Supplementary Material for Camus, Chakraborty, and Reuter, 2025

VM-dataset1-fitness.csv: Competitive fitness of male and female Drosophila melanogaster after feeding protein- or carbohydrate-rich diet as virgins or mated individuals

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.

VM-dataset2-preference.csv: Macronutrient consumption of virgin and mated males and females of Drosophila melanogaster

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. 

VM-dataset3-heat.csv: Thermal tolerance of virgin and mated female Drosophila melanogaster after feeding on protein- or carbohydrate-rich diets

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

VM-dataset4-genelist-female.xlsx: Gene expression changes in female flies exposed to carbohydrate or protein environment. The was examined in mated and virgin flies 

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

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

VM-dataset5-genelist-male.xlsx: Gene expression changes in male flies exposed to carbohydrate or protein environment. 

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) 

VM-dataset6-genelist-female-TF.xlsx: Enriched transcription factor binding sites for DEGs in females

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

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

VM-dataset7-genelist-male-TF.xlsx: Enriched transcription factor binding sites for DEGs in males

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