Natural Populations Of Drosophila Research Articles

Role of Host-Driven Mutagenesis in Determining Genome Evolution of Sigma Virus (DMelSV; Rhabdoviridae) in Drosophila melanogaster.

Sigma virus (DMelSV) is ubiquitous in natural populations of Drosophila melanogaster. Host-mediated, selective RNA editing of adenosines to inosines (ADAR) may contribute to control of viral infection by preventing transcripts from being transported into the cytoplasm or being translated accurately; or by increasing the viral genomic mutation rate. Previous PCR-based studies showed that ADAR mutations occur in DMelSV at low frequency. Here we use SOLiDTM deep sequencing of flies from a single host population from Athens, GA, USA to comprehensively evaluate patterns of sequence variation in DMelSV with respect to ADAR. GA dinucleotides, which are weak targets of ADAR, are strongly overrepresented in the positive strand of the virus, consistent with selection to generate ADAR resistance on this complement of the transient, double-stranded RNA intermediate in replication and transcription. Potential ADAR sites in a worldwide sample of viruses are more likely to be “resistant” if the sites do not vary among samples. Either variable sites are less constrained and hence are subject to weaker selection than conserved sites, or the variation is driven by ADAR. We also find evidence of mutations segregating within hosts, hereafter referred to as hypervariable sites. Some of these sites were variable only in one or two flies (i.e., rare); others were shared by four or even all five of the flies (i.e., common). Rare and common hypervariable sites were indistinguishable with respect to susceptibility to ADAR; however, polymorphism in rare sites were more likely to be consistent with the action of ADAR than in common ones, again suggesting that ADAR is deleterious to the virus. Thus, in DMelSV, host mutagenesis is constraining viral evolution both within and between hosts.

Elevated Linkage Disequilibrium and Signatures of Soft Sweeps Are Common in Drosophila melanogaster.

The extent to which selection and demography impact patterns of genetic diversity in natural populations of Drosophila melanogaster is yet to be fully understood. We previously observed that linkage disequilibrium (LD) at scales of ∼10 kb in the Drosophila Genetic Reference Panel (DGRP), consisting of 145 inbred strains from Raleigh, North Carolina, measured both between pairs of sites and as haplotype homozygosity, is elevated above neutral demographic expectations. We also demonstrated that signatures of strong and recent soft sweeps are abundant. However, the extent to which these patterns are specific to this derived and admixed population is unknown. It is also unclear whether these patterns are a consequence of the extensive inbreeding performed to generate the DGRP data. Here we analyze LD statistics in a sample of >100 fully-sequenced strains from Zambia; an ancestral population to the Raleigh population that has experienced little to no admixture and was generated by sequencing haploid embryos rather than inbred strains. We find an elevation in long-range LD and haplotype homozygosity compared to neutral expectations in the Zambian sample, thus showing the elevation in LD is not specific to the DGRP data set. This elevation in LD and haplotype structure remains even after controlling for possible confounders including genomic inversions, admixture, population substructure, close relatedness of individual strains, and recombination rate variation. Furthermore, signatures of partial soft sweeps similar to those found in the DGRP as well as partial hard sweeps are common in Zambia. These results suggest that while the selective forces and sources of adaptive mutations may differ in Zambia and Raleigh, elevated long-range LD and signatures of soft sweeps are generic in D. melanogaster.

An Indel Polymorphism in the MtnA 3' Untranslated Region Is Associated with Gene Expression Variation and Local Adaptation in Drosophila melanogaster.

Insertions and deletions (indels) are a major source of genetic variation within species and may result in functional changes to coding or regulatory sequences. In this study we report that an indel polymorphism in the 3’ untranslated region (UTR) of the metallothionein gene MtnA is associated with gene expression variation in natural populations of Drosophila melanogaster. A derived allele of MtnA with a 49-bp deletion in the 3' UTR segregates at high frequency in populations outside of sub-Saharan Africa. The frequency of the deletion increases with latitude across multiple continents and approaches 100% in northern Europe. Flies with the deletion have more than 4-fold higher MtnA expression than flies with the ancestral sequence. Using reporter gene constructs in transgenic flies, we show that the 3' UTR deletion significantly contributes to the observed expression difference. Population genetic analyses uncovered signatures of a selective sweep in the MtnA region within populations from northern Europe. We also find that the 3’ UTR deletion is associated with increased oxidative stress tolerance. These results suggest that the 3' UTR deletion has been a target of selection for its ability to confer increased levels of MtnA expression in northern European populations, likely due to a local adaptive advantage of increased oxidative stress tolerance.

