Drosophila Populations Research Articles

Orthologs of Drosophila pointed and Arginine kinase 1 impact sleep in mice

Abstract Model organisms such as Drosophila are powerful tools to study the genetic basis of sleep. Previously, we identified the genes pointed and Arginine kinase 1 using selective breeding for long and short sleep duration in an outbred population of Drosophila. pointed is a transcription factor that is part of the EGFR signaling pathway, while Arginine kinase 1 is involved in proline and arginine metabolism. Conserved orthologs of these genes exist in mice, leading us to hypothesize that they would also impact sleep in a murine model. We generated mutations in the murine orthologs Ets1 and Ckm using CRISPR in a C57BL/6N background, and used video analysis to measure sleep in the mice. Both mutations affected sleep parameters and the effects were observed predominantly in female mice, with males showing fewer differences from littermate controls. The study of natural populations in flies therefore leads to candidate genes with functional conservation on sleep in mammals. This paper is part of the “Genetic and other molecular underpinnings of sleep, sleep disorders, and circadian rhythms including translational approaches” Collection.

Toward the Development of the Trojan Female Technique in Pest Insects: Male-Specific Influence of Mitochondrial Haplotype on Reproductive Output in the Seed Beetle Acanthoscelides obtectus.

Biocontrol techniques that impair reproductive capacity of insect pests provide opportunities to control the dynamics of their populations while minimizing collateral damage to non-target species and the environment. The Trojan Female Technique, or TFT, is a method of the trans-generational fertility-based population control through the release of females that carry mitochondrial DNA mutations that negatively affect male, but not female, reproductive output. TFT is based on the evolutionary hypothesis that, due to maternal inheritance of mitochondria, mutations which are beneficial or neutral in females but harmful in males can accumulate in the mitochondrial genome without selection acting against them. Although TFT has been theoretically substantiated, empirical work to date has focused only on Drosophila melanogaster populations, while the existence of male-biased mutations and the TFT approach in economically important pest species remain unexplored. Here, we examined the sex-specific effects of three distinct and naturally occurring mitochondrial haplotypes (MG1a, MG1d, and MG3b) on several reproductive and life history traits in the seed beetle Acanthoscelides obtectus. Our results revealed that males harboring the MG3b mitotype exhibited lower early fecundity and fertility, while there were no effects on females or longevity in either sex. Our experiments provide support for the existence of the mitochondrial variant that specifically impairs male reproductive output in pest insects. These results can be harnessed to further develop TFT as a novel form of biocontrol with broad applicability to economic pests and disease vector insects.

Pervasive fitness trade-offs revealed by rapid adaptation in large experimental populations of Drosophila melanogaster.

Life-history trade-offs are an inherent feature of organismal biology that evolutionary theory posits play a key role in patterns of divergence within and between species. Efforts to quantify trade-offs are largely confined to phenotypic measurements and the identification of negative genetic-correlations among fitness-relevant traits. Here, we use time-series genomic data collected during experimental evolution in large, genetically diverse populations of Drosophila melanogaster to directly measure the manifestation of trade-offs in response to temporally fluctuating selection pressures on ecological timescales. Specifically, we quantify the genome-wide signal of antagonistic pleiotropy suggestive of trade-offs between reproduction and stress tolerance. We further identify a putative role of two cosmopolitan inversions in these trade-offs, and show that loci responding to selection during lab-based, reproduction selection exhibit signals of fluctuating selection in an outdoor mesocosm exposed to natural environmental conditions. Our results demonstrate the utility of time-series genomic data in revealing the presence and genomic architecture underlying fitness trade-offs, and add credence to models positing a role of generic life history trade-offs in the maintenance of variation in natural populations.

Evolution of mate harm resistance in females from Drosophila melanogaster populations selected for faster development and early reproduction.

