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opencc-by-4.0Apr 2020View details →

Dataset for "Metabolic rate and oxygen radical levels increase but radical generation rate decreases with male age in Drosophila melanogaster sperm"

Metabolic rate, H2O2 level, and ROS production data for D. melanogaster sperm and gut tissue

opencc-zeroMay 2020View details →

Data from: Thoracic underreplication in Drosophila species estimates a minimum genome size and the dynamics of added DNA

Many cells in the thorax of Drosophila were found to stall during replication, a phenomenon known as underreplication. Unlike underreplication in nuclei of salivary and follicle cells, this stall occurs with less than one complete round of replication. This stall point allows precise estimations of early-replicating euchromatin and late-replicating heterochromatin regions, providing a powerful tool to investigate the dynamics of structural change across the genome. We measure underreplication in 132 species across the Drosophila genus and leverage this data to propose a model for estimating the rate at which additional DNA is accumulated as heterochromatin and euchromatin and also predict the minimum genome size for Drosophila. According to comparative phylogenetic approaches, the rates of change of heterochromatin differ strikingly between Drosophila subgenera. While these subgenera differ in karyotype, there were no differences by chromosome number, suggesting other structural changes may influence accumulation of heterochromatin. Measurements were taken for both sexes, allowing the visualization of genome size and heterochromatin changes for the hypothetical path of XY sex chromosome differentiation. Additionally, the model presented here estimates a minimum genome size in Sophophora remarkably close to the smallest insect genome measured to date, in a species over 200 million years diverged from Drosophila.

opencc-zeroJun 2020View details →

Evolution of reduced minimum critical size as a response to selection for rapid pre-adult development in Drosophila melanogaster.

Adult body size in holometabolous insects is directly proportional to the time spent during the larval period. The larval duration can be divided into two parts- (i) pre-critical duration-time required to attain a critical size/critical weight that would result in successful completion of development and metamorphosis even under non-availability of nutrition beyond the time of attainment of critical size, and (ii) post-critical duration-the time duration from attainment of critical size till pupation. It is of interest to decipher the relative contribution of the two larval growth phases (from the hatching of the egg to attainment of critical size or from the attainment of critical size to pupation- post-critical duration) to the final adult size. Many studies using Drosophila melanogaster have shown that, selecting populations for faster development result in the emergence of small adults. Some of these studies have indirectly reported the evolution of smaller critical size. Using two kinds of D. melanogaster populations, one of which is selected for faster/accelerated pre-adult development and the other their ancestral control, we demonstrate that the final adult size is determined by the time spent as larvae post the attainment of critical size despite having increased growth rate during the second larval instar. Our populations under selection for faster per-adult development are exhibiting adaptive-bail out due to intrinsic food limitation as against extrinsic food limitation in the yellow dung fly.

opencc-zeroJun 2020View details →

Data from: Different genetic basis for ADH activity and plasticity in a novel alcohol environment for Drosophila melanogaster

Phenotypic plasticity is known to enhance population persistence (Wang and Althoff, 2019), facilitate adaptive evolution (Levis et al., 2018), and initiate novel phenotypes in novel environments (Levis and Pfennig, 2016). How plasticity can contribute or hinder adaptation to different environments hinges on its genetic architecture. Even though plasticity in many traits is genetically controlled, whether and how plasticity's genetic architecture might change in novel environments is still unclear. Because much of gene expression can be environmentally influenced, each environment may trigger different sets of genes that influence a trait. Using a quantitative trait loci (QTL) approach, we investigated the genetic basis of plasticity in a classic functional trait, alcohol dehydrogenase (ADH) activity in D. melanogaster, across both historical and novel alcohol environments. Previous research in D. melanogaster has also demonstrated that ADH activity is plastic in response to alcohol concentration in substrates used by both adult flies and larvae. We found that across all environments tested, ADH activity was largely influenced by a single QTL encompassing the Adh coding gene and its known regulatory locus, delta-1. After controlling for the allelic variation of the Adh and delta-1 loci, we found additional but different minor QTLs in the 0% and 14% alcohol environments. In contrast, we discovered no major QTL for plasticity itself, including the Adh locus, regardless of the environmental gradients. This suggests that plasticity in ADH activity is likely influenced by many loci with small effects and that the Adh locus is not environmentally sensitive to dietary alcohol.

