Increased transmission of mutations by low-condition females: evidence for condition-dependent DNA repair

Evidence is mounting that mutation rates are sufficiently high for deleterious alleles to be a major evolutionary force affecting the evolution of sex, the maintenance of genetic variation, and many other evolutionary phenomena. Though point estimates of mutation rates are improving, we remain largely ignorant of the biological factors affecting these rates at the individual level. Of special importance is the possibility that mutation rates are condition-dependent with low-condition individuals experiencing more mutation. Theory predicts that such condition dependence would dramatically increase the rate at which populations adapt to new environments and the extent to which populations suffer from mutation load. Despite its importance, there has been little study of this phenomenon in multicellular organisms. Here, we examine whether DNA repair processes are condition-dependent in Drosophila melanogaster. In this species, damaged DNA in sperm can be repaired by maternal repair processes after fertilization. We exposed high- and low-condition females to sperm containing damaged DNA and then assessed the frequency of lethal mutations on paternally derived X chromosomes transmitted by these females. The rate of lethal mutations transmitted by low-condition females was 30% greater than that of high-condition females, indicating reduced repair capacity of low-condition females. A separate experiment provided no support for an alternative hypothesis based on sperm selection.     

High-density populations of diamondback moth have broader host-plant diets

Although ecological specialists exploit a relatively limited resource base, it is unclear whether specialization limits local population density. Here, we focus on the relationship between diet specialization and local population density of a phytophagous insect, the diamondback moth, Plutella xylostella L. (Lepidoptera: Plutellidae). We compared key life history traits and food plant use among five pairs of high- and low-density populations from widely separate geographical areas. Moths from populations that persist at high densities were more generalized in food plant use than moths from low-density populations. In particular, the oviposition preference and larval performance of moths from some high-density populations were less variable across a suite of food plants, suggesting that moths from high- density populations had a broader diet. In addition, low- density populations were less similar to each other, exhibiting opposing preferences for particular plant species. Hence diet breadth may explain some of the persistent differences in the population density of diamondback moths in the field, consistent with the idea that ecological specialization may be generally associated with population density. Received: 19 December 1996 / Accepted: 2 May 1997     

Fitness consequences of larval traits persist across the metamorphic boundary

Metamorphosis is thought to provide an adaptive decoupling between traits specialized for each life-history stage in species with complex life cycles. However, an increasing number of studies are finding that larval traits can carry-over to influence postmetamorphic performance, suggesting that these life-history stages may not be free to evolve independently of each other. We used a phenotypic selection framework to compare the relative and interactive effects of larval size, time to hatching, and time to settlement on postmetamorphic survival and growth in a marine invertebrate, Styela plicata. Time to hatching was the only larval trait found to be under directional selection, individuals that took more time to hatch into larvae survived better after metamorphosis but grew more slowly. Nonlinear selection was found to act on multivariate trait combinations, once again acting in opposite directions for selection acting via survival and growth. Individuals with above average values of larval traits were most likely to survive, but surviving individuals with intermediate larval traits grew to the largest size. These results demonstrate that larval traits can have multiple, complex fitness consequences that persist across the metamorphic boundary; and thus postmetamorphic selection pressures may constrain the evolution of larval traits.     

Transgenerational Effects of Early Life Starvation on Growth,Reproduction, and Stress Resistance in Caenorhabditis elegans

Starvation during early development can have lasting effects that influence organismal fitness and disease risk. We characterized the long-term phenotypic consequences of starvation during early larval development in Caenorhabditis elegans to determine potential fitness effects and develop it as a model for mechanistic studies. We varied the amount of time that larvae were developmentally arrested by starvation after hatching (“L1 arrest”). Worms recovering from extended starvation grew slowly, taking longer to become reproductive, and were smaller as adults. Fecundity was also reduced, with the smallest individuals most severely affected. Feeding behavior was impaired, possibly contributing to deficits in growth and reproduction. Previously starved larvae were more sensitive to subsequent starvation, suggesting decreased fitness even in poor conditions. We discovered that smaller larvae are more resistant to heat, but this correlation does not require passage through L1 arrest. The progeny of starved animals were also adversely affected: Embryo quality was diminished, incidence of males was increased, progeny were smaller, and their brood size was reduced. However, the progeny and grandprogeny of starved larvae were more resistant to starvation. In addition, the progeny, grandprogeny, and great-grandprogeny were more resistant to heat, suggesting epigenetic inheritance of acquired resistance to starvation and heat. Notably, such resistance was inherited exclusively from individuals most severely affected by starvation in the first generation, suggesting an evolutionary bet-hedging strategy. In summary, our results demonstrate that starvation affects a variety of life-history traits in the exposed animals and their descendants, some presumably reflecting fitness costs but others potentially adaptive.     