A high frequency of heritable changes in natural populations of Drosophila melanogaster in Ukraine

Spontaneous mutations are thought to have a stable rate for a given species. If non-adaptive, they appear at low frequencies and are governed by drift. However, environmental factors have been reported to cause spread of non-adaptive mutations in populations, governed by mechanisms, such as genetic assimilation. In the present study, we report a simultaneous appearance of a mutant and apparently non-adaptive C2 vein in Drosophila melanogaster at higher than expected frequencies in several distant populations, which excludes the role of drift or selection as the cause of the reported mutation frequencies. We discuss explanations of the phenomenon, including the role of externalfactors, such as temperature, in the possible genetic assimilation of the trait.

Determination of Genetic Similarities in Natural Populations of Drosophila melanogaster in Savanna Zone of Nigeria Using Microsatellite Markers

This study was carried out to determine genetic similarities in natural population of Drosophila melanogaster in savannah zone of Nigeria using microsatellite markers. A total of 184 D. melanogaster was collected using simple traps baited with banana and baker’s yeast from Northern Guinea (Kaduna), Sudan (Kano) and Sahel (Azare). A total of 40 D. melanogaster were genotyped using 7 sets of microsatellite markers, the bands in the electrophoregramme were analysed and scored using the image LabTM. The result was used to compute dendrogramme based on Nei’s genetic distance using MEGA 6. Result showed that studied population forms two (2) clusters at various degrees of similarities with Sudan savanna and Sahel Savanna forming a cluster at 0.21 then grouped with Northern Guinea Savanna to form the second (2nd) cluster at 0.78 distances, suggesting that Northern Guinea Savanna and Sudan Savanna Drosophila melanogaster populations have a recent common ancestor.

A Quantitative Genomic Approach for Analysis of Fitness and Stress Related Traits in aDrosophila melanogasterModel Population

The ability of natural populations to withstand environmental stresses relies partly on their adaptive ability. In this study, we used a subset of the Drosophila Genetic Reference Panel, a population of inbred, genome-sequenced lines derived from a natural population of Drosophila melanogaster, to investigate whether this population harbors genetic variation for a set of stress resistance and life history traits. Using a genomic approach, we found substantial genetic variation for metabolic rate, heat stress resistance, expression of a major heat shock protein, and egg-to-adult viability investigated at a benign and a higher stressful temperature. This suggests that these traits will be able to evolve. In addition, we outline an approach to conduct pathway associations based on genomic linear models, which has potential to identify adaptive genes and pathways, and therefore can be a valuable tool in conservation genomics.

Choosing mates based on the diet of your ancestors: replication of non-genetic assortative mating in Drosophila melanogaster.

Assortative mating has been a focus of considerable research because of its potential to influence biodiversity at many scales. Sharon et al. (2010) discovered that an inbred strain of Drosophila melanogaster mated assortatively based on the diet of previous generations, leading to initial reproductive isolation without genetic evolution. This behavior was reproduced by manipulating the microbiome independently of the diet, pointing to extracellular bacterial symbionts as the assortative mating cue. To further investigate the biological significance of this result, we attempted to reproduce this phenomenon in an independent laboratory using different genotypes and additional mating assays. Supporting the previous result, we found that a different inbred strain also mated assortatively based on the diets of previous generations. However, we were unable to generate assortative mating in an outbred strain from North Carolina. Our results support the potential for non-genetic mechanisms to influence reproductive isolation, but additional work is needed to investigate the importance of this mechanism in natural populations of Drosophila.