FIGURE 12 in A Revision of the Drosophila spinipes Species Group (Diptera: Drosophilidae)

FIGURE 12. Aedeagus, aedeagal apodeme, and postgonite for most species in the Drosophila spinipes group, lateral views, all to the same scale. Spicules on the phallus are on the inner (mesal) surface. A. D. suma Burla (HS-01). B. D. malagasy n. sp. (HS- 17). C. D. malagasy n. sp. (HS-20). D. D. malagasy n. sp. (HS-22). E. D. cameroonensis n. sp. (HS- 10). F. D. hypandrilata n. sp. (HS- 38). G. sp. D (HS- 03). H. D. freidbergi n. sp. (HS- 06). I. D. nigrospinipes n. sp. (HS-24). J. D. phalloserra n. sp. (HS-07). K. D. phalloserra n. sp. (HS-08). L. D. phalloserra n. sp. (DMSA 140413).

FIGURE 11 in A Revision of the Drosophila spinipes Species Group (Diptera: Drosophilidae)

FIGURE 11. Distiphallus of most species in the Drosophila spinipes group, ventral view, all to the same scale. A. D. cameroonensis n. sp. (HS-10). B. D. freidbergi n. sp. (HS- 06). C. D. hypandrilata n. sp. (HS-38). D. D. malagasy n. sp. (HS- 20). E. D. malagasy n. sp. (HS- 16). F. D. nigrospinipes n. sp. (HS- 24). G. D. phalloserra n. sp. (HS-08). H. D. phalloserra n. sp. (HS- 07). I. D. phalloserra n. sp. (DMSA 140413). J. D. suma Burla (HS-01). K. sp. D (HS-03).

FIGURE 4 in A Revision of the Drosophila spinipes Species Group (Diptera: Drosophilidae)

FIGURE 4. Photomicrographs, dorsolateral view, of the abdomen of several Drosophila spinipes-group species. A-C. D. malagasy n. sp. A.HS-16. B. HS-22. C. HS-18. D. D. nigrospinipes n. sp. (HS-24). E. D. phalloserra n. sp. (HS-07). F. D. suma Burla (HS-01). G. D. spinipes Lamb (NHMUK 014335955).

FIGURE 2 in A Revision of the Drosophila spinipes Species Group (Diptera: Drosophilidae)

FIGURE 2. Distinct or apomorphic features of the Drosophila spinipes species group. A. Lateral view, sp. C (HS-13). B. Same as A, with detail of mouthparts. C. D. nigrospinipes n. sp. (HS-12), dorsolateral view of thorax, showing setal tubercles and spiracular channel. D. Wing, D. malagasy n. sp. (HS-21). Arrow indicates end of dense costal spinules. E-F. SEM of protarsal spines, mesal view of specimen HS-14 (sp. B). Note the shallow longitudinal grooves.

opencc-zeroJul 2020View details →

Data from: The microbiota influences the Drosophila melanogaster life history strategy