Interlocus sexual conflict is predicted to result in sexually antagonistic coevolution between male competitive traits, which are also female-detrimental, and mate harm resistance (MHR) in females. Little is known about the connection between life-history evolution and sexually antagonistic coevolution. Here, we investigated the evolution of MHR in a set of experimentally evolved populations, where mate-harming ability has been shown to have substantially reduced in males as a correlated response to the selection for faster development and early reproduction. We measured mortality and fecundity of females of these populations and those of their matched controls, under different male exposure conditions. We observed that the evolved females were more susceptible to mate harm - suffering from significantly higher mortality under continuous exposure to control males within the twenty-day assay period. Though these evolved females are known to have shorter lifespan, substantially higher mortality was not observed under virgin and single-mating conditions. We used fecundity data to show that this higher mortality in the experimentally evolved females was not due to the cost of egg production, and hence can only be attributed to reduced MHR. Further analysis indicated that this decreased MHR is unlikely to be due purely to the smaller size of these females. Instead, it is more likely to be an indirect experimentally evolved response attributable to the changed breeding ecology, and/or male trait evolution. Our results underline the implications of changes in life history traits, including lifespan, to the evolution of MHR in females.

Do Sex Ratio Distorting Microbes Inhibit the Evolution of Pesticide Resistance? An Experimental Test.

We are still largely reliant on pesticides for the suppression of arthropod pests which threaten human health and food production, but the recent rise of evolved resistance among important pest species has reduced pesticide efficacy. Despite this, our understanding of strategies that effectively limit the evolution of resistance remains weak. Male-killing sex ratio distorting microbes (SRDMs), such as Wolbachia and Spiroplasma, are common among arthropod species. Previous theoretical work has suggested that they could limit adaptive potential in two ways: first, because by distorting sex ratios they reduce the effective population size, and second, because infected females produce no male offspring which restricts gene flow. Here we present the results of a novel experiment in which we test the extent by which these two mechanisms limit the adaptive response of arthropods to pesticide. Using a fully factorial design, we manipulated the adult sex ratio of laboratory populations of Drosophila melanogaster, both in the presence and absence of SRDMs, and exposed these populations to six generations of pesticide poisoning. This design allows the effects of SRDMs on sex ratio and their effects on gene flow to be estimated separately. After six generations, individuals from populations with even sex ratios displayed a higher resistance to pesticide relative to individuals from female-biased populations. By contrast, we found no effect of the presence of SRDMs in host populations on pesticide resistance independent of sex ratio. In addition, males were more susceptible to pesticide than females-this was true of flies from both naïve and previously exposed populations. These findings provide the first empirical proof of concept that sex ratio distortion arising from SRDMs can limit adaptation to pesticides, but cast doubt on the theoretical effect of male-killers limiting adaptation by disrupting gene flow.

Histone H3-K27 and H3-K9 methylation does not predict lifespan in divergent populations of Drosophila melanogaster

A universal theory of aging remains elusive despite decades of research. Traditional gerontological research has focused on genetic alterations as the driving unit of the aging processes. Recent breakthroughs in cellular reprogramming, transgenerational epigenetic inheritance, and molecular aging clocks have motivated theories proposing that the disruption of epigenetic regulation is the proximal cause of aging. The claim that aging is fundamentally an epigenetic process, however, is largely based on studies using clonal cell populations and genetically identical organisms. Consequently, there has been limited experimental evidence demonstrating the correlation between epigenetic differences and longevity differences among genetically diverse populations. To address this gap in literature we leveraged laboratory populations of the model organism Drosophila melanogaster. Using sister populations with evolved differences in longevity after more than 1 500 generations of divergent life history selection, we measured the methylation at the H3K27 and H3K9 sites which have previously been shown to become dysregulated with age. Here we report that there were no differences in the amount of H3K27me3 or H3K9me2 between 3 replicate population pairs of the divergent lines. These results do not support that epigenetic dysregulation is the underlying cause of aging. Future studies investigating additional indicators of epigenetic dysregulation are required to clarify the role of epigenetics in aging.

Continuously fluctuating selection reveals fine granularity of adaptation.

