HiSeq X Ten sequencing
Meyer and Kircher's (https://doi.org/10.1101/pdb.prot5448) library preparation protocol with the addition of Rohland et al.'s (https://doi.org/10.1098/rstb.2013.0624) partial UDG treatment as described in Wasef et al. (https://doi.org/10.3389/fevo.2020.00217). Library underwent whole genome enrichment using baits based on modern domestic dog genomic DNA. After PCR amplifications, ~100  to 500 ng of the library was used for in-solution target enrichment using the dog-based whole genome myBaits® (Arbor Biosciences) using the modification detailed in Wasef et al. (33). Following the manufacture protocol V4, RNA baits used for the target capture enrichment steps were performed with the following modifications: the hybridisation step was performed for 42 hours at 57 °C. The beads, the bead binding buffers, and the washes were heated to 57°C before being used. Post-capture libraries were amplified on beads using HiFi HotStart Uracil+ ReadyMix (Kapa Biosystems) for between 14 and 17 cycles and then visualised using the TapeStation 4000 (Agilent Technologies).