Organisms are locally adapted when members of a population have a fitness advantage in one location relative to conspecifics in other geographies. For example, across latitudinal gradients, some organisms may trade off between traits that maximize fitness components in one, but not both, of somatic maintenance or reproductive output. Latitudinal gradients in life history strategies are traditionally attributed to environmental selection on an animal's genotype, without any consideration of the possible impact of associated microorganisms ("microbiota") on life history traits. Here, we show in Drosophila melanogaster, a key model for studying local adaptation and life history strategy, that excluding the microbiota from definitions of local adaptation is a major shortfall. First, we reveal that an isogenic fly line reared with different bacteria varies the investment in early reproduction versus somatic maintenance. Next, we show that in wild fruit flies, the abundance of these same bacteria was correlated with the latitude and life history strategy of the flies, suggesting geographic specificity of the microbiota composition. Variation in microbiota composition of locally adapted D. melanogaster could be attributed to both the wild environment and host genetic selection. Finally, by eliminating or manipulating the microbiota of fly lines collected across a latitudinal gradient, we reveal that host genotype contributes to latitude-specific life history traits independent of the microbiota and that variation in the microbiota can suppress or reverse the differences between locally adapted fly lines. Together, these findings establish the microbiota composition of a model animal as an essential consideration in local adaptation.

opencc-zeroDec 2018View details →

Data from: Stage- and thermal-specific genetic architecture for preadult viability in natural populations of Drosophila melanogaster

Studying the processes affecting variation for preadult viability is essential to understand the evolutionary trajectories followed by natural populations. This task requires focusing on the complex nature of the phenotype-genotype relationship by taking into account usually neglected aspects of the phenotype and recognizing the modularity between different ontogenetic stages. Here we describe phenotypic variability for viability during the larval and pupal stages in lines derived from three natural populations of Drosophila melanogaster, as well as the variability for phenotypic plasticity and canalization at two different rearing temperatures. The observed phenotypic differences between populations can be attributed both to adaptation to environmental conditions and lack of gene flow between them. According to our results, different aspects of the phenotype (means, plasticity, canalization, plasticity of canalization) are affected by different genetic bases underlying changes in viability in a stage- and environment-specific manner. These findings explain the generalized maintenance of genetic variability for this fitness trait.

opencc-zeroJul 2020View details →

Data from: Neural dysfunction correlates with heat coma and CTmax in Drosophila but does not set the boundaries for heat stress survival

When heated, insects lose coordinated movement followed by the onset of heat coma (critical thermal maximum, CTmax). These traits are popular measures to quantify interspecific and intraspecific differences in insect heat tolerance, and CTmax correlates well with current species distributions of insects, including Drosophila. Here, we examined the function of the central nervous system (CNS) in five species of Drosophila with different heat tolerances, while they were exposed to either constant high temperature or a gradually increasing temperature (ramp). Tolerant species were able to preserve CNS function at higher temperatures and for longer durations than sensitive species, and similar differences were found for the behavioural indices (loss of coordination and onset of heat coma). Furthermore, the timing and temperature (constant and ramp exposure, respectively) for loss of coordination or complete coma coincided with the occurrence of spreading depolarisation (SD) events in the CNS. These SD events disrupt neurological function and silence the CNS, suggesting that CNS failure is the primary cause of impaired coordination and heat coma. Heat mortality occurs soon after heat coma in insects; to examine whether CNS failure could also be the proximal cause of heat death, we used selective heating of the head (CNS) and abdomen (visceral tissues). When comparing the temperature causing 50% mortality (LT50) of each body part versus that of the whole animal, we found that the head was not particularly heat sensitive compared with the abdomen. Accordingly, it is unlikely that nervous failure is the principal/proximate cause of heat mortality in Drosophila.

opencc-zeroDec 2014View details →

Data from: The cost of reinforcement in Drosophila yakuba

When the ranges of two species overlap and the species can hybridize, some individuals may waste gametes on inviable or infertile hybrids. In these cases, enhanced reproductive isolation may evolve as a byproduct of selection against maladaptive hybridization in a process called reinforcement. On the slopes of the African island of São Tomé, Drosophila yakuba and its endemic sister species D. santomea have a well-demarcated hybrid zone. D. yakuba females from within this zone, but not from outside it, show an increase in gametic isolation from males of D. santomea. To understand why reinforced gametic isolation does not spread to the whole geographic range and stays confined to areas of secondary contact, we studied the associated costs of reinforced gametic isolation in D. yakuba by using a combination of natural collections and experimental evolution. We found that D. yakuba males from sympatric populations sire fewer progeny than allopatric males when the female involved in the mating is an allopatric female. The results here shown suggest that the advantageous nature of reinforcement in D. yakuba is local, as its associated costs (i.e., reduced male fertility) might prevent its dispersal outside the hybrid zone.