Temporally fluctuating environmental conditions are a ubiquitous feature of natural habitats. Yet, how finely natural populations adaptively track fluctuating selection pressures via shifts in standing genetic variation is unknown1,2. Here we generated genome-wide allele frequency data every 1-2 generations from a genetically diverse population of Drosophila melanogaster in extensively replicated field mesocosms from late June to mid-December (a period of approximately 12 total generations). Adaptation throughout the fundamental ecological phases of population expansion, peak density and collapse was underpinned by extremely rapid, parallel changes in genomic variation across replicates. Yet, the dominant direction of selection fluctuated repeatedly, even within each of these ecological phases. Comparing patterns of change in allele frequency to an independent dataset procured from the same experimental system demonstrated that the targets of selection are predictable across years. In concert, our results reveala fitness relevance of standing variation that is likely to be masked by inference approaches based on static population sampling or insufficiently resolved time-series data. We propose that such fine-scaled, temporally fluctuating selection may be an important force contributing to the maintenance of functional genetic variation in natural populations and an important stochastic force impacting genome-wide patterns of diversity at linked neutral sites, akin to genetic draft.

Assessing the role of mitonuclear interactions on mitochondrial function and organismal fitness in natural Drosophila populations.

Mitochondrial function depends on the effective interactions between proteins and RNA encoded by the mitochondrial and nuclear genomes. Evidence suggests that both genomes respond to thermal selection and promote adaptation. However, the contribution of their epistatic interactions to life history phenotypes in the wild remains elusive. We investigated the evolutionary implications of mitonuclear interactions in a real-world scenario that sees populations adapted to different environments, altering their geographical distribution while experiencing flow and admixture. We created a Drosophila melanogaster panel with replicate native populations from the ends of the Australian east-coast cline, into which we substituted the mtDNA haplotypes that were either predominant or rare at each cline-end, thus creating putatively mitonuclear matched and mismatched populations. Our results suggest that mismatching may impact phenotype, with populations harboring the rarer mtDNA haplotype suffering a trade-off between aerobic capacity and key fitness aspects such as reproduction, growth, and survival. We discuss the significance of mitonuclear interactions as modulators of life history phenotypes in the context of future adaptation and population persistence.

Selection for greater dispersal in early life increases rate of age-dependent decline in locomotor activity and shortens lifespan.

Locomotor activity is one of the major traits that is affected by age. Greater locomotor activity is also known to evolve in the course of dispersal evolution. However, the impact of dispersal evolution on the functional senescence of locomotor activity is largely unknown. We addressed this knowledge gap using large outbred populations of Drosophila melanogaster selected for increased dispersal. We tracked locomotor activity of these flies at regular intervals until a late age. The longevity of these flies was also recorded. We found that locomotor activity declines with age in general. However interestingly, the activity level of dispersal-selected populations never drops below the ancestry-matched controls, despite the rate of age-dependent decline in activity of the dispersal-selected populations being greater than their respective controls. The dispersal-selected population was also found to have a shorter lifespan as compared to its control, a potential cost of elevated level of activity throughout their life. These results are crucial in the context of invasion biology as contemporary climate change, habitat degradation, and destruction provide congenial conditions for dispersal evolution. Such controlled and tractable studies investigating the ageing pattern of important functional traits are important in the field of biogerontology as well.

Monitoring of the nAChRsα6 G275A spinetoram resistance allele in Drosophila melanogaster populations from New York vineyards.

Spinosyns are a group of naturally occurring and semi-synthetic insecticides with widespread utility in agriculture, including organic production systems. One example is spinetoram (Delegate), which is the only registered insecticide in New York State (for control of Drosophila melanogaster in vineyards) to which vinegar flies have not yet evolved high levels of resistance. However, low levels of resistance have been found in vineyard populations of D. melanogaster, and a highly resistant strain was obtained after only five selections (in the laboratory). We identified the nAChR α6 mutation (G275A) responsible for the resistance and developed a rapid, high-throughput assay for resistance. Surveys of collections made in 2023 show low levels of the resistance allele in four populations. A correlation was observed between vineyard use of spinetoram and frequency of the resistance allele, but not between county-wide use of spinosyns and frequency of the resistance allele. One of the sites we monitored was previously surveyed in 2019 and the frequency of the resistance allele detected in 2023 had increased. Implications of these findings to resistance management of D. melanogaster are discussed. © 2024 Society of Chemical Industry.