Effects of induced variation in anuran larval development on postmetamorphic energy reserves and locomotion

Anuran larvae exhibit high levels of phenotypic plasticity in growth and developmental rates in response to variation in temperature and food availability. We tested the hypothesis that alteration of developmental pathways during the aquatic larval stage should affect the postmetamorphic performance of the Iberian painted frog (Discoglossus galganoi). We exposed tadpoles to different temperatures and food types (animal- vs. plant-based diets) to induce variation in the length of the larval period and body size at metamorphosis. In this species, larval period varied with temperature but was unaffected by diet composition. In contrast, size at metamorphosis was shaped by the interaction between food quality and temperature; tadpoles fed on an animal-based diet became bulkier metamorphs than those fed on plant-based food at high (22°C) but not at low (12°C) temperature. Body condition of newly metamorphosed frogs was unrelated to the temperature or food type experienced during the premetamorphic stage. Frogs maintained at high temperature during the larval period showed reduced jumping ability, especially when fed on the plant-based diet. However, when considering size-independent jumping ability, cold-reared individuals exhibited the lowest performance, and herbivores reared at 17°C the highest. Cold-reared (12°C) frogs accumulated larger amounts of energy reserves than individuals raised at 17°C or 22°C. This was still the case after correction for differences in body mass, thus indicating some size-independent effect of developmental temperature. Despite the higher lipid content of the carnivorous diet, the differences in energy reserves between herbivores and carnivores were relatively weak and associated with differences in body size. These results suggest that the consequences of environmental variation in the larval habitat can extend to the terrestrial phase and influence juvenile growth and survival.     

Age-dependent usage of double-strand-break repair pathways

A DNA double-strand break (DSB) can be repaired by any of several alternative and competing mechanisms. The repaired sequences often differ from the original depending on which mechanism was used so that the cell's "choice" of repair mechanism can have profound genetic consequences. DSBs can accumulate with age , and human diseases that mimic some of the effects of aging, such as increased susceptibility to cancer, are associated with certain defects in DSB repair . The premeiotic germ cells of Drosophila provide a useful model for exploration of the connection between aging and DNA repair because these cells are subject to mortality and other age-related changes , and their DNA repair process is easily quantified. We used Rr3, a repair reporter system in Drosophila, to show that the relative usage of DSB repair mechanisms can change substantially as an organism ages. Homologous repair increased linearly in the male germline from 14% in young individuals to more than 60% in old ones, whereas two other pathways showed a corresponding decrease. Furthermore, the proportion of longer conversion tracts (>156 bp) also increased nearly 2-fold as the flies aged. These findings are relevant to the more general question of how DNA damage and repair are related to aging.     

Developmental trade-offs in caddis flies: increased investment in larval defence alters adult resource allocation

Developmental trade-offs in resource allocation across life-history stages and between different body parts are predicted by life-history theories. However, there is very little empirical evidence that these occur. We investigated these trade-offs in caddis flies by experimentally manipulating larval case construction and thereby silk expenditure. Case building diverts protein resources away from larval stores, which are of major importance to adult development in species with little or no adult feeding. We induced fifth-instar Odontocerum albicorne to build new cases and examined the consequences for the morphology of the resulting adults. Rebuilding did not alter larval food consumption or the date of entering pupation, but shortened the duration of the pupal period. Adults that had been induced to expend more silk as larvae had lighter thoraces and smaller wings than the controls, but their abdomens did not differ significantly in mass or nitrogen content. These results suggest a trade-off between larval silk production and the pattern of resource allocation within the adult. The maintenance of the abdomen is likely to preserve reproductive potential, while the reduction in thoracic and wing investment will have negative consequences for flight and associated activities, and possibly for adult longevity.     

