Skip to main content
Dryad

Data for: Effects of testosterone on gene expression are concordant between sexes but divergent across species of Sceloporus lizards

Cite this dataset

Robinson, Christopher et al. (2024). Data for: Effects of testosterone on gene expression are concordant between sexes but divergent across species of Sceloporus lizards [Dataset]. Dryad. https://doi.org/10.5061/dryad.fj6q57432

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.

README: 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

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

Funding

National Science Foundation, Award: IOS 1755134

National Science Foundation, Award: IOS 2024064

National Science Foundation, Award: IOS 1754934

National Science Foundation, Award: IOS 1755026

United States Department of Agriculture, Award: NJ17321, McIntire-Stennis award