Data from: Shifted levels of sleep and activity under darkness as mechanisms underlying ectoparasite resistance
Data files
Apr 09, 2026 version files 5.98 MB
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Figure_1A_-Response_post-G21_DRYAD_JUNE_24_2024.xlsx
36.28 KB
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Figure_1B_-_RNA-seq_analyses_-_full_data.xlsx
2.56 MB
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Figure_2A_-_G21_stavation_assay_-_plot_-_excel.xlsx
15.40 KB
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Figure_2B_-_Final_lipids.xlsx
10.73 KB
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Figure_2C_-_Final_protein.xlsx
9.32 KB
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Figure_2D_-_Oxygen.xlsx
12.14 KB
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Figure_3A_-_Monitor-C1__C2__C3.txt
1.64 MB
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Figure_3A_-_Monitor-S1_S2_S3.txt
1.64 MB
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Figure_3b_-_sleepboutdurationaverage.csv
8.45 KB
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Figure_3C_-_darkaverage-R-Line.txt
4.66 KB
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Figure_3c_-_light_average.xlsx
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Figure_3d_-_Final-correlation.txt
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Figure_4a_-_restrainted.csv
851 B
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Figure_4b_-_FINAL_-_Day_vs_night.xlsx
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README.md
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Abstract
Parasites harm host fitness and are pervasive agents of natural selection to evolve host defense strategies. Host defensive traits in populations typically show genetic variation, which may be maintained when resistance imposes fitness costs on the host in the absence of parasites. Previously we demonstrated significant evolutionary responses to artificial selection for increasing behavioral immunity to Gamasodes queenslandicus mites in replicate lines of Drosophila melanogaster. Here, we report transcriptional shifts in metabolic processes between selected and control fly lines based on RNA-seq analyses. We also show decreased starvation resistance and increased use of nutrient reserves in flies from mite-resistant lines. Additionally, mite-resistant lines exhibited increased behavioral activity, such as, reduced sleep and elevated oxygen consumption under conditions of darkness. The link between resistance and sleep was confirmed in an independent panel of D. melanogaster genetic lines exhibiting variable sleep durations, showing a positive correlation between mite resistance and reduced sleep. Experimentally restraining the activity of artificially selected mite-resistant flies during exposure to parasites under dark conditions reduced their resistance advantage relative to control flies. The results suggest that ectoparasite resistance in this system involves increased dark-condition activity and metabolic gene expression at the expense of nutrient reserves and starvation resistance.
https://doi.org/10.5061/dryad.ghx3ffbzc
Description of the data and file structure
These are the combined datasets for Benoit et al. 2024. https://www.nature.com/articles/s44323-025-00031-7
Figure 1A - Results from the prolonged selection for mite resistance. Generation is the number of selections conducted. Line is the replicate line for selection. Replicate chamber was used to compare control and selected lines in the same mite parasitism chamber. sex is male or female. Selection treatment is control or selected. Total is the number of flies added. Dead is the number of flies not recovered. Hit is the number with mites attached. Infected is the number of fleas with mites attached or a scar from mite attachment. Uninfected is the number of flies with no scars or mites attached. General linear models were used to examine the interactions between selection status and response variables, where replicates for each selection and control lines are nested as a random effect within the selection and control treatments to establish that effects are significant among control and selected groups.
Figure 1B - Full RNA-seq output from Deseq2. Illumina datasets are available at the National Center for Biotechnology Information’s Sequence Read Archive: Bioproject PRJNA999910. Differential gene expression analysis was performed with DESeq254 with the read counts generated from Kallisto. Filtering in DESeq2 was conducted to remove predicted transcripts with fewer two mapped reads. Selection-specific effects to identify overlapping differences among lines were determined by a nested analysis that included each line and replicates. An adjusted p-value of ≤ 0.01 was used to identify genes as differentially expressed.
Figure 2A - Starvation assay for selected and control flies. Fly represents each replicate. Control male 1-3 represent males from the nonselected lines. Selected male 1-3 represent males from the selected lines. CTmale in a baseline control. Units are in hours. Survival analyses were determined with a Kaplan-Meier test and compared with a general Wilcoxon test.
