DOI: 10.5061/dryad.2v6wwpzzp
title: Data from: Quantifying the phenome-wide response to sex-specific selection in Drosophila melanogaster

description: In species with separate sexes, selection on males causes evolutionary
 change in female traits values (and vice versa) via genetic correlations,
 which has far-reaching consequences for adaptation. Here, we utilise a
 sex-specific form of Robertson’s Secondary Theorem of Natural Selection to
 estimate the expected response to selection for 474 organismal-level
 traits and ~28,000 gene expression traits measured in the Drosophila
 Genetic Reference Panel (DGRP). Across organismal-level traits, selection
 acting on males produced a larger predicted evolutionary response than did
 selection acting on females, even for female traits; while for
 transcriptome traits selection on each sex produced a roughly equal
 average evolutionary response. For most traits, selection on males and
 females was predicted to move average trait values in the same direction,
 though for some traits, selection on one sex increased trait values while
 selection on the other sex decreased them, implying intralocus sexual
 conflict. Our results provide support for the hypothesis that males
 experience stronger selection than females, potentially accelerating
 adaptation in females. Furthermore, sex-opposite responses to selection
 appear to exist for only a small proportion of traits, consistent with
 observations that the inter-sex genetic correlation for fitness is
 positive but less than one in most populations so far studied.
description: We performed a forward citation search of Google Scholar for
 articles that had cited the original DGRP paper (Mackay <em>et
 al.</em>, 2012; this study introduced the resource and is the common
 citation among those that use it) as of January 2022, to obtain line mean
 estimates and associated meta-data for quantitative traits that have been
 measured in the DGRP (Figure 1). We supplemented our search by including
 all articles cited in an influential review of the DGRP (Mackay &
 Huang, 2018) and all datasets included on the DGRP2 web application
 (http://dgrp2.gnets.ncsu.edu/; Mackay <em>et al.</em>, 2012;
 Huang <em>et al.</em>, 2014). In total, we identified 126
 studies that reported line means or raw data for 38,411 phenotypic traits.
 19,259 of these were female traits and 19,081 male traits (the remaining
 71 were estimated from mixed sex groups). 36,280 of these were reported by
 a single study, which measured whole-body expression level for many of the
 known genes in <em>D. melanogaster</em> (Huang <em>et
 al.</em>, 2015). We restricted our analyses to genes that can be
 matched to the GenBank annotation of the <em>D.
 melanogaster</em> transcriptome (Carlson, 2019) and excluded any
 genes on the Y chromosome, leaving 28,536 gene expression traits. Due to
 the size and unique nature of the transcriptome relative to the rest of
 the dataset, we separated our analysis of the phenome into a transcriptome
 component and an organismal-level phenotype component
 (<em>sensu</em> Huang <em>et al.</em>, 2015). For
 analysis, we discarded traits measured in mixed sex groups or individuals
 of unknown sex, traits measured in fewer than 80 DGRP lines, and traits
 that were not measured in homozygous DGRP lines. Two studies that reported
 data for hundreds of traits related to the microbiome (Everett
 <em>et al.</em>, 2020) and metabolome (Jin <em>et
 al.</em>, 2020) were also removed from the dataset; whilst
 potentially interesting, we chose to focus on organismal-level and gene
 expression traits, as these have previously been implicated with sexual
 antagonism (Cox & Calsbeek, 2009; Innocenti & Morrow,
 2010; Wong & Holman, 2023). We retained data from 76 studies, with
 line means for 28,536 gene expression traits (14,268 per sex) and 474
 organismal-level traits, 232 and 242 of which were measured in females and
 males, respectively. For the organismal-level traits we include two
 versions of the dataset: one with trait values expressed in their original
 units and another where for each trait and sex, line means were
 standardised to µ = 0 and = 1. If you wish to use the
 combined DGRP dataset in your own research, we recommend using
 `all.dgrp.phenos_unscaled.csv` or `all.dgrp.phenos_scaled.csv`, in
 conjunction with `meta_data_for_all_traits.csv`. If you wish to download
 the dataset we used for our organismal trait analysis then you'll
 need to filter the data as mentioned in the above paragraph. See the
 Selecting data appropriate for analysis subheading in this report https://tomkeaney.github.io/Secondary_theorem_separate_sexes/Main_analysis.html for instructions and R code for pruning the dataset. Transcriptome data is also provided in this Dryad repository. All other datasets are only inlcuded so that all code can be run. If you want to recompute line means from the individual level data, these data can be found in the `data/data_collation/input/Raw_data_files` folder here: https://github.com/tomkeaney/Secondary_theorem_separate_sexes/tree/main. 
