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Data for 'Genetic variation in trophic avoidance shows fruit flies are generally attracted to bacterial pathogens'
<p>Raw data dn R code for the analysis of data dn generation of all figures in the above referenced paper. Descriptions of each data file are included wihtin the R script. </p>
Calcium imaging of odor responses in the fruit fly mushroom body
<p><strong>Abstract</strong></p> <p>This dataset contains olfactory responses in the third stage of the olfactory circuit in fruit flies: the mushroom body. The responses are recorded with the GCaMP3 sensor. The methods used to collect the data and the procedures to process them are presented in detail in Campbell et al., 2013, Journal of Neuroscience. The dataset was also used in a recent manuscript by Srinivasan et al., 2023.</p> <p><strong>Methods</strong></p> <p>Please refer to Campbell et al., 2013, Journal of Neuroscience for details. Here, we present a description of how the data was collected, the odors presented, and the analysis, excerpted from Campbell et al., 2013.</p> <p><strong>Animal preparation</strong></p> <p>Flies carrying the genetically encoded calcium sensor UAS-GCaMP3 (Tian et al., 2009) were crossed with OK107-Gal4 flies (Connolly et al., 1996) to drive GCaMP3 expression in essentially all KCs (Lee and Luo, 1999; Aso et al., 2009). All experiments were conducted on female F1 heterozygotes from this cross, aged 2–5 d post-eclosion. Procedures for animal preparation were as described previously (Turner et al., 2008; Murthy and Turner, 2010; Honegger et al., 2011). Flies were anesthetized temporarily on ice and inserted into a small hole cut in the recording platform. The animal’s head was tilted forward, exposing the olfactory organs to the odor delivery nozzle located on the underside of the plat- form. The fly was fixed in place with fast-drying epoxy (Devcon 5 min epoxy). The top of the fly was bathed in oxygenated saline (Wilson et al., 2004) and the cuticle overlying the brain was dissected away. Air sacs overlying the MBs were pushed aside, but we did not attempt to remove the perineural sheath. To minimize movement of the brain inside the head capsule, we removed the pulsatile organ at the neck and the probos- cis retractor muscles that pass over the caudal aspect of the optic lobes.</p> <p> </p> <p><strong>Odor delivery </strong></p> <p>The following chemicals were used as stimuli: 2-heptanone (CAS #110-43- 0), 3-octanol (CAS #589-98-0), 6-methyl-5-hepten-2-one (CAS #110-93-0), ␣-humulene (CAS #6753-98-6), benzaldehyde (CAS #100-52-7), ethyl lactate (CAS #97-64-3), ethyl octanoate (CAS #106-32-1), hexanal (CAS #66-25-1), isoamyl acetate (CAS #123-92-2), 4-methylcyclo- hexanol (CAS #589-91-3), methyl octanoate (CAS #111-11-5), diethyl suc- cinate (CAS #123-25-1), pentanal (CAS #110-62-3), butyl acetate (CAS #123-86-4), 1-octen-3-ol (CAS #3391-86-4), 1-hepten-3-ol (CAS #4938-52- 7), and pentyl acetate (CAS #628-63-7). Odors were presented using a custom-built delivery system that uses serial air dilutions to control odor concentration while maintaining a constant total airflow of 1 L/min at the fly. Experiments were conducted at an odor dilution of 1:100 or, where appropriate, adjusted to match the concentrations used behaviorally. We used a photo-ionization detector (Aurora Scientific) to match concentrations between the imaging rig and the T-maze and to monitor odor delivery throughout each imaging ex- periment. Odor pulses were created by switching between clean and odorized air streams using a synchronous two-way valve (N-Research). This final valve was located 50 cm from the fly, leading to a delay of 300 ms between valve switching and the odor reaching the fly. The flow path was 1/8 inch in diameter throughout, which enabled the system to work near atmospheric pressure at these flow rates. The distance of the valve from the fly and the large tubing diameter virtually eliminated pressure transients caused by valve switching, as measured by the photo-ionization detector and a hot-wire anemometer.</p> <p><strong>Calcium imaging</strong></p> <p>Two-photon imaging was performed using a Prairie Ultima system (Prairie Technologies) and a Ti-Sapphire laser (Chameleon XR; Coher- ent) tuned to 920 nm delivering 8 –10 mW at the sample. All images were acquired with Olympus water-immersion objectives (LUMPlanFl/IR, 60x, numerical aperture 0.9; LUMPlanFl/IR, 40x, numerical aperture 0.8). Imaging planes were selected to maximize the number of visibleKCs. Typically imaging frames were 300 x 300 pixels, acquired with a pixel dwell time of 1.6 s, yielding frame rates near 3.8 Hz. On average, 120 KCs (range: 60 –170) were monitored in one plane. Custom MATLAB (MathWorks) routines were used to control odor presentation and synchronize stimulus delivery with data acquisition. Data were acquired in 20 s sweeps with a 1 s odor pulse triggered 8 s after sweep onset. The interstimulus interval was 25 s. Stimuli were presented in randomly interleaved fashion, adjusted so that the same odor was never presented twice in succession.