DOI: 10.5061/dryad.9cnp5hqtt
title: Data from: Maternal deposition of hormones and contaminants shape the gonadal transcriptome in American alligators

description: Environmental conditions influence the maternal deposition of hormones
 into eggs, which is hypothesized to adaptively modify developmental
 outcomes in offspring. However, most ecosystems harbor environmental
 contaminants capable of disrupting endocrine signaling, and maternal
 exposure to these compounds has the potential to further alter offspring
 traits. Studies rarely examine maternally derived hormones and
 contaminants along with offspring phentoypes, and we know little about
 their interrelationships and potential interactions. Here, we measure yolk
 concentrations of 24 endocrine disrupting compounds (EDCs) and 28 steroid
 hormones along with gonadal transcriptomes from two populations of the
 American alligator (Alligator mississippiensis) that differ in
 reproductive development and exposure to EDCs. Using a network-based
 approach, we identify gene expression modules associated with hormones and
 contaminants independently, in combination, or by potential indirect
 influences of EDCs on maternal hormone deposition. We find that yolk
 concentrations of both 17β-estradiol and etiocholanolone differ across
 populations and contribute to substantial variation in gene expression. We
 further provide evidence for the indirect effect of the pesticide,
 methoxychlor, on gonadal gene expression through its relationship with
 17β-estradiol. Our results reveal novel pathways by which maternal
 exposure to environmental contaminants interacts with hormone provisioning
 to affect offspring sexual development.
description: # Maternal deposition of hormones and contaminants shape the gonadal
 transcriptome in American alligators
 [https://doi.org/10.5061/dryad.9cnp5hqtt](https://doi.org/10.5061/dryad.9cnp5hqtt) ## Description of the data and file structure README for APWO21 datasets **Script file**: **APWO21_alignment_trimming_qc** This is the pipeline for qc of raw reads, trimming and alignment of reads to the reference genome **APWO21_read_counting.R** R script for using GenomicAlignments to count reads by gene from BAM files **APWO21_WGCNA.R** R script for running the WGCNA on gene counts **APWO21_analyses.R** R script for comparing concentrations of hormones and contaminants between populations, testing associations between modules and contaminants/hormones, and testing relationships between contaminants and hormones associated with the same module. **Data files** **MEs_horm_contam.csv** Contains module eigengenes from WGCNA and values for components of the developmental endocrine environment that differ across populations clutch - the clutch the egg originated from site - the population the egg originated from columns starting with ME - module eigengene value for each module columns with compound names - concentrations of contaminants or hormones (ng/g) for each sample. PC1 represents the value for the first principal component (see methods) **yolk_OCPs_raw.csv** Raw values for OCP measurements in egg yolk in ng/g. Columns represent individual compounds. egg_id - identifier for individual egg yolk clutch - clutch egg originated from yolk_PCBs_raw.csv Raw values for PCB measurements in egg yolk in ng/g. Columns represent individual compounds. egg_id - identifier for individual egg yolk clutch - clutch egg originated from **HORMONES_RAW.csv** Raw values for hormone measurements in egg yolk in ng/g. Columns represent individual compounds. egg_id - identifier for individual egg yolk clutch - clutch egg originated from APWO21_dev_env_final.csv Filtered dataset of hormones and contaminants by clutch - this is the data used in analyses for gene expression clutch - clutch egg measurement(s) originated from site - population of origin ### Files and variables #### File: MEs\_horm\_contam.csv **Description:** Complete, filtered data frame of module eigengenes and components of the developmental environment that differ between populations ##### Variables * clutch: clutch of origin * site: population of origin  * MEturquoise: eigengene value * MEpink: eigengene value * MEred: eigengene value * MEmagenta: eigengene value * MEblack: eigengene value * MEgreen: eigengene value * MEyellow: eigengene value * MEblue: eigengene