Seasonal variation in life history traits in two Drosophila species.

Seasonal environmental heterogeneity is cyclic, persistent and geographically widespread. In species that reproduce multiple times annually, environmental changes across seasonal time may create different selection regimes that may shape the population ecology and life history adaptation in these species. Here, we investigate how two closely related species of Drosophila in a temperate orchard respond to environmental changes across seasonal time. Natural populations of Drosophila melanogaster and Drosophila simulans were sampled at four timepoints from June through November to assess seasonal change in fundamental aspects of population dynamics as well as life history traits. D.melanogaster exhibit pronounced change across seasonal time: early in the season, the population is inferred to be uniformly young and potentially represents the early generation following overwintering survivorship. D.melanogaster isofemale lines derived from the early population and reared in a common garden are characterized by high tolerance to a variety of stressors as well as a fast rate of development in the laboratory environment that declines across seasonal time. In contrast, wild D.simulans populations were inferred to be consistently heterogeneous in age distribution across seasonal collections; only starvation tolerance changed predictably over seasonal time in a parallel manner as in D.melanogaster. These results suggest fundamental differences in population and evolutionary dynamics between these two taxa associated with seasonal heterogeneity in environmental parameters and associated selection pressures.

Integration, Regulation, and Long-Term Stability of R2 Retrotransposons.

R2 elements are sequence specific non-LTR retrotransposons that exclusively insert in the 28S rRNA genes of animals. R2s encode an endonuclease that cleaves the insertion site and a reverse transcriptase that uses the cleaved DNA to prime reverse transcription of the R2 transcript, a process termed target primed reverse transcription. Additional unusual properties of the reverse transcriptase as well as DNA and RNA binding domains of the R2 encoded protein have been characterized. R2 expression is through co-transcription with the 28S gene and self-cleavage by a ribozyme encoded at the R2 5' end. Studies in laboratory stocks and natural populations of Drosophila suggest that R2 expression is tied to the distribution of R2-inserted units within the rDNA locus. Most individuals have no R2 expression because only a small fraction of their rRNA genes need to be active, and a contiguous region of the locus free of R2 insertions can be selected for activation. However, if the R2-free region is not large enough to produce sufficient rRNA, flanking units - including those inserted with R2 - must be activated. Finally, R2 copies rapidly turnover within the rDNA locus, yet R2 has been vertically maintained in animal lineages for hundreds of millions of years. The key to this stability is R2's ability to remain dormant in rDNA units outside the transcribed regions for generations until the stochastic nature of the crossovers that drive the concerted evolution of the rDNA locus inevitably reshuffle the inserted and uninserted units, resulting in transcription of the R2-inserted units.

Do males matter? Testing the effects of male genetic background on female meiotic crossover rates in Drosophila melanogaster.

Meiotic recombination is a critical genetic process as well as a pivotal evolutionary force. Rates of crossing over are highly variable within and between species, due to both genetic and environmental factors. Early studies in Drosophila implicated female genetic background as a major determinant of crossover rate and recent work has highlighted male genetic background as a possible mediator as well. Our study employed classical genetics to address how female and male genetic backgrounds individually and jointly affect crossover rates. We measured rates of crossing over in a 33 cM region of the Drosophila melanogaster X chromosome using a two-step crossing scheme exploiting visible markers. In total, we measured crossover rates of 10 inbred lines in a full diallel cross. Our experimental design facilitates measuring the contributions of female genetic background, male genetic background, and female by male genetic background interaction effects on rates of crossing over in females. Our results indicate that although female genetic background significantly affects female meiotic crossover rates in Drosophila, male genetic background and the interaction of female and male genetic backgrounds have no significant effect. These findings thus suggest that male-mediated effects are unlikely to contribute greatly to variation in recombination rates in natural populations of Drosophila.

Natural Populations of Drosophila melanogaster Reveal Features of an Uncharacterized Circadian Property: The Lower Temperature Limit of Rhythmicity.

