NextSeq 500 paired end 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 and ligation of unique 7-mer 5' and 3' barcoded adapters during the ligation step (https://doi.org/10.1101/gr.128124.111). Library underwent enrichment for mitochondrial DNA following the protocol described by Mitchell et al. (https://doi.org/10.1098/rsbl.2016.0062) using probes designed based on previously published mtDNA sequences from 24 eutherian mammal species and synthesised by Arbor Biosciences. Enrichment was performed following V1 of the manufacturer's protocol, with the exception that the incubation step was extended to 44 hours (3 hours at 60째C, 12 hours at 55 째C, 12 hours at 50 째C, 17 hours at 55 째C).