</p> <p><strong>Imaging analysis</strong></p> <p>Data were analyzed using MATLAB and R (http://www.R-project.org). To correct for motion within the field of view, frames were aligned using 2D image registration approaches. In many cases, a Fourier-based sub-pixel translation correction was sufficient (Guizar-Sicairos et al., 2008). Some animals required an affine transform to cope with global distortions, such as rotational movement of the brain (Thirion, 1998). Where necessary a nonrigid transform was used to correct more localized dis- tortions (Klein et al., 2010). Fluorescent neural tissue was automatically segmented from the surrounding regions. Pixel intensity values from the area outside this boundary were considered to represent background (tissue autofluorescence plus shot noise) and the mean pixel intensity value from the back- ground was then subtracted from the overall image. To quantify the response of the KCs a small, circular region of interest 6 – 8 pixels in diameter was applied to each cell body. This allowed aver- aging of the pixel intensity values from each cell, treating individual KCs as separate units. Care was taken to ensure that each selected cell re- mained within its region of interest over the whole imaging session. Response amplitudes were calculated as the mean change in fluorescence (dF/F) in the 0.5– 4.5 s window after stimulus onset. A statistical test originally described in Honegger et al. (2011) was used to determine whether a KC responded significantly on a given trial. Briefly, the SD of the baseline activity was obtained 8 s before stimulus onset. The response time course was then smoothed using a five-point running average to control for outliers. The peak dF/F in the 0.5– 4.5 s window after stimulus onset was determined. The response was judged to be significant if this peak was 2.33 SDs greater than the baseline, which corresponds to a one-tailed significance test where alpha = 0.01.</p> <p><br> <strong>References</strong></p> <p>Aso Y, Grübel K, Busch S, Friedrich AB, Siwanowicz I, Tanimoto H (2009) The mushroom body of adult Drosophila characterized by GAL4 drivers. J Neurogenet 23:156 –172. </p> <p>Connolly JB, Roberts IJ, Armstrong JD, Kaiser K, Forte M, Tully T, O’Kane CJ (1996) Associative learning disrupted by impaired Gs signaling in Drosophila mushroom bodies. Science 274:2104 –2107.</p> <p>Honegger KS, Campbell RA, Turner GC (2011) Cellular-resolution population imaging reveals robust sparse coding in the Drosophila mushroom body. J Neurosci 31:11772–11785.</p> <p>Lee T, Luo L (1999) Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis. Neuron 22:451– 461.</p> <p>Murthy M, Turner GC (2010) In vivo whole-cell recordings in the Drosophila brain. In: Drosophila neurobiology methods: a laboratory manual (Zhang B, Waddell S, Freeman M, eds). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.</p> <p>Srinivasan, S., Daste, S., Modi, M., Turner, G., Fleischmann, A. & Navlakha, S (2023). Stochastic coding: a conserved feature of odor representations and its implications for odor discrimination. bioRxiv.</p> <p>Thirion JP (1998) Image matching as a diffusion process: an analogy with Maxwell’s demons. Med Image Anal 2:243–260.</p> <p>Tian L, Hires SA, Mao T, Huber D, Chiappe ME, Chalasani SH, Petreanu L, Akerboom J, McKinney SA, Schreiter ER, Bargmann CI, Jayaraman V, Svoboda K, Looger LL (2009) Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators. Nat Methods 6:875–881.</p> <p>Turner GC, Bazhenov M, Laurent G (2008) Olfactory representations by Drosophila mushroom body neurons. J Neurophysiol 99:734 –746.</p> <p>Wilson RI, Turner GC, Laurent G (2004) Transformation of olfactory representations in the Drosophila antennal lobe. Science 303:366–370.</p> <p><strong>Usage notes</strong></p> <p>The files are all in csv format, and can be easily opened in R or Python or other programming languages.</p> <p>Please see the README.md file for directions on how to use the data.</p> <p>The dataset included here is broken into two parts. The main dataset was the one that was chiefly used in the Campbell and Srinivasan papers, with the second part containing 7 additional datasets that were used in some figures. A fuller description is available in the README.md file.</p>
Fig. 2 in Notes on the frugivorous fruit fly (Diptera: Tephritidae) fauna of western Africa, with description of a new Dacus species
Fig. 2. Ecoregion boundaries of West Guinean Lowland Forest (1), East Guinean Forest (2), Nigerian Lowland Forest (3), Cross-Nigerian Transition Forest (4), West Sudanian Savannah (5), Guinean Forest Savannah Mosaic (6), Jos Plateau Forest Grassland Mosaic (7), Central African Mangroves (8), with sites of collecting events for Tephritidae (open circles).