Most cyclic biological processes are under control of a circadian molecular timing system that synchronizes these phenomena to the 24-h day. One generic property of circadian-controlled processes is that they operate within a specific temperature range, below which the manifestation of rhythm ceases. Little is known about the evolutionary relevance of the lower temperature limit of rhythmicity or about the mechanism underlying the loss of overt circadian behavior below this lower limit, especially in one model organism of chronobiology, Drosophila melanogaster. Natural populations of Drosophila are evolving under divergent selection pressures and so provide a source of diversity necessary to address these issues. Using lines derived from African populations, we find that there is natural variation in the expression of rhythmic behavior under low-temperature conditions. We found evidence that this variability is evolutionarily relevant at extremely low temperature (12 °C) because high-altitude populations exhibit selection for locally adapted genomes that contribute to rhythmic behavior. Lines resistant to 15 °C show an additional layer of diversity in their response to temperature extremes because some lines are resistant to low temperature (15 °C) only, whereas others are cross-resistant to high and low temperature (15 °C and 30 °C). Genetic analysis of one cold-resistant circadian line at 15 °C reveals that the phenotype maps to the X-chromosome but not to the core clock genes, per and sgg. Analysis of the central clock cells of this line reveals that maintenance of rhythm is associated with robust clock function, which is compromised in a standard laboratory strain. These data indicate that the cold-resistant circadian phenotype is clock based. This study highlights the importance of using natural populations to inform us of the basic features of circadian traits, especially those that might be under temperature-based selection.

Fecundity as one of possible factors contributing to the dominance of the wMel genotype of Wolbachia in natural populations of Drosophila melanogaster

Alphaproteobacteria of the genus Wolbachia are common intracellular endosymbionts of a variety of insects. Their successful spread over a vast range of host taxa is often attributed to selective advantages conferred by the bacteria to infected individuals. Among the known diversity of Wolbachia pipientis infecting Drosophila melanogaster, a single genotype, wMel, within the wMel strain has been found to dominate over other genotypes world-wide. Genotyping of D. melanogaster wild populations from Ukraine reveals a relatively high frequency of the wMel genotype, although 31 % flies from an Uman’ population are infected with the rare genotype wMelCS. We demonstrate that wMelCS-infected females have lower fecundity compared to wMel-infected flies, which might be the cause of wMel prevalence in D. melanogaster populations. We report no difference in the bacterial transmission rate between these two bacterial genotypes. However, we observed an association between transmission fidelity of Wolbachia and genotype of D. melanogaster indicating that Wolbachia-host relationships in this case are more complex. Furthermore our study reveals fluctuations in Wolbachia infection rates in wMel-infected populations.

Developmental thermal plasticity among Drosophila melanogaster populations.

Many biotic and abiotic variables influence the dispersal and distribution of organisms. Temperature has a major role in determining these patterns because it changes daily, seasonally and spatially, and these fluctuations have a significant impact on an organism's behaviour and fitness. Most ecologically relevant phenotypes that are adaptive are also complex and thus they are influenced by many underlying loci that interact with the environment. In this study, we quantified the degree of thermal phenotypic plasticity within and among populations by measuring chill-coma recovery times of lines reared from egg to adult at two different environmental temperatures. We used sixty genotypes from six natural populations of Drosophila melanogaster sampled along a latitudinal gradient in South America. We found significant variation in thermal plasticity both within and among populations. All populations exhibit a cold acclimation response, with flies reared at lower temperatures having increased resistance to cold. We tested a series of environmental parameters against the variation in population mean thermal plasticity and discovered the mean thermal plasticity was significantly correlated with altitude of origin of the population. Pairing our data with previous experiments on viability fitness assays in the same populations in fixed and variable environments suggests an adaptive role of this thermal plasticity in variable laboratory environments. Altogether, these data demonstrate abundant variation in adaptive thermal plasticity within and among populations.

