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opencc-by-4.0Oct 2016View details →

Read-mapping for next-generation sequencing data (Drosophila melanogaster)

Code, logs and quality-control data for whole-genome resequencing of Sussex-LHM and RG Drosophila melanogaster. Mapping code is in the archive lhm_mapping_scripts.zip Mapping logs are in the in the archive lhm_mapping_logs.zip Other zip archives contain the quality control data. The pre-print manuscript for this data is available on biorxiv: "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample" http://biorxiv.org/content/early/2016/10/17/081554 doi: http://dx.doi.org/10.1101/081554

opencc-by-4.0May 2017View details →

Adult Wing images from Drosophila sechellia and D. simulans

These are images of adult wings from two Drosophila species that were dissected by Christian Marier (in the Dworkin lab) and imaged by Ian Dworkin in 2015. Strains were provided by the Wittkopp lab at the University of Michigan. Flies were reared in the Wittkopp lab by Richard Lusk. Adults were stored in 70% ethanol prior to dissection and mounting in 70% glycerol. All images were taken on an Olympus BX-51 microscope on a 4X objective (40X total magnification) and captured with a DP30BW digital camera using Olympus DP controller (V.3,1,1208) software. All images were collected for geometric morphometric analysis. Dsim = Drosophila simulans Dsech = Drosophila sechellia f VS M is for male and female.

opencc-by-4.0Jun 2017View details →

Genome-wide estimation of linkage disequilibrium-independent SNPs in Drosophila melanogaster (Sussex LHM).

Uses R to create SNP density across each chromosome arm. Uses Plink 1.9 to select independent SNPs with step sizes corresponding to chromosome density. Output data is combined_chromosomes_lhm_indep.txt a list of SNP IDs.

opencc-by-4.0Oct 2023View details →

Different spectral sensitivities of ON- and OFF-motion pathways enhance the detection of approaching color objects in Drosophila - Processed Data

Processed data and code for plotting figures for the paper:"Different spectral sensitivities of ON- and OFF-motion pathways enhance the detection of approaching color objects in Drosophila", by Kit D. Longden, Edward M. Rogers, Aljoscha Nern, Heather Dionne, Michael B. Reiser.Data (compressed results folder) and plotting code (compressed src folder) are MATLAB files (see READ_ME for version information and toolboxes). The Source Data excel file also contains the data plotted in the paper figures.

opencc-zeroNov 2023View details →

Data from: A dynamical model of growth and maturation in Drosophila

The decision to stop growing and mature into an adult is a critical point in development that determines adult body size, impacting multiple aspects of an adult's biology. In many animals, growth-cessation is a consequence of hormone release that appears to be tied to attainment of particular body size or condition. Nevertheless, the size-sensing mechanism animals use to initiate hormone synthesis is poorly understood. Here we develop a simple mathematical model of growth cessation in Drosophila melanogaster, which is ostensibly triggered by attainment of a critical weight early in the last instar. Attainment of critical weight is correlated with synthesis of the steroid hormone ecdysone, which causes a larva to stop growing, pupate and metamorphose into the adult form. Our model suggests that, contrary to expectation, the size-sensing mechanism that initiates metamorphosis occurs before the larva reaches critical weight; that is, the critical-weight phenomenon is a downstream consequence of an earlier size-dependent developmental decision, not a decision point itself. Further, this size-sensing mechanism does not require a direct assessment of body size, but emerges from the interactions between body size, ecdysone and nutritional signaling. Because many aspects of our model are evolutionarily conserved among all animals, the model may provide a general framework for understanding how animals commit to maturing from their juvenile to adult form.

opencc-by-4.0Oct 2015View details →

Fig. 1 in Constant fluctuating asymmetry but not directional asymmetry along the geographic distribution of Drosophila antonietae (Diptera, Drosophilidae)

Fig. 1. Locations of the sampled populations of Drosophila antonietae. Serrana (21◦ 14Ɩ S, 47◦ 34Ɩ W), Itirapina (22◦16Ɩ S, 47◦48Ɩ W), Guarapuava (25◦17Ɩ S, 51◦53Ɩ W), Cantagalo (25◦25Ɩ S, 52◦04Ɩ W), Santiago (29◦ 23Ɩ S, 54◦44Ɩ W).

