Genotype-by-environment interactions influence the composition of the Drosophila seminal proteome

Ejaculate proteins are key mediators of post-mating sexual selection and sexual conflict, as they can influence both male fertilization success and female reproductive physiology. However, the extent and sources of genetic variation and condition dependence of the ejaculate proteome are largely unknown. Such knowledge could reveal the targets and mechanisms of post-mating selection and inform about the relative costs and allocation of different ejaculate components, each with its own potential fitness consequences. Here, we used liquid chromatography coupled with tandem mass spectrometry to characterize the whole-ejaculate protein composition across twelve isogenic lines of Drosophila melanogaster that were reared on a high- or low-quality diet. We discovered new proteins in the transferred ejaculate and inferred their origin in the male reproductive system. We further found that the ejaculate composition was mainly determined by genotype identity and genotype-specific responses to larv..., We derived all individuals from 12 independent isogenic lines (hereafter: “isolines”) of D. melanogaster, created through 15 generations of full-sibling inbreeding from an outbred population (approx. 1,000 adults with overlapping generations). Previous studies have reported significant genetic variation in ejaculate traits across these isolines [11,32,41]. Using isogenic lines allowed us to subject multiple individuals of each genotype simultaneously to different treatments, thereby separating genotypic from treatment effects. To establish the different developmental treatments, we transferred groups of 40 first-instar larvae to food vials, filled with either standard cornmeal medium (75 g glucose, 100 g fresh yeast, 55 g cornmeal, 8 g agar, 10 g flour, 15 ml Nipagin antimicrobial agent per litre medium) or a nutrient-restricted, less favourable version. For the latter, we diluted (9-fold) the standard medium in water and agar to a final agar concentration of 15 g/L. The standard female..., Usage notes
There are two supplementary table:
–      “Table_S1_dataset”: the datasets used in this study.
–      “Table_S2_analysis_output”: the output of the analysis.
There are 2 R-scripts:
–      “code”: the R-code used to produce the results of this study.
–      “code_Fig.S4AC”: a second R-code used to produce Fig. S4A, S4B and S4C.
The Mass Spectrometer data, which the analysis is based on:
–      “raw_MS_file_TMT_A-E”: The raw data as obtained using Proteome Discoverer v2.5 (Thermo Fisher Scientific), searching against the D. melanogaster protein database containing only the longest isoform for each protein (r6.32; Thurmond et al, 2019, n = 13,813 entries).
The thorax length data:
–      “thorax_length”: the thorax length of 35 focal males and standard females per isoline-treatment combination.
And 2 additional files used for the analysis:
–      “bothContrasts”: the proteins that were differentially expressed relative to diet or isoline prior to FDR correction (from Fig. 2 and ...