DOI: 10.25387/g3.30375490
title: Supplementary Material for Camus, Chakraborty, and Reuter, 2025

description: <strong>VM-dataset1-fitness.csv:</strong> <strong>Competitive fitness of male and female </strong><em><strong>Drosophila melanogaster</strong></em><strong> after feeding protein- or carbohydrate-rich diet as virgins or mated individuals</strong>
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The dataset contains the following variables:
-  vial: a vial ID, specific to the diet treatment
-  diet: the diet treatment, P = protein rich, C = carbohydrate-rich
-  sex: the sex of the triplet of focal flies (male or female)
-  rep: the replicate vial, specific to a combination of diet, sex and status
-  status: mating status of the focal individuals during feeding (mated or virgin)
-  total: total amount of liquid diet consumed in ul
-  pro.ug: amount of protein consumed by flies (ug)
-  carb.ug: amount of carbohydrate consumed by flies (ug)
-  egg: number of eggs laid in the female fecundity assay
-  red, brown, total: number of offspring with red or brown eyes (fathered by focal and competitor males, respectively) and total eclosed in the male fertilisation assay.
-  prop.red: proportion of red-eyed offspring eclosed in the male fertilisation assay, calculated from red and total.
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<strong>VM-dataset2-preference.csv:</strong> <strong>Macronutrient consumption of virgin and mated males and females of </strong><em><strong>Drosophila melanogaster</strong></em>
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The dataset contains the following variables:
-  status: mating status of the focal individuals during feeding, mated or virgin
-  sex: the sex of the triplet of focal flies
-  vial: a vial ID, specific to the diet treatment
-  pro(ul), carb(ul): the quantity of liquid media consumed from the capillary containing the liquid protein and carbohydrate diet, respectively. Evaporation has already been controlled for in these calculations. 
-  pro(ug), carb(ug): liquid volume converted into ug of protein and carbohydrate consumed. Obtained by multiplying the previous 2 columns (pro(ul), carb(ul)) by 32.5, which is the concentration of protein/carb in the stock solutions. 
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<strong>VM-dataset3-heat.csv:</strong> <strong>Thermal tolerance of virgin and mated female </strong><em><strong>Drosophila melanogaster</strong></em><strong> after feeding on protein- or carbohydrate-rich diets</strong>
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The dataset contains the following variables:
-  run: the experimental run, 1 or 2
-  side: the side of the rack onto which a tube was clipped, A or B
-  status: mating status of the individuals, mated or virgin
-  diet: the diet treatment, P = protein rich, C = carbohydrate-rich
-  minute, second: the recorded number of minutes and seconds until heat coma
-  totalminutes: the total time until heat coma in minutes
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<strong>VM-dataset4-genelist-female.xlsx:</strong> <strong>Gene expression changes in female flies exposed to carbohydrate or protein environment. The was examined in mated and virgin flies</strong> 
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The dataset contains four tabs: 
1.  diet: fold genes in our model where we look at overall diet effects (carbohydrate-to-protein)
2.  mating status: genes in our model where we look at overall mating status effects (virgin-to-mated)
3.  D+M: genes in our model that showed additive diet + mating status effects
4.  DxM: genes in our model that show interactive diet x mating status effects
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Each tab has the same column headers: 
-  S: did we observe an overall “mating Status” effect (Yes or No)
-  D: did we observe an overall “Diet” effect (Yes or No)
-  SD: did we observe an interactive “mating status x diet” effect (Yes or No)
-  combo: combining S, D and SD columns into one. 
-  FLYBASE: Flybase ID 
-  ENTREZID: Entrez ID
-  SYMBOL: NCBI ID 
-  GENENAME: Gene name
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<strong>VM-dataset5-genelist-male.xlsx: Gene expression changes in male flies exposed to carbohydrate or protein environment.</strong> 
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The dataset contains the following variables [one tab]:
-  FLYBASE: Flybase ID 
-  ENTREZID: Entrez ID
-  SYMBOL: NCBI ID 
-  GENENAME: Gene name
-  logFC: Log fold change going from a carbohydrate environment to a protein environment
-  logCPM: log counts per million – number of reads mapped to the given gene
-  F: F-value for the fold change 
-  PValue: significance value for the fold change difference
-  FDR: False discovery rate corrected p-value
-  dir: direction of fold change (U = up, D = down) 
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<strong>VM-dataset6-genelist-female-TF.xlsx: Enriched transcription factor binding sites for DEGs in females</strong>
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The dataset contains four tabs: 
1.  diet: fold genes in our model where we look at overall diet effects (carbohydrate-to-protein)
2.  mating status: genes in our model where we look at overall mating status effects (virgin-to-mated)
3.  D+M: genes in our model that showed additive diet + mating status effects
4.  DxM: genes in our model that show interactive diet x mating status effects
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Each tab has the same column headers: 
-  motif: predicted transcription factor binding site motif
-  NES: Normalised Enrichment Score of the motif from the TF motif database. This value is calculated -for each motif- based on the AUC distribution of all the motifs for the gene-set. Those motifs that pass the given threshold are considered significant.
-  AUC: Area Under the Curve
-  TF_hc_pred: predictiontion of high confidence of transcription factor binding
-  nEnrGenes: Number of genes in having the transcription factor binding site motif
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<strong>VM-dataset7-genelist-male-TF.xlsx:</strong> <strong>Enriched transcription factor binding sites for DEGs in males</strong>
 
The dataset contains the following columns:
-  motif: predicted transcription factor binding site motif
-  NES: Normalised Enrichment Score of the motif from the TF motif database. This value is calculated -for each motif- based on the AUC distribution of all the motifs for the gene-set. Those motifs that pass the given threshold are considered significant.
-  AUC: Area Under the Curve
-  TF_hc_pred: predictiontion of high confidence of transcription factor binding
-  nEnrGenes: Number of genes in having the transcription factor binding site motif