WGBS of  Parus major females
The preparation and sequencing of whole-genome bisulfite libraries of the four samples used in this study was performed by the Roy J. Carver Biotechnology Centre (University of Illinois at Urbana-Champaign, USA) together with the other samples of the experiment (see above). Shotgun genomic libraries (with read length of 150 nucleotides) were prepared with the Hyper Library construction kit from kapa Biosystems (Roche) and treated with the EZ DNA Methylation Lightning kit from Zymo Research. Libraries were pooled, quantitated by qPCR and each pool was sequenced for 151 cycles from both ends of the fragments (i.e. paired-end) on a S4 flow cell using a NovaSeq 6000. Samples selected for this study were sequenced on the same lane. Because WGBS data showed high duplication rates (Table S2), library preparation and sequencing were performed twice for all samples and data from both runs were merged. See Table S2 for unique read counts per sample and run.