Static and Dynamic Factors Limit Chromosomal Replication Complexity in Escherichia coli,Avoiding Dangers of Runaway Overreplication

We define chromosomal replication complexity (CRC) as the ratio of the copy number of the most replicated regions to that of unreplicated regions on the same chromosome. Although a typical CRC of eukaryotic or bacterial chromosomes is 2, rapidly growing Escherichia coli cells induce an extra round of replication in their chromosomes (CRC = 4). There are also E. coli mutants with stable CRC∼6. We have investigated the limits and consequences of elevated CRC in E. coli and found three limits: the “natural” CRC limit of ∼8 (cells divide more slowly); the “functional” CRC limit of ∼22 (cells divide extremely slowly); and the “tolerance” CRC limit of ∼64 (cells stop dividing). While the natural limit is likely maintained by the eclipse system spacing replication initiations, the functional limit might reflect the capacity of the chromosome segregation system, rather than dedicated mechanisms, and the tolerance limit may result from titration of limiting replication factors. Whereas recombinational repair is beneficial for cells at the natural and functional CRC limits, we show that it becomes detrimental at the tolerance CRC limit, suggesting recombinational misrepair during the runaway overreplication and giving a rationale for avoidance of the latter.     

Dietary fatty acids promote sleep through a taste‐independent mechanism

Consumption of foods that are high in fat contribute to obesity and metabolism‐related disorders. Dietary lipids are comprised of triglycerides and fatty acids, and the highly palatable taste of dietary fatty acids promotes food consumption, activates reward centers in mammals and underlies hedonic feeding. Despite the central role of dietary fats in the regulation of food intake and the etiology of metabolic diseases, little is known about how fat consumption regulates sleep. The fruit fly, Drosophila melanogaster, provides a powerful model system for the study of sleep and metabolic traits, and flies potently regulate sleep in accordance with food availability. To investigate the effects of dietary fats on sleep regulation, we have supplemented fatty acids into the diet of Drosophila and measured their effects on sleep and activity. We found that flies fed a diet of hexanoic acid, a medium‐chain fatty acid that is a by‐product of yeast fermentation, slept more than flies starved on an agar diet. To assess whether dietary fatty acids regulate sleep through the taste system, we assessed sleep in flies with a mutation in the hexanoic acid receptor Ionotropic receptor 56D, which is required for fatty acid taste perception. We found that these flies also sleep more than agar‐fed flies when fed a hexanoic acid diet, suggesting the sleep promoting effect of hexanoic acid is not dependent on sensory perception. Taken together, these findings provide a platform to investigate the molecular and neural basis for fatty acid‐dependent modulation of sleep.     

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. 2. It is hypothesised that an Allee effect in D. melanogaster larvae arises from an increased efficiency of a group of larvae to temper fungal growth on their feeding substrate. To test this hypothesis, standard apple substrates were infested with specified numbers of larvae, and their survival and development were monitored. A potential beneficial effect of the presence of adult flies was also investigated by incubating a varying number of adults on the substrate before introducing the larvae. Adults inoculate substrates with yeast, on which the larvae feed. 3. Fungal growth was related negatively to larval survival and the size of the emerging flies. Although the fungal growth on the substrate was largely reduced at increased larval densities, the measurements of fitness components indicated no Allee effect between larval densities and larval fitness, but rather indicated larval competition. 4. In contrast, increased adult densities on the substrates prior to larval development yielded higher survival of the larvae, larger emerging flies, and also reduced fungal growth on the substrates. Hence, adults enhanced the quality of the larval substrate and significant benefits of aggregated oviposition in fruit flies were shown. Experiments with synthetic pheromone indicated that the aggregation pheromone itself did not contribute directly to the quality of the larval resource. 5. The interaction among adults, micro‐organisms, and larval growth is discussed in relation to the consequences for total fitness.     