opencc-zeroJun 2020View details →

Identification of a genetic network for an ecologically relevant behavioral phenotype in Drosophila melanogaster

Pupation site choice of Drosophila third-instar larvae is critical for the survival of individuals, as pupae are exposed to various biotic and abiotic dangers while immobilized during the 3-4 days of metamorphosis. This singular behavioural choice is sensitive to both environmental and genetic factors. Here we developed a high-throughput phenotyping approach to assay the variation in pupation height in Drosophila melanogaster, while controlling for possibly confounding factors. We find substantial variation of mean pupation height among sampled natural stocks and we show that the Drosophila Genetic Reference Panel (DGRP) captures this variation. Using the DGRP stocks for genome wide association (GWA) mapping, 16 loci involved in determining pupation height could be resolved. The candidate genes in these loci are enriched for high expression in the larval central nervous system. A genetic network could be constructed from the candidate loci, which places scrib at the centre, plus other genes known to be involved in nervous system development, such as Egfr and p53. Using gene disruption lines, we could functionally validate several of the initially identified loci, as well as additional loci predicted from network analysis. Our study shows that the combination of high throughput phenotyping with a genetic analysis of variation captured from the wild can be used to approach the genetic dissection of an environmentally relevant behavioural phenotype.

Data from: The dynamic transmission of positional information in stau-mutants during Drosophila embryogenesis.

It has been suggested that Staufen (Stau) is key in controlling the variability of the posterior boundary of the Hb anterior domain (xHb). However, its underlying mechanism is elusive. Here, we quantified the dynamic 3D expression of segmentation genes in Drosophila embryos. With improved control of measurement errors, we show xHb of stau- mutants reproducibly moves posteriorly by 10% of the embryo length (EL) to the wild type (WT) position in the nuclear cycle (nc) 14, and its variability at short time windows is comparable as that of the WT. Moreover, for stau- mutants, the upstream Bicoid (Bcd) gradients show equivalent relative intensity noise to that of the WT in nc12-nc14, and the downstream Even-skipped (Eve) and cephalic furrow (CF) show the same positional errors as the WT. Our results indicate that threshold-dependent activation and self-organized filtering are not mutually exclusive but could both be implemented in early Drosophila embryogenesis.

Dataset and scripts from: Predicting temperature mortality and selection in natural Drosophila populations

The study develops and validates a theoretical model to predict thermal mortality under natural conditions, based on measurements of mortality performed in the laboratory at multiple constant temperatures. The theoretical model first fits a thermal tolerance landscape, which describes how survival probability is affected by both temperature and exposure time, to the empirical measurements of mortality obtained in the laboratory under controlled conditions. Then, employing a numerical approximation to the analytical solution based on differential calculus, it combines this tolerance landscape with ambient temperature records in natural settings to predict the survival probability curve under these thermal conditions. These predictions were validated by contrasting predicted and observed mortality curves in 11 Drosophila species under three different warming rates, reported in the literature, which were virtually indistinguishable. Having validated the model, the study then examines how mortality should be affected by climate change in a natural population of Drosophila subobscura from Santiago, Chile, employing temperature records for this location during 1984 - 1991 and 2014 - 2018. The cumulative mortality predicted from temperature records closely resemble the periods of population collapse recorded for this population during the Austral summer and, according to the model, warming temperatures in the past 30 years may have advanced this period by almost a month. This methodology is highly general and can in principle be employed to predict temperature mortality in small ectotherms under any varying thermal regime.