description: # Data from: Quantifying the phenome-wide response to sex-specific
 selection in Drosophila melanogaster
 [https://doi.org/10.5061/dryad.2v6wwpzzp](https://doi.org/10.5061/dryad.2v6wwpzzp) ## Description of the data and file structure Data concern a vast range of quantitative traits measured across the Drosophila genetic reference panel. With these data you can run all analyses presented in the associated manuscript. If you would like to use the dataset for your own analysis, download `meta_data_for_all_traits.csv` and either `all.dgrp.phenos_unscaled.csv` or `all.dgrp.phenos_scaled.csv` depending on whether you want to use traits expressed on their original scale or on a standardised scale (mean = 0, SD = 1). Read [this](https://tomkeaney.github.io/Secondary_theorem_separate_sexes/Data_collation.html) to see how we collated the dataset and conducted quality control. Read [this](https://tomkeaney.github.io/Secondary_theorem_separate_sexes/Main_analysis.html) to see how we further cleaned this dataset in preparation for our specific analyses. ### Files and variables ### File: meta\_data\_for\_all\_traits.csv ##### Variables * Trait: the name of the trait.  * Lines measured: the number of DGRP lines the trait was measured in. * Sex: traits were measured female, males or with pooled sexes (these are removed for analysis). * Life_stage: traits were measured in juveniles (larvae) or adults. * Trait guild: a loose categorisation of the trait, used to aid visualisation. * Trait description: a short summary of the trait and how it was measured. * Reference: the study that collected the trait data. ### File: all.dgrp.phenos\_unscaled.csv ##### Variables * line: the DGRP line number that was phenotyped. * Trait: the trait that was measured. * trait_value: the mean value of the trait, in raw units. * Reference: the study that collected the trait data. ### File: all.dgrp.phenos\_scaled.csv **Description:** identical to `all.dgrp.phenos_unscaled.csv`, except that trait values are standardised to have mean = 0 and standard deviation = 1. ### File: dgrp\_phenos\_calculated\_from\_raw\_data.csv **Description:** trait values that we calculated from individual level data, when line means weren't available. All variables have been detailed above. See this [page](https://tomkeaney.github.io/Secondary_theorem_separate_sexes/Get_line_means_from_raw_data.html) for all modelling details. If you want to re-run the models, the data can be found [here](https://github.com/tomkeaney/Secondary_theorem_separate_sexes/tree/main/data/data_collation/input/Raw_data_files). ### File: trait\_names.rds **Description:** the nice trait names come from here. Used in Figures and Tables. ### File: dgrp\_phenos\_calculated\_from\_raw\_data\_meta\_data.csv **Description:** meta-data for the traits that we needed to find line means for. All variables have been described above. ### File: all.line.mean.phenos\_metadata.csv **Description:** all the meta-data from the studies that provide line means. Everything has already been described. Included so that the code runs. ### File: gene\_anntotations.csv **Description:** gene annotation data downloaded from `GenBank` using the `org.Dm.eg.db` R package provided by `BiocManager`. ##### Variables * FBID: flybase ID. * gene_name: the name of the gene. * gene_symbol: an abbreviated form of the name. * entrez_id: the ID given to the gene in the NCBI's database for gene-specific information. Entrez is the a keyword-searching program used. * chromosome: the chromosome the gene is found on. ### File: all\_dmel\_genes.csv **Description:** GenBank annotation of the *D. melanogaster* transcriptome. All variables are as per `gene\_anntotations.csv`. ### File: all.line.mean.phenos.csv **Description:** all the line mean data. Everything has already been described. Included so that the code runs. ### File: dgrp.array.exp.female.txt **Description:** gene names, DGRP line IDs with a 1 or 2 prefix indicating whether this was the first or second measurement and the mean, whole-body expression for the gene. Measured in adult females. Data comes from [Huang et al. (2015)](https://pubmed.ncbi.nlm.nih.gov/26483487/). ### File: dgrp.array.exp.male.txt **Description:** gene names, DGRP line IDs with a 1 or 2 prefix indicating whether this was the first or second measurement and the mean, whole-body expression for the gene. Measured in adult males. Data comes from [Huang et al. (2015)](https://pubmed.ncbi.nlm.nih.gov/26483487/). ## Code/software All analyses were run in `R`. A detailed description of the code is available here: [https://tomkeaney.github.io/Secondary_theorem_separate_sexes/About.html](https://tomkeaney.github.io/Secondary_theorem_separate_sexes/About.html). ## Access information Other publicly accessible locations of the data: * [https://github.com/tomkeaney/Secondary_theorem_separate_sexes](https://github.com/tomkeaney/Secondary_theorem_separate_sexes)