Adaptation to divergent larval diets in the medfly,Ceratitis capitata

Variation in diet can influence the timing of major life‐history events and can drive population diversification and ultimately speciation. Proximate responses of life histories to diet have been well studied. However, there are scant experimental data on how organisms adapt to divergent diets over the longer term. We focused on this omission by testing the responses of a global pest, the Mediterranean fruitfly, to divergent selection on larval diets of different nutritional profiles. Tests conducted before and after 30 generations of nutritional selection revealed a complex interplay between the effects of novel larval dietary conditions on both plastic and evolved responses. There were proximate‐only responses to the larval diet in adult male courtship and the frequency of copulation. Males on higher calorie larval diets consistently engaged in more bouts of energetic courtship. In contrast, following selection, larval development time, and egg to adult survival showed evidence of evolved divergence between diet regimes. Adult body size showed evidence for adaptation, with flies being significantly heavier when reared on their “own” diet. The results show the multifaceted responses of individuals to dietary selection and are important in understanding the extreme generalism exhibited by the medfly.     

Alleles underlying larval foraging behaviour influence adult dispersal in nature

The dispersal and migration of organisms have resulted in the colonisation of nearly every possible habitat and ultimately the extraordinary diversity of life. Animal dispersal tendencies are commonly heterogeneous (e.g. long vs. short) and non‐random suggesting that phenotypic and genotypic variability between individuals can contribute to population‐level heterogeneity in dispersal. Using laboratory and field experiments, we demonstrate that natural allelic variation in a gene underlying a foraging polymorphism in larval fruit flies (for), also influences their dispersal tendencies as adults. Rover flies (for^R; higher foraging activity) have consistently greater dispersal tendencies and are more likely to disperse longer distances than sitter flies (for^s; lower foraging activity). Increasing for expression in the brain and nervous system increases dispersal in sitter flies. Our study supports the notion that variation in dispersal can be driven by intrinsic variation in food‐dependent search behaviours and confirms that single gene pleiotropic effects can contribute to population‐level heterogeneity in dispersal.     

Dietary protein content affects evolution for body size, body fat and viability in Drosophila melanogaster

The ability to use different food sources is likely to be under strong selection if organisms are faced with natural variation in macro-nutrient (protein, carbohydrate and lipid) availabilities. Here, we use experimental evolution to study how variable dietary protein content affects adult body composition and developmental success in Drosophila melanogaster. We reared flies on either a standard diet or a protein-enriched diet for 17 generations before testing them on both diet types. Flies from lines selected on protein-rich diet produced phenotypes with higher total body mass and relative lipid content when compared with those selected on a standard diet, irrespective of which of the two diets they were tested on. However, selection on protein-rich diet incurred a cost as flies reared on this diet had markedly lower developmental success in terms of egg-to-adult viability on both medium types, suggesting a possible trade-off between the traits investigated.     

Diet quality mitigates intraspecific larval competition in Drosophila suzukii

The invasive frugivore Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) utilizes a wide range of host plants and damages important fruit crops, including blueberries, cherries, blackberries, raspberries, and strawberries. Field infestations of D. suzukii often exceed one larva per berry, suggesting that intraspecific competition may frequently occur. Because dietary resources are also likely to vary across the host range of D. suzukii, we designed a laboratory assay to measure larval performance across diets of varying quality: a standard artificial diet, a fruit‐based medium, a low‐protein, and a low‐carbohydrate diet. We manipulated egg density across these diets to provide increasing levels of competition and measured larval performance by observing survival to pupation and adulthood, and development times for both life stages. Although increasing density generally negatively impacted D. suzukii performance across diets, the magnitude of these impacts varied by diet type. Drosophila suzukii performance was generally similar in fruit and standard diets, although larval development was more rapid in fruit diets at lower densities. Even at low densities (5 or 10 eggs per arena), survival was reduced and development time increased in low‐protein diets relative to standard and fruit diets. At the two highest larval densities (20 or 40 eggs per arena), survivorship was reduced in low‐carbohydrate diets as compared to standard and fruit diets. There is evidence that larvae compensated in both low‐quality diets by extending development time, which could have consequences for population dynamics. Population models for use in D. suzukii management may need to account for both host nutritional quality and relative competition to accurately predict turnover and geographic expansion.     