Evolution and development of Drosophila melanogaster under different thermal conditions affected cell sizes and sensitivity to paralyzing hypoxia

Environmental gradients cause evolutionary and developmental changes in the cellular composition of organisms, but the physiological consequences of these effects are not well understood. Here, we studied experimental populations of Drosophila melanogaster that had evolved in one of three selective regimes: constant 16 °C, constant 25 °C, or intergenerational shifts between 16 °C and 25 °C. Genotypes from each population were reared at three developmental temperatures (16 °C, 20.5 °C, and 25 °C). As adults, we measured thorax length and cell sizes in the Malpighian tubules and wing epithelia of flies from each combination of evolutionary and developmental temperatures. We also exposed flies from these treatments to a short period of nearly complete oxygen deprivation to measure hypoxia tolerance. For genotypes from any selective regime, development at a higher temperature resulted in smaller flies with smaller cells, regardless of the tissue. At every developmental temperature, genotypes from the warm selective regime had smaller bodies and smaller wing cells but had larger tubule cells than did genotypes from the cold selective regime. Genotypes from the fluctuating selective regime were similar in size to those from the cold selective regime, but their cells of either tissue were the smallest among the three regimes. Evolutionary and developmental treatments interactively affected a fly’s sensitivity to short-term paralyzing hypoxia. Genotypes from the cold selective regime were less sensitive to hypoxia after developing at a higher temperature. Genotypes from the other selective regimes were more sensitive to hypoxia after developing at a higher temperature. Our results show that thermal conditions can trigger evolutionary and developmental shifts in cell size, coupled with changes in body size and hypoxia tolerance. These patterns suggest links between the cellular composition of the body, levels of hypoxia within cells, and the energetic cost of tissue maintenance. However, the patterns can be only partially explained by existing theories about the role of cell size in tissue oxygenation and metabolic performance.

Polymorphism-Aware Models in RevBayes: Species Trees, Disentangling Balancing Selection, and GC-Biased Gene Conversion.

The role of balancing selection is a long-standing evolutionary puzzle. Balancing selection is a crucial evolutionary process that maintains genetic variation (polymorphism) over extended periods of time; however, detecting it poses a significant challenge. Building upon the Polymorphism-aware phylogenetic Models (PoMos) framework rooted in the Moran model, we introduce a PoMoBalance model. This novel approach is designed to disentangle the interplay of mutation, genetic drift, and directional selection (GC-biased gene conversion), along with the previously unexplored balancing selection pressures on ultra-long timescales comparable with species divergence times by analyzing multi-individual genomic and phylogenetic divergence data. Implemented in the open-source RevBayes Bayesian framework, PoMoBalance offers a versatile tool for inferring phylogenetic trees as well as quantifying various selective pressures. The novel aspect of our approach in studying balancing selection lies in polymorphism-aware phylogenetic models' ability to account for ancestral polymorphisms and incorporate parameters that measure frequency-dependent selection, allowing us to determine the strength of the effect and exact frequencies under selection. We implemented validation tests and assessed the model on the data simulated with SLiM and a custom Moran model simulator. Real sequence analysis of Drosophila populations reveals insights into the evolutionary dynamics of regions subject to frequency-dependent balancing selection, particularly in the context of sex-limited color dimorphism in Drosophila erecta.

Integrating mRNA transcripts and genomic information into genomic prediction.

Genomic prediction has emerged as a pivotal technology for the genetic evaluation of livestock, crops, and for predicting human disease risks. However, classical genomic prediction methods face challenges in incorporating biological prior information such as the genetic regulation mechanisms of traits. This study introduces a novel approach that integrates mRNA transcript information to predict complex trait phenotypes. To evaluate the accuracy of the new method, we utilized a Drosophila population that is widely employed in quantitative genetics researches globally. Results indicate that integrating mRNA transcript data can significantly enhance the genomic prediction accuracy for certain traits, though it does not improve phenotype prediction accuracy for all traits. Compared with GBLUP, the prediction accuracy for olfactory response to dCarvone in male Drosophila increased from 0.256 to 0.274. Similarly, the accuracy for cafe in male Drosophila rose from 0.355 to 0.401. The prediction accuracy for survival_paraquat in male Drosophila is improved from 0.101 to 0.138. In female Drosophila, the accuracy of olfactory response to 1hexanol increased from 0.147 to 0.210. In conclusion, integrating mRNA transcripts can substantially improve genomic prediction accuracy of certain traits by up to 43%, with range of 7% to 43%. Furthermore, for some traits, considering interaction effects along with mRNA transcript integration can lead to even higher prediction accuracy.

