DOI: 10.5061/dryad.fj6q57432
title: Data for: Effects of testosterone on gene expression are concordant between sexes but divergent across species of Sceloporus lizards

description: Hormones mediate sexual dimorphism by regulating sex-specific patterns of
 gene expression, but it is unclear how much of this regulation involves
 sex-specific hormone levels versus sex-specific transcriptomic responses
 to the same hormonal signal. Moreover, transcriptomic responses to
 hormones can evolve, but the extent to which hormonal pleiotropy in gene
 regulation is conserved across closely related species is not well
 understood. We addressed these issues by elevating testosterone levels in
 juvenile females and males of three Sceloporus lizard species prior to
 sexual divergence in circulating testosterone, then characterizing
 transcriptomic responses in the liver. In each species, more genes were
 responsive to testosterone in males than in females, suggesting that early
 developmental processes prime sex-specific transcriptomic responses to
 testosterone later in life. However, overall transcriptomic responses to
 testosterone were concordant between sexes, with no genes exhibiting
 sex-by-treatment interactions. By contrast, hundreds of genes exhibited
 species-by-treatment interactions, particularly when comparing distantly
 related species with different patterns of sexual dimorphism, suggesting
 evolutionary lability in gene regulation by testosterone. Collectively,
 our results indicate that early organizational effects may lead to
 sex-specific differences in the magnitude, but not the direction, of
 transcriptomic responses to testosterone, and that the hormone-genome
 interface accrues regulatory changes over evolutionary time.
description: # Data for: Effects of testosterone on gene expression are concordant
 between sexes but divergent across species of Sceloporus lizards ##
 Overview
 [https://doi.org/10.5061/dryad.fj6q57432](https://doi.org/10.5061/dryad.fj6q57432) README code and data file explanation for: "Effects of testosterone on gene expression are concordant between sexes but divergent across species of *Sceloporus* lizards" Robinson CD, MD Hale, CL Cox, HB John-Alder, and RM Cox. 2024. Effects of testosterone on gene expression are concordant between sexes but divergent across species of *Sceloporus* lizards. The American Naturalist.  Email addresses and ORCIDs: CDR*, corresponding author: [cdr4ua@virginia.edu](mailto:cdr4ua@virginia.edu); 0000-0002-1874-4660 MDH: [mhale@hivresearch.org](mailto:mhale@hivresearch.org); 0000-0003-0338-847X CLC: [ccox@fiu.edu](mailto:ccox@fiu.edu); 0000-0002-9424-8482 HBJ-A: [henry.john-alder@rutgers.edu](mailto:henry.john-alder@rutgers.edu); 0000-0001-5036-592X RMC: [rmc3u@virginia.edu](mailto:rmc3u@virginia.edu); 0000-0001-8325-111X All authors contributed to data collection. Code was written by CDR.  ## Description of the data and file structure The following data files are used: morphological_data.csv ReadCounts.csv See below for column identification.  **morphological_data.csv** ID - column containing the individual ID for each individual Species - column containing the species to which each individual belongs ``` SCME - Sceloporus merriami SCUN - Sceloporus undulatus SCVI - Sceloporus virgatus ``` Sex - column containing the sex of each individual ``` F - Female M - Male ``` Treatment - column containing information about the implant recieved by an individual ``` CONT - Control implant TEST - Testosterone implant ``` SVL - column containing the snout-to-vent length (SVL) of each individual, measured in millimeters Mass - column containing the mass of each individual, measured in grams Test_conc - column containing the circulating level of testosterone at the time of tissue collection for each individual, measured in nanograms per milliliter ``` N/A - Three testosterone values are missing in the dataset and therefore Not Available. The assay failed for these individuals. Analysis of testosterone levels excluded them. ``` **ReadCounts.csv** Geneid - column containing the Gene ID Chr - column containing information about which chromosome a gene resides on Start - column containing information about the position on the chromosome a gene begins End - column containing information about the position on the chromosome a gene ends Strand - column containing information about which strand each exon resides on Length - column containing information about the number of basepairs in a gene Every remaining column is an individual ID, with each datum representing the number of transcripts counted for each gene (row) ## Code/Software The following packages and versions are used for this dataset: edgeR v3.38.4 DESeq2 v1.42.0 plyr v1.8.9 dplyr v1.1.4 ggplot2 v3.4.4 rospca v1.0.4 cowplot v1.1.1 To install edgeR and DESeq2, use bioconductor. Specifically, use the following code: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("edgeR") BiocManager::install("DESeq2") The R code for all analyses and figures is provided in the file: TestosteroneManip_Code.R