PElement Activity and Molecular Structure inDrosophila melanogasterPopulations from Firtina Valley, Turkey

In order to study P element dynamics in natural populations of Drosophila melanogaster, 88 isofemale lines were examined from the Firtina Valley, Turkey. The P-M gonadal dysgenesis characteristics and the molecular patterns of P and KP elements were analyzed. Gonadal dysgenesis tests showed a slight variation both for P activity and P susceptibility, however the results showed a predominant M' phenotype for this region. The P and KP element were also characterized by polymerase chain reaction. The molecular analyses showed that all the populations examined had the entire 1.15 kb KP element. The molecular patterns of KP elements were the same for the populations studied. No clear relationship was found between phenotype and genomic P element composition. The correlations between the level of gonadal dysgenesis percentage (as an index for P activity and P susceptibility) and several geoclimatic factors were tested, and no general effects of altitude, temperature, rainfall, or humidity were found. The theoretical P' strain, which is very rare in natural populations, was also recorded for this region.

Indy gene variation in natural populations confers fitness advantage and life span extension through transposon insertion

Natural selection acts to maximize reproductive fitness. However, antagonism between life span and reproductive success frequently poses a dilemma pitting the cost of fecundity against longevity. Here, we show that natural populations of Drosophila melanogaster harbor a Hoppel transposon insertion variant in the longevity gene Indy (I'm not dead yet), which confers both increased reproduction and longevity through metabolic changes. Heterozygosity for this natural long-lived variant has been maintained in isolates despite long-term inbreeding under laboratory conditions and advantageously confers increased fecundity. DNA sequences of variant chromosome isolates show evidence of selective sweep acting on the advantageous allele, suggesting that natural selection acts to maintain this variant. The transposon insertion also regulates Indy expression level, which has experimentally been shown to affect life span and fecundity. Thus, in the wild, evolution reaffirms that the mechanism of heterozygote advantage has acted upon the Indy gene to assure increased reproductive fitness and, coincidentally, longer life span through regulatory transposon mutagenesis.

P element activity and molecular structure in Drosophila melanogaster populations from Firtina Valley, Turkey.

In order to study P element dynamics in natural populations of Drosophila melanogaster , 88 isofemale lines were examined from the Firtina Valley, Turkey. The P-M gonadal dysgenesis characteristics and the molecular patterns of P and KP elements were analyzed. Gonadal dysgenesis tests showed a slight variation both for P activity and P susceptibility, however the results showed a predominant M' phenotype for this region. The P and KP element were also characterized by polymerase chain reaction. The molecular analyses showed that all the populations examined had the entire 1.15 kb KP element. The molecular patterns of KP elements were the same for the populations studied. No clear relationship was found between phenotype and genomic P element composition. The correlations between the level of gonadal dysgenesis percentage (as an index for P activity and P susceptibility) and several geoclimatic factors were tested, and no general effects of altitude, temperature, rainfall, or humidity were found. The theoretical P' strain, which is very rare in natural populations, was also recorded for this region.

The puzzle of Wolbachia spreading out through natural populations of Drosophila melanogaster

The endosymbiotic bacteria Wolbachia are widely spread in natural populations of arthropods all over the world. This phenomenon, according to the current views, may be due either to so called reproductive parasitism (modification of sexual reproduction) or to mutualistic interrelationships with the host organism, since the bacteria are transmitted transovarially. Wolbachia are extremely widespread in natural populations and laboratory lineages of Drosophila melanogaster though they do not cause any known modifications of this insect sexual reproduction that could influence the bacteria frequency in the populations. It is found out that Wolbachia effects on drosophila reproductive processes can only consist in low-level of cytoplasmic incompatibility within laboratory lineages; in natural drosophila populations even such an effect has not been detected. The attempts to explain the wide spread of Wolbachia among representatives of D. melanogaster through fitness increasing of infected individuals were not successful either. Data obtained thereupon are contradictive and the results are not versatile. Meanwhile, there are some incomplete data on the bacteria affecting drosophila sexual behavior, expression of certain genes, ferrum metabolism. It is shown that the bacteria enhance individual resistance to RNA-viruses that, under natural conditions, infect fruit flies rather frequently, but the mechanisms of the phenomenon remain uncertain as well as the commonness of the phenomenon itself. Thus, at the one hand, it can be stated that infection by Wolbachia leads to a rather complex effect on D. melanogaster while, at the other hand, the reasons behind the wide spread of Wolbachia in natural populations of D. melanogaster still remain unclear.

