Data for: Effects of testosterone on gene expression are concordant between sexes but divergent across species of Sceloporus lizards
Data files
Jul 06, 2024 version files 24.33 MB
-
morphological_data.csv
2.82 KB
-
ReadCounts.csv
24.32 MB
-
README.md
3.41 KB
Abstract
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.
Overview
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; 0000-0002-1874-4660
MDH: mhale@hivresearch.org; 0000-0003-0338-847X
CLC: ccox@fiu.edu; 0000-0002-9424-8482
HBJ-A: henry.john-alder@rutgers.edu; 0000-0001-5036-592X
RMC: 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