Effects of larval diet on development rates and reproductive maturation of male and female Mediterranean fruit flies

Abstract Mediterranean fruit fly Ceratitis capitata (Diptera: Tephritidae) larvae are capable of developing in one of many hosts that may vary greatly in quality. We hypothesized that they will respond to the larval environment in a manner beneficial to their subsequent reproductive performance. Accordingly, we investigated the effects of various larval diets (varying in the amount of protein and sugar they contain) on the size, development time, nutritional status and reproductive maturation (ovarian development and onset of sexual behaviour) of females and males. We found that flies which undergo larval development in artificial host fruit that contain sugar and protein ('protein-fed') were larger, developed faster and emerged with more nutritional reserves than flies that were protein-deprived as larvae. Protein-fed males, regardless of their size, became sexually active before males that developed in hosts with no protein. Protein-fed females produced more mature eggs than protein-deprived ones. Moreover, protein-fed females tended to copulate sooner than females that developed in hosts with no protein. In addition, regardless of female larval diet, females with more mature eggs tended to copulate sooner than females with less mature eggs. In light of these results, the importance of the larval environment for adult reproductive success is discussed.     

Multiple-pathway analysis of double-strand break repair mutations in Drosophila

The analysis of double-strand break (DSB) repair is complicated by the existence of several pathways utilizing a large number of genes. Moreover, many of these genes have been shown to have multiple roles in DSB repair. To address this complexity we used a repair reporter construct designed to measure multiple repair outcomes simultaneously. This approach provides estimates of the relative usage of several DSB repair pathways in the premeiotic male germline of Drosophila. We applied this system to mutations at each of 11 repair loci plus various double mutants and altered dosage genotypes. Most of the mutants were found to suppress one of the pathways with a compensating increase in one or more of the others. Perhaps surprisingly, none of the single mutants suppressed more than one pathway, but they varied widely in how the suppression was compensated. We found several cases in which two or more loci were similar in which pathway was suppressed while differing in how this suppression was compensated. Taken as a whole, the data suggest that the choice of which repair pathway is used for a given DSB occurs by a two-stage “decision circuit” in which the DSB is first placed into one of two pools from which a specific pathway is then selected.     

Impacts of dietary amino acid composition and microbial presence on preference and performance of immature Lucilia sericata (Diptera: Calliphoridae)

1. As primary colonisers of ephemeral resources, the common green bottle fly, Lucilia sericata, must exercise efficient resource exploitation strategies to maximise fitness. Foraging incurs costs, so the efficient evaluation of resources is essential for individuals relying on fragmented patches whose dissimilarity may result in fitness consequences for offspring. Thus, selective pressures between carrion‐using insects and carrion‐associated microbes are expected to occur. 2. Microbes play a pivotal role in adult fly assessment of resources via production of volatile organic compounds (VOCs) resulting from the breakdown of essential amino acids. If one assumes that chemoreception of these VOCs provides public information regarding the corresponding essential amino acids, the resulting effects on maternal decision‐making could impact larval resource exploitation. 3. The essential amino acids phenylalanine, methionine, valine, and tryptophan, the corresponding VOCs of which are known fly attractants, were used to construct imbalanced diets with and without antimicrobial treatment to investigate the impact of suboptimal food sources on larval L. sericata. 4. The results of this study demonstrate that both amino acid composition and microbial presence influence behaviour, with larvae displaying a preference for untreated diets lacking methionine and a complete reversal in preference for antimicrobial‐treated diets. This interaction between diet and antimicrobial treatment indicates that the presence of microbes that produce essential amino acids may impact larval resource utilisation strategies. This investigation into larval performance on diets deficient in amino acids that provide important VOC cues to maternal flies provides a stepping stone for dissecting larval behavioural strategies on ephemeral resources when faced with limited choices.     

