Early developmental carry-over effects on exploratory behaviour and DNA methylation in wild great tits (Parus major)
Data files
Feb 16, 2024 version files 57.08 KB
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Barcode_file_epiGBS2_B9-B10.xlsx
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CORLOC_WH_2018.xlsx
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juveniles_epiGBS_2018_WH.txt
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juveniles_tested_age.txt
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Postfledging_biometry_WH_2018.xlsx
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README.md
Abstract
Adverse, postnatal conditions experienced during development are known to induce lingering effects on morphology, behaviour, reproduction and survival. Despite the importance of early developmental stress for shaping the adult phenotype, it is largely unknown which molecular mechanisms allow for the induction and maintenance of such phenotypic effects once the early environmental conditions are released. Here we aimed to investigate whether lasting early developmental phenotypic changes are associated with post-developmental DNA methylation changes. We used a cross-foster and brood size experiment in great tit (Parus major) nestlings, which induced post-fledging effects on biometric measures and exploratory behaviour, a validated personality trait. We investigated whether these post-fledging effects are associated with DNA methylation levels of CpG sites in erythrocyte DNA. Individuals raised in enlarged broods caught up on their developmental delay after reaching independence and became more explorative as days since fledging passed, while the exploratory scores of individuals that were raised in reduced broods remained stable. Although we previously found that brood enlargement hardly affected pre-fledging methylation levels, we found 420 CpG sites that were differentially methylated between fledged individuals that were raised in small versus large sized broods. A considerable number of the affected CpG sites were located in or near genes involved in metabolism, growth, behaviour and cognition. Since the biological functions of these genes line up with the observed post-fledging phenotypic effects of brood size, our results suggest that DNA methylation provides organisms the opportunity to modulate their condition once the environmental conditions allow it. In conclusion, this study shows that nutritional stress during early development associates with indirect, carry-over effects on DNA methylation. We propose that treatment-associated DNA methylation differences arise as a consequence of pre-fledging phenotypic changes, rather than that they cause early environmentally-induced effects.
README
All data related to the paper "Early developmental carry-over effects on exploratory behaviour and DNA methylation in wild great tits (Parus major)"
by Bernice Sepers, Koen Verhoeven and Kees van Oers.
Explanation of column names that are included in many data files: NIOO_ID = identity of an individual great tit (Parus major); NB_origin = brood of origin, the number of the nest box where an individual was born; NB_rearing = brood of origin, the number of the nest box where an individual was raised; Pair or CF_pair = cross-foster pair (individuals were swapped withing a pair of broods when they were nestlings); Treatment = brood size manipulation treatment, either reduced (i.e. raised in an experimentally reduced brood) or enlarged (i.e. raised in an experimentally enlarged brood) or other (not part of this experiment).
"CORLOC_WH_2018.xlxs" includes the exploration scores and affiliated information about the juveniles involved in this study. Column explanations: aprilDayhatching = day of hatching in April days (since the first of April); CORLOC = exploration score from the novel environment test, calculated as the sum of all movements corrected for date (Dingemanse et al., 2002); aprilDay_testing = day on which the novel environment test occurred, in April days; Age_testing = age on which the novel environment test occurred, in days since hatching.
"Postfledging_biometry_WH_2018.xlxs" includes biometry data divided over three sheets:
- sheet "weight", column explanation: weight_postfl_gr = weight in grams on the day of catching (one day before the novel environment test).
- sheet "delta_weight", column explanations: weight_postfl_gr = eight in grams on the day of catching (one day before the novel environment test); weight_d14_gr = weight in grams on day 14 after hatching (day of hatching being day 0); delta_weight_gr = weight_postfl_gr minus weight_d14_gr.
- sheet "p3", column explanation: length of the third primary (counting from the outside of the wing) in mm on the day of the novel environment test.
"juveniles_tested_age.txt", column explanation: Age_testing = age on which the individuals were blood sampled, in days since hatching.
"juveniles_epiGBS_2018_WH.txt", column explanation: File = methylation call file name, output of the epiGBS2 pipeline.
"Barcode_file_epiGBS2_B9-B10.xlxs" includes the unique barcode combinations needed to demultiplex the raw epiGBS2 data on NCBI. 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 = Sample name; 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.
Any cells that contain "NA" represent missing values or the column does not apply to that individual.
"Rscript_postfl_biometry_corloc_WH_2018.R" includes the script to assess a treatment effect on behavioural and biometry data.
"Rscript_filtering_postfl_meth_2018_WH.R" includes the script to filter the DNA methylation (epiGBS2) data.
"Rscript_stats_postfl_meth_2018_WH.R" includes the script to assess a treatment effect on DNA methylation.
"Rscript_stats_interaction_postfl_meth_2018_WH.R" includes the script to assess a days since fledging-dependent treatment effect on DNA methylation.
"Annotation_meth_2018_WH.R" includes the script to annotate CpG sites.
- The multiplexed epiGBS2 reads are available on NCBI under BioProject ID PRJNA208335 under the SRA accessions SRX21758799 and SRX21758800.
- 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.