The neurodevelopmental genes alan shepard and Neuroglian contribute to female mate preference in African Drosophila melanogaster.

Mate choice is a key trait that determines fitness for most sexually reproducing organisms, with females often being the choosy sex. Female preference often results in strong selection on male traits that can drive rapid divergence of traits and preferences between lineages, leading to reproductive isolation. Despite this fundamental property of female mate choice, very few loci have been identified that contribute to mate choice and reproductive isolation. We used a combination of population genetics, quantitative complementation tests, and behavioural assays to demonstrate that alan shepard and Neuroglian contribute to female mate choice, and could contribute to partial reproductive isolation between populations of Drosophila melanogaster. Our study is among the first to identify genes that contribute to female mate preference in this historically important system, where female preference is an active premating barrier to reproduction. The identification of loci that are primarily known for their roles in neurodevelopment provides intriguing questions of how female mate preference evolves in populations via changes in sensory system and higher learning brain centres.

Modeling Length Changes in De Novo Open Reading Frames during Neutral Evolution.

For protein coding genes to emerge de novo from a non-genic DNA, the DNA sequence must gain an open reading frame (ORF) and the ability to be transcribed. The newborn de novo gene can further evolve to accumulate changes in its sequence. Consequently, it can also elongate or shrink with time. Existing literature shows that older de novo genes have longer ORF, but it is not clear if they elongated with time or remained of the same length since their inception. To address this question we developed a mathematical model of ORF elongation as a Markov-jump process, and show that ORFs tend to keep their length in short evolutionary timescales. We also show that if change occurs it is likely to be a truncation. Our genomics and transcriptomics data analyses of seven Drosophila melanogaster populations are also in agreement with the model's prediction. We conclude that selection could facilitate ORF length extension that may explain why longer ORFs were observed in old de novo genes in studies analysing longer evolutionary time scales. Alternatively, shorter ORFs may be purged because they may be less likely to yield functional proteins.

Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection.

Inferring the demographic history of populations provides fundamental insights into species dynamics and is essential for developing a null model to accurately study selective processes. However, background selection and selective sweeps can produce genomic signatures at linked sites that mimic or mask signals associated with historical population size change. While the theoretical biases introduced by the linked effects of selection have been well established, it is unclear whether ancestral recombination graph (ARG)-based approaches to demographic inference in typical empirical analyses are susceptible to misinference due to these effects. To address this, we developed highly realistic forward simulations of human and Drosophila melanogaster populations, including empirically estimated variability of gene density, mutation rates, recombination rates, purifying, and positive selection, across different historical demographic scenarios, to broadly assess the impact of selection on demographic inference using a genealogy-based approach. Our results indicate that the linked effects of selection minimally impact demographic inference for human populations, although it could cause misinference in populations with similar genome architecture and population parameters experiencing more frequent recurrent sweeps. We found that accurate demographic inference of D. melanogaster populations by ARG-based methods is compromised by the presence of pervasive background selection alone, leading to spurious inferences of recent population expansion, which may be further worsened by recurrent sweeps, depending on the proportion and strength of beneficial mutations. Caution and additional testing with species-specific simulations are needed when inferring population history with non-human populations using ARG-based approaches to avoid misinference due to the linked effects of selection.

A Metabolomic Approach to Investigate the Effect of Phytonutrients on Proteostasis and Metabolic Pathways in Drosophila melanogaster

