Data for: A predominant role of genotypic variation in both expression of sperm competition genes and paternity success in Drosophila melanogaster
Data files
Aug 31, 2023 version files 427.64 MB
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Patlar_Civetta_data_Acp36de.txt
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Patlar_Civetta_data_SP.txt
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Patlar_Civetta_PaternityData.txt
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README.md
Abstract
The study focuses on investigating the impact of both environmental and genotypic variations on the expression of sperm competition genes and relative paternity success (i.e. second male paternity; P2) in Drosophila melanogaster. To address this, the research leverages the Drosophila Genetic Reference Panel (DGRP) inbred lines and introduces manipulation of developmental population density, specifically larval density. This experimental design allows for the examination of the effects of genotype, environment, and potential genotype-environment interactions (GEI) on the expression of seminal fluid genes, namely Sex Peptide, Acp36DE, and CG9997 and sperm competitiveness. In light of the observed genotypic influence on genes' expression, a genome-wide association study (GWAS) was also conducted for Sex Peptide and Acp36DE.
README
Data: A predominant role of genotypic variation in both expression of sperm competition genes and paternity success in Drosophila melanogaster
***** Data text file "Patlar_Civetta_PaternityData" *****
Column A: Female ID: Individual ID assigned for each individual female used in the experiment
Column B: FemaleBot: The ID of replicates of bottles where virgin females were collected
Column C: MaleID: Individual ID assigned for each individual male used in the experiment
Column D: BSCcode: ID assigned to Drosophila Reference Panel Lines by Bloomingtoon Stock Center
Column E: DGRPcode: ID assigned to Drosophila Reference Panel Lines by publisher*~
Column F: Replicate: Replicate ID for Block - Environment combinations
Column G: Block: Block ID for experiment blocks
Column H: Env: Larval treatment levels as different environments (Low: Low larval density, High: High larval density)
Column I: seen: The first mating activity between couples were observed by watching (y) or not observed by watching (n).
Column J: secmate: The second mating was watched and seen (y) or not seen meaning second mating did not occur (n).
Column K: Vial1: The number off offspring counted from Vial 1.
Column L: gfp2: The number of gfp offpsing counted in Vial 2.
Column M: nogfp2: The number of wild type offpsing conted ion Vial 2.
Column N: gfp3: The number of gfp offpsing counted in Vial 3.
Column O: nogfp3: The number of wild type offpsing conted ion Vial 3.
Column P: gfp: Total number of gfp offspring from Vial 2 and 3.
Column Q: nogfp: Total number of wild type offspring from Vial 2 and 3.
Column R: paternity: The ratio of the number of wild type offsping to the total number of wild type and gfp offpsing from Vial 2 and 3.
*~ Mackay, T., Richards, S., Stone, E. et al. The Drosophila melanogaster Genetic Reference Panel. Nature 482, 173–178 (2012).
https://doi.org/10.1038/nature10811
***** Data text file "Patlar_Civetta_data_Acp36de" and "Patlar_Civetta_data_SP" *****
Two text files consist of Genome Wide Association Study results (gwas.top.annot) obtained through DGRP2 website~ for gene Acp26DE and Sex Peptide (SP).
Column 1: "ID" Identification code for variant
Column 2: "MinorAllele" Allele second most frequently observed
Column 3: "MajorAllele" Allele most frequently observed
Column 4: "MAF" Minor allele frequency, i.e. second highest allele frequency, from each frequency source
Column 5: "MinorAlleleCount" Allele count second most frequently observed among samples
Column 6: "MajorAlleleCount" Allele count first most frequently observed among samples
Column 7: "SinglePval" p values are from simple regression
Column 8: "SingleMixedPval" p values are from mixed effects model
Column 9: "CHR" Chromosomal location of variant
Column 10: "BP" Sequence position of variant
Column 11: "null" Variation class/type of variant
Column 12: "fdr" adjusted p-value based on false discovery rate that is used for Manhatton plot
~http://dgrp.gnets.ncsu.edu/
Usage notes
Data sets are uploaded as text files.