Puma concolor Mitochondrial DNA Sequence Files from Illumina HiSeq

Mitochondrial DNA was extracted from skin tissue and purified using a phenol: chloroform protocol and MinElute PCR Purification Kit with modifications to retain short DNA fragments following clean lab protocols for ancient DNA. Libaries were made using the Meyer & Kircher protocol with modifications for ancient DNA. The library was then enriched for endogenous DNA using the MyCroarray MyBaits kit with biotinylated RNA probes which bind to the desired DNA, with one exception. Sample BE813 was not enriched as it had sufficient DNA without enrichment. Samples were multiplexed on a single lane and sequenced on the Illumina HiSeq. Once the sequence files were generated, we removed adapter sequences and artifacts created by the library process, merged forward and reverse reads with 11 nt overlap and a combined phred quality score of merged sites greater than 20. Sequence reads were then aligned to the complete Puma concolor mitochondrial genome available on Genbank (accession number NC_016470) using the Burrows-Wheeler Aligner (BWA). Samples were processed and potential PCR duplicate reads removed using the Samtools package version 1.2 (using htslib 1.2.1) with default settings.