Bregje Wertheim

Genome-wide gene expression in response to parasitoid attack in Drosophila

BackgroundParasitoids are insect parasites whose larvae develop in the bodies of other insects. The main immune defense against parasitoids is encapsulation of the foreign body by blood cells, which subsequently often melanize. The capsule sequesters and kills the parasite. The molecular processes involved are still poorly understood, especially compared with insect humoral immunity.ResultsWe explored the transcriptional response to parasitoid attack in Drosophila larvae at nine time points following parasitism, hybridizing five biologic replicates per time point to whole-genome microarrays for both parasitized and control larvae. We found significantly different expression profiles for 159 probe sets (representing genes), and we classified them into 16 clusters based on patterns of co-expression. A series of functional annotations were nonrandomly associated with different clusters, including several involving immunity and related functions. We also identified nonrandom associations of transcription factor binding sites for three main regulators of innate immune responses (GATA/srp-like, NF-κB/Rel-like and Stat), as well as a novel putative binding site for an unknown transcription factor. The appearance or absence of candidate genes previously associated with insect immunity in our differentially expressed gene set was surveyed.ConclusionMost genes that exhibited altered expression following parasitoid attack differed from those induced during antimicrobial immune responses, and had not previously been associated with defense. Applying bioinformatic techniques contributed toward a description of the encapsulation response as an integrated system, identifying putative regulators of co-expressed and functionally related genes. Genome-wide studies such as ours are a powerful first approach to investigating novel genes involved in invertebrate immunity.

Quantification of food intake in Drosophila

Measurement of food intake in the fruit fly Drosophila melanogaster is often necessary for studies of behaviour, nutrition and drug administration. There is no reliable and agreed method for measuring food intake of flies in undisturbed, steady state, and normal culture conditions. We report such a method, based on measurement of feeding frequency by proboscis-extension, validated by short-term measurements of food dye intake. We used the method to demonstrate that (a) female flies feed more frequently than males, (b) flies feed more often when housed in larger groups and (c) fly feeding varies at different times of the day. We also show that alterations in food intake are not induced by dietary restriction or by a null mutation of the fly insulin receptor substrate chico. In contrast, mutation of takeout increases food intake by increasing feeding frequency while mutation of ovoD increases food intake by increasing the volume of food consumed per proboscis-extension. This approach provides a practical and reliable method for quantification of food intake in Drosophila under normal, undisturbed culture conditions.

Allee effect in larval resource exploitation in Drosophila : an interaction among density of adults, larvae, and micro-organisms

Abstract 1. Aggregation pheromones can evolve when individuals benefit from clustering. Such a situation can arise with an Allee effect, i.e. a positive relationship between individual fitness and density of conspecifics. Aggregation pheromone in Drosophila induces aggregated oviposition. The aim of the work reported here was to identify an Allee effect in the larval resource exploitation by Drosophila melanogaster, which could explain the evolution of aggregation pheromone in this species.

Ejaculate depletion patterns evolve in response to experimental manipulation of sex ratio in Drosophila melanogaster

Abstract We assessed the extent to which traits related to ejaculate investment have evolved in lines of Drosophila melanogaster that had an evolutionary history of maintenance at biased sex ratios. Measures of ejaculate investment were made in males that had been maintained at male-biased (MB) and female-biased (FB) adult sex ratios, in which levels of sperm competition were high and low, respectively. Theory predicts that when the risk of sperm competition is high and mating opportunities are rare (as they are for males in the MB populations), males should increase investment in their few matings. We therefore predicted that males from the MB lines would (1) exhibit increased investment in their first mating opportunities and (2) deplete their ejaculates at a faster rate when mating multiply, in comparison to FB males. To investigate these predictions we measured the single mating productivity of males from three replicates each of MB and FB lines mated to five wild-type virgin females in succession. In contrast to the first prediction, there was no evidence for differences in productivity between MB and FB line males in their first matings. The second prediction was upheld: mates of MB and FB males suffered increasingly reduced productivity with successive matings, but the decline was significantly more pronounced for MB than for FB males. There was a significant reduction in the size of the accessory glands and testes of males from the MB and FB regimes after five successive matings. However, the accessory glands, but not testes, of MB males became depleted at a significantly faster rate than those of FB males. The results show that male reproductive traits evolved in response to the level of sperm competition and suggest that the ability to maintain fertility over successive matings is associated with the rate of ejaculate, and particularly accessory gland, depletion.

