors of a different genotype. However, we document increasing among population variation in phenotypic plasticity due to random genetic drift. Several reasons are explored to explain these results including the possibility that the use of highly inbred lines to make inferences about the evolution of genetically variable populations may be misleading.
Data from: Epidermal growth factor receptor and transforming growth factor-beta signaling contributes to variation for wing shape in Drosophila melanogaster
Wing development in Drosophila is a common model system for the dissection of genetic networks and their roles during development. In particular, the RTK and TGF-beta regulatory networks appear to be involved with numerous aspects of wing development, including patterning, cell determination, growth, proliferation, and survival in the developing imaginal wing disc. However, little is known as to how subtle changes in the function of these genes may contribute to quantitative variation for wing shape, per se. In this study 50 insertional mutations, representing 43 loci in the RTK, Hedgehog, TGF-beta pathways, and their genetically interacting factors were used to study the role of these networks on wing shape. To concurrently examine how genetic background modulates the effects of the mutation, each insertion was introgressed into two wild-type genetic backgrounds. Using geometric morphometric methods, it is shown that the majority of these mutations have profound effects on shape but not size of the wing when measured as heterozygotes. To examine the relationships between how each mutation affects wing shape hierarchical clustering was used. Unlike previous observations of environmental canalization, these mutations did not generally increase within-line variation relative to their wild-type counterparts. These results provide an entry point into the genetics of wing shape and are discussed within the framework of the dissection of complex phenotypes.
Data from: Past and present resource availability affect mating rate but not choice in Drosophila melanogaster
The choices of when, where, and with whom to mate represent some of the most important decisions an individual can make to increase their fitness. Several studies have shown that the resources available to an individual during development can dramatically alter their mating rate later in life, and even the choice of mate. However, an individual's surroundings and available resources can change rapidly, and it is not clear how quickly the redistribution of resources towards reproduction can change. To address this important question, we measured mating rate and mate choice among Drosophila melanogaster males that were manipulated in terms of both past resources (control vs. starvation) and the resources available during mate choice (food vs. no food). We found that males given access to ample resources prior to mate choice showed higher mating rates than those that were starved, in agreement with previous studies. However, we also found that this effect can be reversed quickly, as starved males given the opportunity to mate in a high-quality environment mated at frequencies equivalent to their fed counterparts. While past and present resources affected mating rate, they did not affect mate choice, as males mated with high quality females at high frequencies regardless of their condition and environment. Our results show that both current condition as well as the promise of future resources can dramatically influence individuals' investment into reproduction, and that such mating decisions are extremely plastic and reliant on environmental cues.
Data from: Temporal variation favors the evolution of generalists in experimental populations of Drosophila melanogaster
In variable environments, selection should favor generalists that maintain fitness across a range of conditions. However, costs of adaptation may generate fitness trade-offs and lead to some compromise between specialization and generalization that maximizes fitness. Here, we evaluate the evolution of specialization and generalization in 20 populations of Drosophila melanogaster experimentally evolved in constant and variable thermal environments for 3 years. We developed genotypes from each population at two temperatures after which we measured fecundity across eight temperatures. We predicted that constant environments would select for thermal specialists and that variable environments would select for thermal generalists. Contrary to our predictions, specialists and generalists did not evolve in constant and spatially variable environments, respectively. However, temporal variation produced a type of generalist that has rarely been considered by theoretical models of developmental plasticity. Specifically, genotypes from the temporally variable selective environment were more fecund across all temperatures than were genotypes from other environments. These patterns suggest certain allelic effects and should inspire new directions for modeling adaptation to fluctuating environments.
Data from: Behavioural response to combined insecticide and temperature stress in natural populations of Drosophila melanogaster
Insecticide resistance evolves extremely rapidly, providing an illuminating model for the study of adaptation. With climate change reshaping species distribution, pest and disease vector control needs rethinking to include the effects of environmental variation and insect stress physiology. Here we assessed how both long term adaptation of populations to temperature and immediate temperature variation affects the genetic architecture of DDT insecticide response in Drosophila melanogaster. Mortality assays and behavioral assays based on continuous activity monitoring were used to assess the interaction between DDT and temperature on three field-derived populations from climate extremes (Raleigh for warm temperate, Tasmania for cold oceanic and Queensland for hot tropical). The Raleigh population showed the highest mortality to DDT whereas the Queensland population, epicentre for derived alleles of the resistance gene Cyp6g1, showed the lowest. Interaction between insecticide and temperature strongly affected mortality, particularly for the Tasmanian population. Activity profiles analyzed using self-organizing maps show the insecticide promoted an early response while elevated temperature promoted a later response. These distinctive early or later activity phases revealed similar responses to temperature and DDT dose alone but with more or less genetic variance depending on the population. This change in genetic variance among populations suggests that selection particularly depleted genetic variance for DDT response in the Queensland population. Finally, despite similar (co)variation between traits in benign conditions, the genetic responses across population differed under stressful conditions. This showed how stress-responsive genetic variation only reveals itself in specific conditions and thereby escapes potential trade-offs in benign environments.
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Allen Brain Atlas
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