Dynamic evolution of euchromatic satellites on the X chromosome in Drosophila melanogaster and the simulans clade

ABSTRACTSatellite DNAs (satDNAs) are among the most dynamically evolving components of eukaryotic genomes and play important roles in genome regulation, genome evolution, and speciation. Despite their abundance and functional impact, we know little about the evolutionary dynamics and molecular mechanisms that shape satDNA distributions in genomes. Here we use high-quality genome assemblies to study evolutionary dynamics of two complex satDNAs, Rsp-like and 1.688 gm/cm3, in Drosophila melanogaster and its three nearest relatives in the simulans clade. We show that large blocks of these repeats are highly dynamic in the heterochromatin, where their genomic location varies across species. We discovered that small blocks of satDNA that are abundant in X chromosome euchromatin are similarly dynamic, with repeats changing in abundance, location, and composition among species. We detail the proliferation of a rare satellite (Rsp-like) across the X chromosome in D. simulans and D. mauritiana. Rsp-like spreads by inserting into existing clusters of the older, more abundant 1.688 satellite, in events that were likely facilitated by microhomology-mediated repair pathways. We show that Rsp-like is abundant on extrachromosomal circular DNA in D. simulans, which may have contributed to its dynamic evolution. Intralocus satDNA expansions via unequal exchange and the movement of higher-order repeats also contribute to the fluidity of the repeat landscape. We find evidence that euchromatic satDNA repeats experience cycles of proliferation and diversification somewhat analogous to bursts of transposable element proliferation. Our study lays a foundation for mechanistic studies of satDNA proliferation and the functional and evolutionary consequences of satDNA movement.

opencc-zeroMar 2020View details →

Development and testing of a novel Killer-Rescue self-limiting gene drive system in Drosophila melanogaster

Here we report the development and testing of a novel self-limiting gene drive system, Killer-Rescue, in Drosophila melanogaster. This system is composed of an auto-regulated Gal4 Killer (K) and a Gal4-activated Gal80 Rescue (R). Overexpression of Gal4 is lethal, but in the presence of R activation of Gal80 leads to much lower levels of Gal4 and rescue of lethality. We demonstrate that with a single 2:1 engineered to wildtype release, K drives R through the population and after nine generations more than 98% of the population carry R and less than 2% of the population are wildtype flies. We discuss how this simple Killer-Rescue gene drive system may be readily adapted for population replacement in a human health pest, Aedes aegypti, or for population suppression in an agricultural pest, Drosophila suzukii.

Data from: How gut microbiome interactions affect nutritional traits of Drosophila melanogaster

Most research on the impact of the gut microbiome on animal nutrition is designed to identify the effects of single microbial taxa and single metabolites of microbial origin, without considering the potentially complex network of interactions among co-occurring microorganisms. Here, we investigate how different microbial associations and their fermentation products affect host nutrition, using Drosophila melanogaster colonized with three gut microorganisms (the bacteria Acetobacter fabarum and Lactobacillus brevis and the yeast Hanseniaspora uvarum) in all seven possible combinations. Some microbial effects on host traits could be attributed to single taxa (e.g. yeast-mediated reduction of insect development time), while other effects were sex-specific and driven by among-microbe interactions (e.g. male lipid content determined by interactions between the yeast and both bacteria). Parallel analysis of nutritional indices of microbe-free flies administered different microbial fermentation products (acetic acid, acetoin, ethanol and lactic acid) revealed a single consistent effect: that the lipid content of both male and female flies is reduced by acetic acid. This effect was recapitulated in male flies colonized with both yeast and Acetobacter, but not for any microbial treatment in females nor in males with other microbial complements. These data suggest that the effect of microbial fermentation products on host nutritional status is strongly context-dependent, with respect to both the combination of associated microorganisms and host sex. Taken together, our findings demonstrate that among-microbe interactions can play a critically important role in determining the physiological outcome of host-microbiome interactions in Drosophila and, likely, in other animal hosts.