opencc-by-4.0Jun 2022View details →

A re-analysis of an existing Drosophila melanogaster dataset reveals a new set of genes involved in post-mating response

The figures and tables presented here are part of a manuscript submitted for publication by Chloe J. Bennett and Rodolfo Aramayo entitled: "A re-Analysis of an existing Drosophila melanogaster dataset reveals a new set of genes involved in post-mating response" Abstract RNA sequencing (RNA-seq) is a commonly used method to identify changes in gene expression between two conditions. The analysis of RNA-seq output is complicated, with the possibility of getting different results from the same raw data. We developed and deployed four parallel pipelines to reanalyze an existing dataset of two female Drosophila melanogaster tissue types before and after mating. The Drosophila post-mating response (PMR) is a well-characterized suite of changes that occur after mating, accompanied by a flux in gene expression. In comparing our study with the previous analysis of this dataset, we find our results to be more stringent, though we do identify a number of significant genes not found before. We also found variation among our own separate experiments, with gene-to-transcript isoform number and index building playing important roles in outcome. Finally, we identified a set of genes found by our pipeline that were not identified by the previous study and proposed potential roles for these genes in post-mating biology. Together, this work presents a critique of current RNA-seq analysis techniques and proposes multiple workflow adjustments that can increase the sensitivity, specificity, and stringency of differential gene expression studies.

opencc-zeroApr 2024View details →

Data from: Tissue-specific O-GlcNAcylation profiling identifies substrates in translational machinery in the Drosophila mushroom body contributing to olfactory learning

O-GlcNAcylation is a dynamic post-translational modification that diversifies the proteome. Its dysregulation is associated with neurological disorders that impair cognitive function, and yet identification of phenotype-relevant candidate substrates in a brain-region-specific manner remains unfeasible. By combining an O-GlcNAc binding activity derived from Clostridium perfringens OGA (CpOGA) with TurboID proximity labeling in Drosophila, we developed an O-GlcNAcylation profiling tool that translates O-GlcNAc modification into biotin conjugation for tissue-specific candidate substrates enrichment. We mapped the O-GlcNAc interactome in major brain regions of Drosophila and found that components of the translational machinery, particularly ribosomal subunits, were abundantly O-GlcNAcylated in the mushroom body of Drosophila brain. Hypo-O-GlcNAcylation induced by ectopic expression of active CpOGA in the mushroom body decreased local translational activity, leading to olfactory learning deficits that could be rescued by dMyc overexpression-induced increase of protein synthesis. Our study provides a useful tool for future dissection of tissue-specific functions of O-GlcNAcylation in Drosophila and suggests a possibility that O-GlcNAcylation impacts cognitive function via regulating regional translational activity in the brain.

opencc-zeroDec 2021View details →

Desiccation stress acts as cause as well as cost of dispersal in Drosophila melanogaster

Environmental stress is one of the important causes of biological dispersal. At the same time, the process of dispersal itself can incur and/or increase susceptibility to stress for the dispersing individuals. Therefore, in principle, stress can serve as both a cause and a cost of dispersal. We studied these potentially contrasting roles of a key environmental stress (desiccation) using Drosophila melanogaster. By modulating water and rest availability, we asked whether: (a) dispersers are individuals that are more susceptible to desiccation stress, (b) dispersers pay a cost in terms of reduced resistance to desiccation stress, (c) dispersal evolution alters the desiccation cost of dispersal, and (d) females pay a reproductive cost of dispersal. We found that desiccation was a clear cause of dispersal in both sexes, as both male and female dispersal propensity increased with increasing duration of desiccation. However, the desiccation cost of dispersal was male-biased, a trend unaffected by dispersal evolution. Instead, females paid a fecundity cost of dispersal. We discuss the complex relationship between desiccation and dispersal, which can lead to both positive and negative associations. Furthermore, the sex differences highlighted here may translate into differences in movement patterns, thereby giving rise to sex-biased dispersal patterns.

opencc-zeroJan 2022View details →

Thermal tolerance in Drosophila: repercussions for distribution, community coexistence and responses to climate change