Fig. 1 in Notes on the frugivorous fruit fly (Diptera: Tephritidae) fauna of western Africa, with description of a new Dacus species
Fig. 1. Country boundaries of Ivory Coast (1), Ghana (2), Togo (3), Benin (4) and Nigeria (5) with sites of collecting events for Tephritidae (open circles).
Figs 31–34. Ichneumonopsis burmensis Hardy, 1973, biological traits. 31 in A revision of Ichneumonopsis Hardy, 1973 (Diptera: Tephritidae: Dacinae: Gastrozonini), Oriental bamboo-shoot fruit flies
Figs 31–34. Ichneumonopsis burmensis Hardy, 1973, biological traits. 31. Bamboo shoots of the host plant, Pseudoxytenanthera albociliata, at the edge of an abandoned field in northern Thailand in November. The shoots are 2–5 m tall and up to 2 cm wide at the base. 32. Bamboo internode (ca 7 mm wide) infested by an I. burmensis larva. The internode is located at the tip of the bamboo shoot, because the apical 4–5 internodes have died and fallen to the ground. 33. A fully-grown I. burmensis larva (length ca 14 mm) that has started to bite off strips of vascular bundles from the bamboo shoot wall (on the right) in order to create a cocoon. 34. I. burmensis puparium (length ca 8 mm) located in the internode cavity at the base of the infested internode. The upper part of the internode has broken off. Side branches growing from the basal bud were partly removed.
Figs 22–24. Ichneumonopsis spp., epandrium. 22. I. burmensis Hardy, 1973, anterior view. 23. I. burmensis Hardy, 1973, lateral view. 24 in A revision of Ichneumonopsis Hardy, 1973 (Diptera: Tephritidae: Dacinae: Gastrozonini), Oriental bamboo-shoot fruit flies
Figs 22–24. Ichneumonopsis spp., epandrium. 22. I. burmensis Hardy, 1973, anterior view. 23. I. burmensis Hardy, 1973, lateral view. 24. Ichneumonopsis taiwanensis sp. nov., lateral view.
Figs 10–12 in A revision of Ichneumonopsis Hardy, 1973 (Diptera: Tephritidae: Dacinae: Gastrozonini), Oriental bamboo-shoot fruit flies
Figs 10–12. Ichneumonopsis spp., thorax, lateral view. 10. I. burmensis Hardy, 1973. 11. I. hancocki sp. nov. 12. I. taiwanensis sp. nov.
Figs 7–9 in A revision of Ichneumonopsis Hardy, 1973 (Diptera: Tephritidae: Dacinae: Gastrozonini), Oriental bamboo-shoot fruit flies
Figs 7–9. Ichneumonopsis spp., head and thorax, dorsal view. 7. I. burmensis Hardy, 1973. 8. I. hancocki sp. nov. 9. I. taiwanensis sp. nov.
Figs 2–4. Ichneumonopsis spp., habitus. 2. I. burmensis Hardy, 1973 in A revision of Ichneumonopsis Hardy, 1973 (Diptera: Tephritidae: Dacinae: Gastrozonini), Oriental bamboo-shoot fruit flies
Figs 2–4. Ichneumonopsis spp., habitus. 2. I. burmensis Hardy, 1973, ♀. 3. I. hancocki sp. nov., holotype, ♂. 4. I. taiwanensis sp. nov., holotype, ♀.
Data and scripts for the analysis of fruit flies' species distributions in Reunion island
<p>Data and scripts supporting the analyses of the joint species distributions of eight Tephritids species in La Réunion island.</p>
Fig. 6 in The Taxonomy And Phylogenetic Relationships Of Species In The Bactrocera Musae Complex Of Fruit Flies (Diptera: Tephritidae: Dacinae) In Papua New Guinea
Fig. 6. Neighbour joining tree showing relationships between CO1 haplotypes from species in the Bactrocera musae complex. Values at nodes are for 1000 bootstrap replicates of the maximum likelihood calculations using the Kimura two-parameter model of sequence evolution (left) and Bayesian posterior probability (right). Clade A = B. musae, Clade B = B. rufivitta, Clade C = B. contermina. Note: the numbers at the branch tips represent the field collection codes given to individual specimens.