value * MEbrown: eigengene value * MEgrey: eigengene value * temp: incubation temperature group * Trichlorobiphenyl: concentration (ng/g) * Tetrachlorobiphenyl: concentration (ng/g) * Epoxyheptachlor: concentration (ng/g) * Endosulfan.I: concentration (ng/g) * p..p..DDE: concentration (ng/g) * Endosulfan.II: concentration (ng/g) * Endrin.Aldehyde: concentration (ng/g) * DDT: concentration (ng/g) * Endrin.Ketone: concentration (ng/g) * Methoxychlor: concentration (ng/g) * Estrone: concentration (ng/g) * Estradiol: concentration (ng/g) * Etiocholanolone: concentration (ng/g) * X5b.tetrahydrocortisol: concentration (ng/g) * PC1: value for first principle component of contaminants and hormones differing between populations (see methods) * OCP_sum: sum of OCP concentrations (ng/g) * PCB_sum: sum of PCB concentrations (ng/g) #### File: AP\_WO\_dev\_env\_final.csv **Description:** Complete, filtered data frame of all components of the developmental environment that differ between populations  ##### Variables * Trichlorobiphenyl: concentration (ng/g) * Tetrachlorobiphenyl: concentration (ng/g) * Epoxyheptachlor: concentration (ng/g) * Endosulfan.I: concentration (ng/g) * p..p..DDE: concentration (ng/g) * Endosulfan.II: concentration (ng/g) * Endrin.Aldehyde: concentration (ng/g) * DDT: concentration (ng/g) * Endrin.Ketone: concentration (ng/g) * Methoxychlor: concentration (ng/g) * Estrone: concentration (ng/g) * Estradiol: concentration (ng/g) * Etiocholanolone: concentration (ng/g) * X5b.tetrahydrocortisol: concentration (ng/g) * PC1: value for first principle component of contaminants and hormones differing between populations (see methods) * clutch: clutch egg originated from * site: population of origin  * OCP_sum: sum of OCP concentrations (ng/g) * PCB_sum: sum of PCB concentrations (ng/g) #### File: yolk\_HORMONEs\_raw\.csv **Description:** Raw hormone date ##### Variables * clutch: clutch of origin * egg_id: id of egg yolk for measurement  * DHP:  concentration (ng/g) * 20b_DHP: concentration (ng/g) * cortisone: concentration (ng/g) * cortisol: concentration (ng/g) * estrone: concentration (ng/g) * estradiol: concentration (ng/g) * progesterone: concentration (ng/g) * etiocholanolone: concentration (ng/g) * testosterone: concentration (ng/g) * androstenedione: concentration (ng/g) * 5b_dihydrocortisol: concentration (ng/g) * 5b_tetrahydrocortisol: concentration (ng/g) * b_cortol: concentration (ng/g) * 5b_dihydrocortisone: concentration (ng/g) * pregnanedione: concentration (ng/g) * pregnenolone: concentration (ng/g) * 17a_hydroxyprogesterone: concentration (ng/g) * deoxycorticosterone: concentration (ng/g) * 11_deoxycortisol: concentration (ng/g) * corticosterone: concentration (ng/g) * 11_ketotestosterone: concentration (ng/g) * 17a_hydroxypregnenolone: concentration (ng/g) * 11b_hydroxyprogesterone: concentration (ng/g) * 5b_tetrahydrocorticosterone: concentration (ng/g) * 11_tetrahydrocorticosterone: concentration (ng/g) * 5b_corticosterone: concentration (ng/g) * 20b_dihydrocorticosterone: concentration (ng/g) * pregnanolone: concentration (ng/g) #### File: yolk\_OCPs\_raw\.csv **Description:** Raw OCP data ##### Variables * egg_id: id of egg yolk for measurement  * clutch: clutch of origin  * alpha: concentration (ng/g) * beta: concentration (ng/g) * gama: concentration (ng/g) * delta: concentration (ng/g) * Heptachlor: concentration (ng/g) * Aldrin: concentration (ng/g) * Epoxyheptachlor: concentration (ng/g) * Endosulfan_I: concentration (ng/g) * ppDDE: concentration (ng/g) * Dieldrin: concentration (ng/g) * Endrin: concentration (ng/g) * Endosulfan_II: concentration (ng/g) * Endrin_Aldehyde: concentration (ng/g) * DDT: concentration (ng/g) * Endrin_Ketone: concentration (ng/g) * Methoxychlor:  concentration (ng/g) * Total: sum of OCP concentrations (ng/g) #### File: yolk\_PCBs\_raw\.csv **Description:** Raw PCB data ##### Variables * egg_id: id of egg yolk for measurement * clutch: clutch of origin * site: population of origin * Monochlorobiphenyl: concentration (ng/g) * Dichlorobiphenyl: concentration (ng/g) * Trichlorobiphenyl: concentration (ng/g) * Tetrachlorobiphenyl: concentration (ng/g) * Pentachlorobiphenyl: concentration (ng/g) * Hexachlorobiphenyl: concentration (ng/g) * Heptachlorobiphenyl: concentration (ng/g) * Octachlorobiphenyl: concentration (ng/g)