Here we combined controlled experiments and field surveys to determine if estimates of heat tolerance predict distributional ranges and phenology of different Drosophila species in southern South America. We contrasted thermal death time curves, which consider both magnitude and duration of the challenge to estimate heat tolerance, against the thermal range where populations are viable based on field surveys in an 8-yr longitudinal study. We observed a strong correspondence of the physiological limits, the thermal niche for population growth, and the geographic ranges across studied species, which suggests that the thermal biology of different species provides a common currency to understand how species will respond to warming temperatures both at a local level and throughout their distribution range. Our approach represents a novel analytical toolbox to anticipate how natural communities of ectothermic organisms will respond to global warming.

opencc-by-4.0Dec 2021View details →

Natural variation in Drosophila shows weak pleiotropic effects

Pleiotropy is the phenomenon that a gene affects multiple phenotypes. The extent of pleiotropy is still disputed, mainly because of power issues. A further challenge is that empirical tests of pleiotropy are restricted to a small subset of all possible phenotypes. To overcome these limitations, we propose a new measurement of pleiotropy, which integrates across many phenotypes and multiple generations to improve power. We infer pleiotropy from the fitness cost imposed by frequency changes of pleiotropic loci. Mixing Drosophila simulans populations, which adapted independently to the same new environment using different sets of genes we show that the adaptive frequency changes have been accompanied by measurable fitness costs. Unlike previous studies characterizing the molecular basis of pleiotropy, we show that many loci, each with weak effects, contribute to genome-wide pleiotropy. We propose that the costs of pleiotropy were reduced by the modular architecture of gene expression, which facilitated adaptive gene expression changes with low impact on other functions.

opencc-zeroApr 2022View details →

A genome-wide test for paternal indirect genetic effects on lifespan in Drosophila melanogaster

Exposing sires to various environmental manipulations has demonstrated that paternal effects can be non-trivial also in species where male investment in offspring is almost exclusively limited to sperm. Whether paternal effects also have a genetic component (i.e. paternal indirect genetic effects - PIGEs) in such species is however largely unknown, primarily because of methodological difficulties separating indirect from direct effects of genes. PIGEs may nevertheless be important, since they have the capacity to contribute to evolutionary change. Here we use Drosophila genetics to construct a breeding design that allows testing nearly complete haploid genomes (>99%) for PIGEs. Using this technique, we estimate the variance in male lifespan due to PIGEs among four populations and compare this to the total paternal genetic variance (the sum of paternal indirect and direct genetic effects). Our results indicate that a substantial part of the total paternal genetic variance results from PIGEs. A screen of 38 haploid genomes, randomly sampled from a single population, suggests that PIGEs also influence variation in lifespan within populations. Collectively, our results demonstrate that PIGEs may constitute an underappreciated source of phenotypic variation.

opencc-zeroApr 2022View details →

Data from: Pre-copulatory reproductive behaviours are preserved in Drosophila melanogaster infected with bacteria

The activation of the immune system upon infection exerts a huge energetic demand on an individual, likely decreasing available resources for other vital processes, like reproduction. The factors that determine the trade-off between defensive and reproductive traits remain poorly understood. Here, we exploit the experimental tractability of the fruit fly Drosophila melanogaster to systematically assess the impact of immune system activation on pre-copulatory reproductive behaviour. Contrary to expectations, we found that male flies undergoing an immune activation continue to display high levels of courtship and mating success. Similarly, immune-challenged female flies remain highly sexually receptive. By combining behavioural paradigms, a diverse panel of pathogens and genetic strategies to induce the fly immune system, we show that pre-copulatory reproductive behaviours are preserved in infected flies, despite the significant metabolic cost of infection.

opencc-zeroMay 2022View details →

Dataset and software to analyze and simulate neuronal morphogenesis in Drosophila class IV da neurons

The highly ramified arbors of neuronal dendrites provide the substrate for the high connectivity and computational power of the brain. Altered dendritic morphology is associated with neuronal diseases. Many molecules have been shown to play crucial roles in shaping and maintaining dendrite morphology. Yet, the underlying principles by which molecular interactions generate branched morphologies are not understood. To elucidate these principles, we visualized the growth of dendrites throughout larval development of Drosophila sensory neurons and discovered that the tips of dendrites undergo dynamic instability, transitioning rapidly and stochastically between growing, shrinking, and paused states. By incorporating these measured dynamics into a novel, agent-based computational model, we showed that the complex and highly variable dendritic morphologies of these cells are a consequence of the stochastic dynamics of their dendrite tips. These principles may generalize to branching of other neuronal cell-types, as well as to branching at the subcellular and tissue levels.