The interaction between dispersal, the Allee effect and scramble competition affects population dynamics

Many organisms experience an Allee effect: their populations do not grow optimally at low densities. In addition, individuals compete with one another at high densities. The Allee effect and competition thus create a lower and an upper bound to local population size. Local populations can, however, be connected through dispersal. By using a spatio-temporal integro-difference simulation model, parameterized for Drosophila melanogaster, we explore the consequences of the Allee effect, scramble competition and dispersal for different combinations of resource distributions, initial adult distributions and densities, modes of dispersal and boundary conditions. We found that the initial distribution and density of adults determines whether a population can establish, while resource availability, the ability to reach resources and heterogeneity are mainly responsible for subsequent population persistence. In our model heterogeneity was introduced by the distribution of resources, the initial adult distribution, and the boundary conditions. Although local population dynamics are inherently unstable, overall stability can be attained by (re)colonization processes. The averaged dynamics of the total population turned out to be reasonably smooth, so apparently upper and lower local population bounds, coupled with dispersal, created an effective stable mean population density for the system as a whole. This suggests that stable mean population densities for spatial populations can be emergent properties appearing at sufficiently large scales, as opposed to inherent properties occurring at all scales. We also found, in agreement with most literature but contrary to some recent literature, that population persistence can be facilitated by a leptokurtic dispersal mode, which has higher probabilities of traveling both short and long distances, but smaller probability of traveling intermediate distances than random dispersal.

The mode of evolution of aggregation pheromones in Drosophila species

Aggregation pheromones are used by fruit flies of the genus Drosophila to assemble on breeding substrates, where they feed, mate and oviposit communally. These pheromones consist of species‐specific blends of chemicals. Here, using a phylogenetic framework, we examine how differences among species in these pheromone blends have evolved. Theoretical predictions, genetic evidence, and previous empirical analysis of bark beetle species, suggest that aggregation pheromones do not evolve gradually, but via major, saltational shifts in chemical composition. Using pheromone data for 28 species of Drosophila we show that, unlike with bark beetles, the distribution of chemical components among species is highly congruent with their phylogeny, with closely related species being more similar in their pheromone blends than are distantly related species. This pattern is also strong within the melanogaster species group, but less so within the virilis species group. Our analysis strongly suggests that the aggregation pheromones of Drosophila exhibit a gradual, not saltational, mode of evolution. We propose that these findings reflect the function of the pheromones in the ecology of Drosophila, which does not hinge on species specificity of aggregation pheromones as signals.

Behavioural plasticity in support of a benefit for aggregation pheromone use in Drosophila melanogaster

We explored behavioural plasticity in the use of aggregation pheromone in the fruit fly Drosophila melanogaster Meigen (Diptera: Drosophilidae). Based on previous field observations, we formulated two hypotheses on a benefit of using aggregation pheromone for aggregated oviposition. One hypothesis concerns a benefit to the females themselves, where reduced harassment by males can enhance oviposition rate; the other concerns a benefit to their offspring, where larvae can exploit arduous substrates more efficiently. We derive contrasting expectations on the strength of the behavioural response to pheromone for substrates that differ in nutritional quality to larvae. High quality substrates relax the strength of larval competition, which allows for stronger aggregative responses of the females, but conversely, it may yield aggregation less necessary when the benefit is related to resource exploitation by the larvae. In indoor and outdoor dual choice set‐ups, we tested the behavioural responses of the adults to the aggregation pheromone with substrates of varying quality, and examined oviposition behaviour. The response of adults to the aggregation pheromone was strong and robust for low quality substrates, but significantly weaker for a high quality substrate. This supports the hypothesis on a benefit to the larvae. Females retained aggregation pheromones in the absence of oviposition substrates for at least 24 h. In the outdoor set‐up, substrate with aggregation pheromone received more than three times as many eggs as control substrates, and this was directly related to the number of adults that visited each substrate. Per capita, oviposition rates were not different for differently sized aggregations, and consequently, no evidence was found in support of the hypothesis on reduced harassment. The combination of aggregation pheromone possession and a mutualistic relationship with micro‐organisms for Drosophila and other insects is discussed.