Fig. 7 in The Taxonomy And Phylogenetic Relationships Of Species In The Bactrocera Musae Complex Of Fruit Flies (Diptera: Tephritidae: Dacinae) In Papua New Guinea
Fig. 7. Diagram showing clustering of individuals at (A) the highest hierarchical level of structuring in the Bactrocera musae complex using STRUCTURE, and (B) the sub-group structuring into two further clusters of the individuals from the red cluster in A. Vertical bars represent individuals and colours denote the proportion of ancestry from each cluster based on eight microsatellite loci. Note at the highest level (A), individuals are clearly assigned to either the B. musae or the 'others' cluster. At the next level (B), individuals from the 'others' cluster are assigned to either the B. rufivitta cluster (red) or the B. contermina cluster (green). Note: The numbers below the vertical bars represent the field collection codes given to individual specimens.
Figure 1 in Detection of Male Mediterranean Fruit Flies (Diptera: Tephritidae): Performance of Trimedlure Relative to Capilure and Enriched Ginger Root Oil
Figure 1. Capture of C. capitata males in TML- versus CPL-baited Jackson traps for 3 replicates in an Oahu coffee field. Abscissa represents period of lure ageing, where 0 weeks represents fresh lures. Bar heights indicate mean of 20 traps per lure type; error bars represent + 1 SE. Symbols above bars show results of the Tukey HSD test comparing the 2 lures for each ageing category, where an asterisk indicates P <0.001 and ns indicates no significant difference.
Fig. 3. Cytochrome c oxidase subunit I in Analysis of COI gene, prevalence, and intensity of the bat fly Cyclopodia greeffi on roosting straw-coloured fruit bat Eidolon helvum in Southwest Nigeria
Fig. 3. Cytochrome c oxidase subunit I (COI) gene sequence phylogeny showing the relationship between Cyclopodia greeffi and other species of the same and different genera. Values obtained from Bayesian posterior are presented as supports at the nodes. BI – Bayesian posterior probability value.
Fig. 2. Cyclopodia greeffi. a in Analysis of COI gene, prevalence, and intensity of the bat fly Cyclopodia greeffi on roosting straw-coloured fruit bat Eidolon helvum in Southwest Nigeria
Fig. 2. Cyclopodia greeffi. a. Thorax, dorsal: ctenidia with thick blunt teeth. b, c, d. Abdomen ventral: b. sternite 1–2 bearing ctenidium, with about 40–44 blunt teeth; c. male, claspers long and slender, pigmented at the apex, fifth sternite with 8 spines; d. female, truncate abdomen, sternite with two curved rows of spine.
Fig. 6 in Analysis of COI gene, prevalence, and intensity of the bat fly Cyclopodia greeffi on roosting straw-coloured fruit bat Eidolon helvum in Southwest Nigeria
Fig. 6. Regression distribution plot of Cyclopodia greeffi infestation intensity on Eidolon helvum weight for both sexes and seasons.
Fig. 1. a, b, c. C in Analysis of COI gene, prevalence, and intensity of the bat fly Cyclopodia greeffi on roosting straw-coloured fruit bat Eidolon helvum in Southwest Nigeria
Fig. 1. a, b, c. C. greeffi parasites on the straw-coloured fruit bat Eidolon helvum. a. fur around the right side of shoulder and neck region; b. ventral side of the wing (patagium) region below the right forearm; c. ventral side of the abdominal region. Arrows are pointing to the location of the bat flies.
Fig. 5 in Analysis of COI gene, prevalence, and intensity of the bat fly Cyclopodia greeffi on roosting straw-coloured fruit bat Eidolon helvum in Southwest Nigeria
Fig. 5. Density distribution plot of intensity of infestation of Cyclopodia greeffi on Eidolon helvum showing seasonal bimodal distribution.
Fig. 4 in Analysis of COI gene, prevalence, and intensity of the bat fly Cyclopodia greeffi on roosting straw-coloured fruit bat Eidolon helvum in Southwest Nigeria
Fig. 4. Density distribution plot of intensity of Cyclopodia greeffi infestation on Eidolon helvum for sexes and seasons.
F I G U R E 3 in Oviposition by the oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), on five citrus types in a laboratory
F I G U R E 3 Mean (±1 SE) proportion of time female Bactrocera dorsalis spent on aggression, grooming, oviposition, probing, being inactive, and walking and tasting on (a) damaged and (b) undamaged citrus types and a positive control (Golden Delicious apple). Citrus types investigated were Golden Delicious apple, Delta Valencia orange, Eureka lemon, Glen Ora navel orange, Nadorcott mandarin and Star Ruby grapefruit. Each female was observed for 20 min.
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Allen Brain Atlas
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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