opencc-zeroJun 2022View details →

Raw data from: Inter- and intra-specific variation in mycotoxin tolerance: A study of four Drosophila species

Many mycophagous Drosophila species have adapted to tolerate high concentrations of mycotoxins, an ability not reported in any other eukaryotes. Although an association between mycophagy and mycotoxin tolerance has been established in many Drosophila species, the genetic mechanisms of the tolerance are unknown. This study presents the inter- and intraspecific variation in the mycotoxin tolerance trait. We studied the mycotoxin tolerance in four Drosophila species from four separate clades within the immigrans-tripunctata radiation from two distinct locations. The effect of mycotoxin treatment on 20 isofemale lines per species was studied using seven gross phenotypes: survival to pupation, survival to eclosion, development time to pupation and eclosion, thorax length, fecundity, and longevity. We observed interspecific variation among four species, with D. falleni being the most tolerant, followed by D. recens, D. neotestacea, and D. tripunctata, in that order. The results also revealed geographical variation and intraspecific genetic variation in mycotoxin tolerance. This report provides the foundation for further delineating the genetic mechanisms of the mycotoxin tolerance trait.

opencc-zeroSep 2022View details →

Distinct signals of clinal and seasonal allele frequency change at eQTLs in Drosophila melanogaster

Populations of short-lived organisms can respond to spatial and temporal environmental heterogeneity through local adaptation. However, the comparative signals of local adaptation across space and time remains poorly understood. Here, we examined patterns of allele frequency change across a latitudinal cline and between seasons at previously reported expression quantitative trait loci (eQTLs). We divided eQTLs into groups by utilizing differential expression profiles of fly populations collected across latitudinal clines or exposed to different environmental conditions. In general, we find that eQTLs are enriched for clinally varying polymorphisms, and that these eQTLs change in frequency in concordant ways across the cline and in response to starvation and chill-coma. The enrichment of eQTLs among seasonally varying polymorphisms is more subtle, and the direction of allele frequency change at eQTLs appears to be somewhat idiosyncratic. Taken together, we suggest that clinal adaptation at eQTLs is at least partially distinct from seasonal adaptation.

FIG. 1 in The Drosophila funebris Species Group in North America (Diptera: Drosophilidae)

FIG. 1. Heads, frontal views, of native North American species of the Drosophila funebris group. A. D. limpiensis (ex: type locality: Limpia Canyon, Texas). B. D. macrospina (ex: Rochester, NY). C. D. subfunebris (ex: type series: Pasadena, CA). D. D. trispina (ex: type series: Earp, CA). To the same scale.

FIG. 8 in The Drosophila funebris Species Group in North America (Diptera: Drosophilidae)

FIG. 8. Detail of apices of aedeagi (ventral views) of native North American species of the D. funebris group (all to the same scale). A. D. limpiensis. B. D. macrospina (ex: New Orleans, LA). C. D. macrospina (ex: Piqua, OH). D. D. macrospina (ex: Missouri). E. D. trispina. F. D. subfunebris.

FIG. 2 in The Drosophila funebris Species Group in North America (Diptera: Drosophilidae)

FIG. 2. Heads, lateral views, of native North American species of the Drosophila funebris group. A. D. limpiensis (ex: Limpia Canyon, TX). B. D. macrospina (ex: Piqua, OH). C. D. subfunebris (ex: Pasadena, CA). D. D. trispina (ex: Earp, CA). To the same scale.

FIG. 5 in The Drosophila funebris Species Group in North America (Diptera: Drosophilidae)

FIG. 5. Male genitalia of native North American species of the Drosophila funebris group, ventral views (to same scale). A. D. limpiensis (ex: Limpia Canyon, TX). B. D. macrospina (ex: St. Catherine's Island, GA). C. D. macrospina (ex: Rochester, NY). D. D. subfunebris (ex: Pasadena, CA). E. D. trispina (ex: Earp, CA).