AbstractThe use of Drosophila melanogaster as a biological platform to study the effect of diet and food bioactives on the metabolome remains a highly unexplored subject. Aiming to establish alternative solutions for the investigation of nutritional interventions with bioactive natural products by employing LC-MS-based metabolomics approaches, we assessed the effect of a phytonutrient-rich extract from the endemic Mediterranean plant Cichorium spinosum (stamnagkàthi) on a Drosophila population. The extractʼs modulating effect on the proteostasis network and metabolism of young D. melanogaster flies was evaluated. Furthermore, an untargeted metabolomics approach, employing a C18 UPLC-ESI-Orbitrap-HRMS/MS platform, permitted the detection of several biomarkers in the metabolic profile of Drosophila’s tissues; while targeted amino acid quantification in Drosophila tissue was simultaneously performed by employing aTRAQ labeling and an ion-pairing UPLC-ESI-SWATH-HRMS/MS platform. The detected metabolites belong to different chemical classes, and statistical analysis with chemometrics tools was utilized to reveal patterns and trends, as well as to uncover potential class-distinguishing features and possible biomarkers. Our findings suggest that Drosophila can serve as a valuable in vivo model for investigating the role of bioactive phytoconstituents, like those found in C. spinosum’s decoction, on diverse metabolic processes. Additionally, the fruit fly represents a highly effective platform to investigate the molecular mechanisms underlying sex differences in diverse aspects of nutrition and physiology in higher metazoans.

Spatial structure imposes sex-specific costs but does not reduce interlocus sexual conflict

Abstract Spatial structure is a common feature of all naturally occurring populations. Theoretically, spatial structuring of a habitat could modulate the intensity of interlocus sexual conflict (ISC) in a population, possibly by modulating intersexual encounter rate. We tested this theory using laboratory populations of Drosophila melanogaster by measuring male-induced decline in female fitness in three-patch habitat systems with two alternative habitat types: structured–interconnected and unstructured. Our results on reproductive and survival costs in females suggested significant costs attributable to male presence (i.e. ISC) and to living on structured habitat. However, there was only weak evidence supporting the theory of modulation of ISC by habitat structuring only. Through a follow-up experiment, we also showed that the effect of habitat on ISC is robust to the alteration of female conditions. Therefore, it appears that spatial structuring per se is unlikely to modulate ISC but can impose additional survival costs. We also showed that this survival cost could be sex specific, possibly reflecting female-biased spontaneous dispersal.

Natural Diversity of Cuticular Pheromones in a Local Population of Drosophila after Laboratory Acclimation.

Experimental studies of insects are often based on strains raised for many generations in constant laboratory conditions. However, laboratory acclimation could reduce species diversity reflecting adaptation to varied natural niches. Hydrocarbons covering the insect cuticle (cuticular hydrocarbons; CHCs) are reliable adaptation markers. They are involved in dehydration reduction and protection against harmful factors. CHCs can also be involved in chemical communication principally related to reproduction. However, the diversity of CHC profiles in nature and their evolution in the laboratory have rarely been investigated. Here, we sampled CHC natural diversity in Drosophila melanogaster flies from a particular location in a temperate region. We also measured cis-Vaccenyl acetate, a male-specific volatile pheromone. After trapping flies using varied fruit baits, we set up 21 D. melanogaster lines and analysed their pheromones at capture and after 1 to 40 generations in the laboratory. Under laboratory conditions, the broad initial pheromonal diversity found in male and female flies rapidly changed and became more limited. In some females, we detected CHCs only reported in tropical populations: the presence of flies with a novel CHC profile may reflect the rapid adaptation of this cosmopolitan species to global warming in a temperate area.

Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species.

The X chromosome, being hemizygous in males, is exposed one-third of the time increasing the visibility of new mutations to natural selection, potentially leading to different evolutionary dynamics than autosomes. Recently, we found an enrichment of hard selective sweeps over soft selective sweeps on the X chromosome relative to the autosomes in a North American population of Drosophila melanogaster. To understand whether this enrichment is a universal feature of evolution on the X chromosome, we analyze diversity patterns across 6 commonly studied Drosophila species. We find an increased proportion of regions with steep reductions in diversity and elevated homozygosity on the X chromosome compared to autosomes. To assess if these signatures are consistent with positive selection, we simulate a wide variety of evolutionary scenarios spanning variations in demography, mutation rate, recombination rate, background selection, hard sweeps, and soft sweeps and find that the diversity patterns observed on the X are most consistent with hard sweeps. Our findings highlight the importance of sex chromosomes in driving evolutionary processes and suggest that hard sweeps have played a significant role in shaping diversity patterns on the X chromosome across multiple Drosophila species.