DNA methylation associates with sex-specific effects of experimentally increased yolk testosterone in wild nestlings
Data files
Dec 13, 2024 version files 278.86 KB
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barcode_files_epiGBS2020_B19-B23.xlsx
20.40 KB
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HS_data.xlsx
33.16 KB
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info_nestlings_epigbs.txt
14.41 KB
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README.md
5.29 KB
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video_data.xlsx
205.59 KB
Abstract
Maternal hormones can profoundly impact offspring physiology and behaviour in sex-dependent ways. Yet little is known on the molecular mechanisms linking these maternal effects to offspring phenotypes. DNA methylation, an epigenetic mechanism, is suggested to facilitate maternal androgens’ effects. To assess whether phenotypic changes induced by maternal androgens associate with DNA methylation changes, we experimentally manipulated yolk testosterone levels in wild great tit eggs (Parus major) and quantified phenotypic and DNA methylation changes in the hatched offspring. While we found no effect on the handing stress response, increased yolk testosterone levels decreased the begging probability, emphasised sex-differences in fledging mass and affected methylation at 763 CpG sites, but always in a sex-specific way. These sites associated with genes involved in growth, oxidative stress and reproduction, suggesting sex-specific trade-offs to balance the costs and benefits of exposure to high yolk testosterone levels. Future studies should assess if these effects extend beyond the nestling stage and impact fitness.
README: DNA methylation associates with sex-specific effects of experimentally increased yolk testosterone in wild nestlings
All data and scripts related to the manuscript "DNA methylation associates with sex-specific effects of experimentally increased yolk testosterone in wild nestlings"
by Bernice Sepers, Suvi Ruuskanen, Tjomme van Mastrigt and Kees van Oers.
Explanation of column names that are included in many data files: ID = identity of an individual great tit (Parus major); brood_origin = brood of origin, the number of the nest box where an individual was born; brood_rearing = brood of rearing, the number of the nest box where an individual was raised; treatment = experimental treatment group, either testosterone (i.e. hatched from egg injected with testosterone + sesame oil) or control (i.e. hatched from egg injected with sesame oil); sex = sex of the individual.
- "HS_data.xlsx" includes the raw handling stress data (sheet HS) and the handling stress estimates (sheet HS_ESTIMATES) for each nestling on day 14 after hatching. Column explanations: april_date = April day on which the breath rate (i.e. handling stress test) was recorded; temperature = air temperature in °C at the test location; bout = bout number (15 seconds) within one minute; breath rate = number of breaths (breast movements) per bout; time minutes = time in minutes since midnight; estimate = handling stress estimate.
- "video_data.xlsx" includes the video data, including nestling food solicitation behaviour, on day eight after hatching. Column explanations: visit_number = parental visit number; recorded_brood = recorded brood, i.e. brood of rearing; fed_ID = ID of the nestling that received the prey item; fed_treatment = treatment of the nestling that received the prey item; fed_sex = sex of the nestling that received the prey item; fed_brood_origin = brood of origin of the nestling that received the prey item; ID_all = nestling ID; brood_origin_all = brood of origin; begging_all = indicates which nestlings showed a begging response right before feeding (1 = begging response shown, 0 = no begging response shown); fed_all = indicates which nestling received the prey item (1 = received the prey item, 0 = did not receive the prey item); treatment_all = experimental treatment group; sex_all = nestling sex.
- "barcode_files_epiGBS2020_B19-B23.xlsx" includes the unique barcode combinations needed to demultiplex the raw DNA methylation (epiGBS2) data on NCBI (see below). Column name explanation: Flowcell = sequencing flowcell; Lane = sequencing lane; Barcode_R1 = barcode ligated to the 5 prime – 3 prime DNA strands (i.e. R1 or BA); Barcode_R2 = barcode ligated to the 3 prime – 5 prime DNA strands (i.e. R2 or CO); Sample = individual; ENZ_R1 = restriction enzyme; ENZ_R2 = restriction enzyme; Wobble_R1 = length (in nucleotides) of the random nucleotide sequence (i.e. UMI) in the adapter of the 5 prime – 3 prime DNA strands; Wobble_R2 = length (in nucleotides) of the random nucleotide sequence (i.e. UMI) in the adapter of the 3 prime – 5 prime DNA strands; Species = study species.
- "info_nestlings_epigbs.txt" includes nestling information to link to the DNA methylation data. Column name explanation: File_location = location of the DNA methylation call file name, output of the epiGBS2 pipeline.
Any cells that contain "NA" represent missing values or the column does not apply to that individual.
- "Rscript_HS.R" includes the script to analyse the nestling handling stress data in "HS_data.xlsx"
- "Rscript_video.R" includes the script to analyse the video data (nestling food solicitation behaviour and feeding) in "video_data.xlsx".
- "Rscript_brood_characteristics.R" includes the script to analyse the incubation length data, the clutch size data, the hatching success data and the egg weight data. The data are archived in the SPI-Birds Database (https://spibirds.org/en) and can be requested.
- "Rscript_biometry_nestlings.R" includes the script to analyse the nestling biometry data (weight on day two, six, eight and 14 and tarsus length on day 14). The data are archived in the SPI-Birds Database (https://spibirds.org/en) and can be requested.
- "Rscript_methylation_filtering.R" includes the script to filter the DNA methylation (epiGBS2) data.
- "Rscript_methylation_analyses.R" includes the script to analyse the DNA methylation data.
- "Rscript_methylation_annotation.R" includes the script to annotate CpG sites.
- The raw genomic epiGBS2 reads are available on NCBI under BioProject PRJNA208335 under the SRA accessions SRX22027777, SRX22027778, SRX22027779, SRX22027780 and SRX22027781.
- The epiGBS2 bioinformatics pipeline can be accessed on github (https://github.com/nioo-knaw/epiGBS2).
For more information on data collection and analysis, please refer to the published manuscript and the Supplementary Material. Also, please feel free to contact Bernice Sepers (b.sepers@nioo.knaw.nl or bernice.sepers@uni-bielefeld.de) or Kees van Oers (k.vanoers@nioo.knaw.nl) if you have any further questions or comments.