Figure 2B - Lipid utilization rates for selected and control flies. Control is nonselected lines, and selected were developed for increased resistance to ectoparasitic mites. Samples are C# for control lines replicate and S# for select line replicate. CT is the base population. Rate is the μg/fly/hour of lipid utilization
Figure 2C - Protein utilization rates for selected and control flies. Control is nonselected lines, and selected were developed for increased resistance to ectoparasitic mites. Samples is C# for control lines replicate and S# for select line replicate. CT is the base population. Rate is the μg/fly/hour of protein utilization
Figure 2D - Oxygen consumption rates for selected and control flies. C is nonselected lines and S were developed for increased resistance to ectoparasitic mites. Line is the replicate selection or control lines. Oxygen is the μl Oxygen/dry mass mg/hour. Data from day is when oxygen was measured during the photophase, and night was during the scotophase (two sheets).
Figure 3A - DAM system activity (Trikinetics - Locomotor Activity Monitor 25 (LAM25) system (TriKinetics Inc., Waltham, MA, USA) and the DAMSystem3 Data Collection Software data for control (C) and Selected (S) lines. Monitor C1-C3 is the control (nonselected lines) and monitor S1-S3 is the selected lines. There are two data sets provided one for the control monitors (C1-C3) and one for the selected (S1-S3). Data collected with the DAMSystem3 was processed using the Rethomics platform in R with its associated packages including behavr, ggetho, damr and sleepr. Specific data sets over based on the number of beam crossed per minute and compared based on the relative levels (unitless).
Figure 3B - Relative sleep duration for selected and control flies. Sleep was determined with Rethomics platform in R with its associated packages including behavr, ggetho, damr and sleepr. C is nonselected lines and S were developed for increased resistance to ectoparasitic mites. Line is the replicate selection or control lines. Value are average sleep duration in seconds.
Figure 3C - Activity for selected and control flies. Activity was determined with Rethomics platform in R with its associated packages including behavr, ggetho, damr and sleepr. C is nonselected lines and S were developed for increased resistance to ectoparasitic mites. Line is the replicate selection or control lines. Value are average beam breaks per minute during the day (light) or night (dark).
Figure 3D - Sleep levels in relation to levels of parasitism. Sleep was determined with Rethomics platform in R with its associated packages including behavr, ggetho, damr and sleepr. C is nonselected lines and S were developed for increased resistance to ectoparasitic mites. Sleep amount in minutes. Number for lines represents the Bloomington Fly Stock ID. Sleep value is in total minutes per 24 hours.
Figure 4A - Mite parasitism selected and control flies following restraint. Control is nonselected lines and selected were developed for increased resistance to ectoparasitic mites. Line is the replicate selection or control lines. Restrained is if the fly was prevented from moving as described. Proportion in the number of flies that had evidence of parasitism.
Figure 4B - Parasitism levels for selected and control flies under dark or light conditions. C is nonselected lines and S were developed for increased resistance to ectoparasitic mites. Line is the replicate selection or control lines. Infected is the number of flies with mites attached or scars from mite attachment. Uninfected is the number of flies with no scars or mites attached. General linear models were used to examine the interactions between selection status and response variables, where replicates for each selection and control lines are nested as a random effect within the selection and control treatments to establish that effects are significant among control and selected groups.
Files and variables
File: Benoit_et_al._2024.zip
Description: Complete dataset for Figures 1-4 and Table S1
Figure 1A - Results from the prolonged selection for mite resistance.
Figure 1B - Full RNA-seq output from Deseq2.
Figure 2A - Starvation assay for selected and control flies.
Figure 2B - Lipid utilization rates for selected and control flies.
Figure 2C - Protein utilization rates for selected and control flies.
Figure 2D - Oxygen consumption rates for selected and control flies.
Figure 3A - DAM system activity data for control (C) and Selected (S) lines
Figure 3B - Sleep duration for selected and control flies.
Figure 3C - Activity for selected and control flies.
Figure 3D - Sleep levels in relation to levels of parasitism
Figure 4A - Mite parasitism selected and control flies following restraint.
Figure 4B - Parasitism levels for selected and control flies under dark or light conditions.
Access information
Other publicly accessible locations of the data:
- Illumina datasets are available at the National Center for Biotechnology Information’s Sequence Read Archive: Bioproject PRJNA999910