Identification of Mob2, a Novel Regulator of Larval Neuromuscular Junction Morphology, in Natural Populations of Drosophila melanogaster

Although evolutionary changes must take place in neural connectivity and synaptic architecture as nervous systems become more complex, we lack understanding of the general principles and specific mechanisms by which these changes occur. Previously, we found that morphology of the larval neuromuscular junction (NMJ) varies extensively among different species of Drosophila but is relatively conserved within a species. To identify specific genes as candidates that might underlie phenotypic differences in NMJ morphology among Drosophila species, we performed a genetic analysis on one of two phenotypic variants we found among 20 natural isolates of Drosophila melanogaster. We discovered genetic polymorphisms for both positive and negative regulators of NMJ growth segregating within the variant line. Focusing on one subline, that displayed NMJ overgrowth, we mapped the phenotype to Mob2 [Monopolar spindle (Mps) one binding protein 2)], a gene encoding a Nuclear Dbf2 (Dumbbell formation 2)-Related (NDR) kinase activator. We confirmed this identification by transformation rescue experiments and showed that presynaptic expression of Mob2 is necessary and sufficient to regulate NMJ growth. Mob2 interacts in a dominant, dose-dependent manner with tricornered but not with warts, to cause NMJ overgrowth, suggesting that Mob2 specifically functions in combination with the former NDR kinase to regulate NMJ development. These results demonstrate the feasibility and utility of identifying genetic variants affecting NMJ morphology in natural populations of Drosophila. These variants can lead to discovery of new genes and molecular mechanisms that regulate NMJ development while also providing new information that can advance our understanding of mechanisms that underlie nervous system evolution.

Latitudinal Variation in Starvation Resistance is Explained by Lipid Content in Natural Populations of Drosophila melanogaster

One of the most common environmental stressors is a shortage or suboptimal quality of food, thus all animals deal with periods of starvation. In the present study we examine variation in starvation resistance, longevity and body lipid content and the correlations between traits along an environmental gradient using isofemale lines recently derived from natural populations of Drosophila melanogaster from South America. The use of isofemale lines and controlled rearing laboratory conditions allows us to investigate within and among population components of genetic variation and the potential associations among starvation resistance, longevity and body lipid content. All these traits were analyzed separately in females and males, improving our understanding of sexual dimorphism. Our results revealed significant differences among populations in starvation resistance and longevity. Actually, the opposing latitudinal cline detected for starvation resistance suggests that natural selection played an essential role in shaping the pattern of geographic variation in this trait. Moreover, we also detected a positive relationship between starvation resistance and body lipid content in both sexes, providing evidence for a physiological and/or evolutionary association between these traits. Conversely, starvation resistance was not correlated with longevity indicating that these traits might be enabled to evolve independently. Finally, our study reveals that there is abundant within population genetic variation for all traits that may be maintained by sex-specific effects.

Discovery of Trypanosomatid Parasites in Globally Distributed Drosophila Species

Microbial parasites of animals include bacteria, viruses, and various unicellular eukaryotes. Because of the difficulty in studying these microorganisms in both humans and disease vectors, laboratory models are commonly used for experimental analysis of host-parasite interactions. Drosophila is one such model that has made significant contributions to our knowledge of bacterial, fungal, and viral infections. Despite this, less is known about other potential parasites associated with natural Drosophila populations. Here, we surveyed sixteen Drosophila populations comprising thirteen species from four continents and Hawaii and found that they are associated with an extensive diversity of trypanosomatids (Euglenozoa, Kinetoplastea). Phylogenetic analysis finds that Drosophila-associated trypanosomatids are closely related to taxa that are responsible for various types of leishmaniases and more distantly related to the taxa responsible for human African trypanosomiasis and Chagas disease. We suggest that Drosophila may provide a powerful system for studying the interactions between trypanosomatids and their hosts.