Effect of plant oils on quality parameters of Bactrocera tryoni (Froggatt) reared on liquid larval diet

Liquid larval diets have been developed for several tephritid fruit flies including Queensland fruit fly, Bactrocera tryoni (Frogatt) (Q‐fly). In liquid diets, wheat germ oil (WGO) is usually added to improve performance in some quality parameters of reared flies, especially flight ability. However, for some flies, other plant oils may be more readily available, cheaper or produce flies of superior performance. In the present study, four alternative types of plant oils – rice bran, canola, vegetable, and sesame – were incorporated into a fruit fly liquid larval diet to replace the currently used wheat germ oil and their efficacy on the quality parameters of reared Q‐fly was compared to diets containing wheat germ oil or no oil. The quality parameters included: total pupal yield (N), pupal recovery (%), larval duration (days), pupal weight (mg), adult emergence (%), adult fliers (%), rate of fliers (%), sex ratio (%), F₁ egg/female/day and egg hatching (%). There were significant differences among treatments in performance of Q‐fly. Vegetable oil appeared better in terms of total pupal yield, percentage of pupal recovery, percentage of adult emergence, percentage of fliers, mean egg/female/day and % F₁ egg hatch compared with other oil treatments, especially from that of WGO treated diet. The result suggests that WGO can be substituted with rice bran and vegetable oil to improve the liquid larval diet for rearing of B. tryoni, with vegetable oil being the best replacement.     

Predicting Disease Risk Using Bootstrap Ranking and Classification Algorithms

Genome-wide association studies (GWAS) are widely used to search for genetic loci that underlie human disease. Another goal is to predict disease risk for different individuals given their genetic sequence. Such predictions could either be used as a “black box” in order to promote changes in life-style and screening for early diagnosis, or as a model that can be studied to better understand the mechanism of the disease. Current methods for risk prediction typically rank single nucleotide polymorphisms (SNPs) by the p-value of their association with the disease, and use the top-associated SNPs as input to a classification algorithm. However, the predictive power of such methods is relatively poor. To improve the predictive power, we devised BootRank, which uses bootstrapping in order to obtain a robust prioritization of SNPs for use in predictive models. We show that BootRank improves the ability to predict disease risk of unseen individuals in the Wellcome Trust Case Control Consortium (WTCCC) data and results in a more robust set of SNPs and a larger number of enriched pathways being associated with the different diseases. Finally, we show that combining BootRank with seven different classification algorithms improves performance compared to previous studies that used the WTCCC data. Notably, diseases for which BootRank results in the largest improvements were recently shown to have more heritability than previously thought, likely due to contributions from variants with low minimum allele frequency (MAF), suggesting that BootRank can be beneficial in cases where SNPs affecting the disease are poorly tagged or have low MAF. Overall, our results show that improving disease risk prediction from genotypic information may be a tangible goal, with potential implications for personalized disease screening and treatment.     

Evidence of a Mild Mutator Phenotype in Cambodian Plasmodium falciparum Malaria Parasites

Malaria control efforts have been continuously stymied by drug-resistant strains of Plasmodium falciparum, which typically originate in Southeast Asia prior to spreading into high-transmission settings in Africa. One earlier proposed explanation for Southeast Asia being a hotbed of resistance has been the hypermutability or “Accelerated Resistance to Multiple Drugs” (ARMD) phenotype, whereby multidrug-resistant Southeast Asian parasites were reported to exhibit 1,000-fold higher rates of resistance to unrelated antimalarial agents when compared to drug-sensitive parasites. However, three recent studies do not recapitulate this hypermutability phenotype. Intriguingly, genome sequencing of recently derived multidrug-resistant Cambodian isolates has identified a high proportion of DNA repair gene mutations in multidrug-resistant parasites, suggesting their potential role in shaping local parasite evolution. By adapting fluctuation assays for use in P. falciparum, we have examined the in vitro mutation rates of five recent Cambodian isolates and three reference laboratory strains. For these studies we also generated a knockout parasite line lacking the DNA repair factor Exonuclease I. In these assays, parasites were typed for their ability to acquire resistance to KAE609, currently in advanced clinical trials, yielding 13 novel mutations in the Na⁺/H⁺-ATPase PfATP4, the primary resistance determinant. We observed no evidence of hypermutability. Instead, we found evidence of a mild mutator (up to a 3.4-fold increase in mutation rate) phenotype in two artemisinin-resistant Cambodian isolates, which carry DNA repair gene mutations. We observed that one such mutation in the Mismatch Repair protein Mlh1 contributes to the mild mutator phenotype when modeled in yeast (scmlh1-P157S). Compared to basal rates of mutation, a mild mutator phenotype may provide a greater overall benefit for parasites in Southeast Asia in terms of generating drug resistance without incurring detrimental fitness costs.