Evolution of a Cellular Immune Response in Drosophila: A Phenotypic and Genomic Comparative Analysis

Understanding the genomic basis of evolutionary adaptation requires insight into the molecular basis underlying phenotypic variation. However, even changes in molecular pathways associated with extreme variation, gains and losses of specific phenotypes, remain largely uncharacterized. Here, we investigate the large interspecific differences in the ability to survive infection by parasitoids across 11 Drosophila species and identify genomic changes associated with gains and losses of parasitoid resistance. We show that a cellular immune defense, encapsulation, and the production of a specialized blood cell, lamellocytes, are restricted to a sublineage of Drosophila, but that encapsulation is absent in one species of this sublineage, Drosophila sechellia. Our comparative analyses of hemopoiesis pathway genes and of genes differentially expressed during the encapsulation response revealed that hemopoiesis-associated genes are highly conserved and present in all species independently of their resistance. In contrast, 11 genes that are differentially expressed during the response to parasitoids are novel genes, specific to the Drosophila sublineage capable of lamellocyte-mediated encapsulation. These novel genes, which are predominantly expressed in hemocytes, arose via duplications, whereby five of them also showed signatures of positive selection, as expected if they were recruited for new functions. Three of these novel genes further showed large-scale and presumably loss-of-function sequence changes in D. sechellia, consistent with the loss of resistance in this species. In combination, these convergent lines of evidence suggest that co-option of duplicated genes in existing pathways and subsequent neofunctionalization are likely to have contributed to the evolution of the lamellocyte-mediated encapsulation in Drosophila.

Polyploidy in Animals: Effects of Gene Expression on Sex Determination, Evolution and Ecology

Polyploidy is rarer in animals than in plants. Why? Since Mullers observation in 1925, many hypotheses have been proposed and tested, but none were able to completely explain this intriguing fact. New genomic technologies enable the study of whole genomes to explain the constraints on or consequences of polyploidization, rather than focusing on specific genes or life history characteristics. Here, we review a selection of old and recent literature on polyploidy in animals, with emphasis on the consequences of polyploidization for gene expression patterns and genomic network interactions. We propose a conceptual model to contrast various scenarios for changes in genomic networks, which may serve as a framework to explain the different evolutionary dynamics of polyploidy in animals and plants. We also present new insights of genetic sex determination in animals and our emerging understanding of how animal sex determination systems may hamper or enable polyploidization, including some recent data on haplodiploids. We discuss the role of polyploidy in evolution and ecology, using a gene regulation perspective, and conclude with a synopsis regarding the effects of whole genome duplications on the balance of genomic networks. See also the sister articles focusing on plants by Ashman et al. and Madlung and Wendel in this themed issue.

Genomic changes under rapid evolution: selection for parasitoid resistance

In this study, we characterize changes in the genome during a swift evolutionary adaptation, by combining experimental selection with high-throughput sequencing. We imposed strong experimental selection on an ecologically relevant trait, parasitoid resistance in Drosophila melanogaster against Asobara tabida. Replicated selection lines rapidly evolved towards enhanced immunity. Larval survival after parasitization increased twofold after just five generations of selection. Whole-genome sequencing revealed that the fast and strong selection response in innate immunity produced multiple, highly localized genomic changes. We identified narrow genomic regions carrying a significant signature of selection, which were present across all chromosomes and covered in total less than 5% of the whole D. melanogaster genome. We identified segregating sites with highly significant changes in frequency between control and selection lines that fell within these narrow ‘selected regions’. These segregating sites were associated with 42 genes that constitute possible targets of selection. A region on chromosome 2R was highly enriched in significant segregating sites and may be of major effect on parasitoid defence. The high genetic variability and small linkage blocks in our base population are likely responsible for allowing this complex trait to evolve without causing widespread erosive effects in the genome, even under such a fast and strong selective regime.