DOI: 10.5061/dryad.hqbzkh1pf
title: Early developmental carry-over effects on exploratory behaviour and DNA methylation in wild great tits (Parus major)

description: 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.
description: 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 (). --- 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 ( or
 ) or Kees van Oers
 () if you have any further questions or
 comments.