Data from: Maternal deposition of hormones and contaminants shape the gonadal transcriptome in American alligators
Data files
Dec 11, 2024 version files 32.82 KB
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AP_WO_dev_env_final.csv
3 KB
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MEs_horm_contam.csv
7.23 KB
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README.md
7.15 KB
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yolk_HORMONEs_raw.csv
10.05 KB
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yolk_OCPs_raw.csv
4.28 KB
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yolk_PCBs_raw.csv
1.10 KB
Abstract
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.
README: Maternal deposition of hormones and contaminants shape the gonadal transcriptome in American alligators
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)