Mitochondrial results
Unsurprisingly, the sensitivity of Illumina sequencing recovered mitochondrial PCR products which were not easily deciphered from agarose gel electrophoresis. PCR success, as determined solely from gel electrophoresis, was a poor indicator of template existence in low quality samples for mitochondrial DNA. All museum samples recovered the 300 bp fragment of cytochrome b , despite only an average of 11% PCR success in the LQMS. The haplotypes recovered here matched with others in a rangewide study of G. oregonensis (Yuan, 2020).
Three haplotypes were recovered, and all of the LQMS recovered high quality, reliable sequences. The lowest coverage was in MVZ 2088 which still had minimally 98.6% reads above Q20 and 95.2% reads Q30 and above. From the limited coverage in this sample (22.7x average) there were only about 7 expected sequencing errors. The low error rate combined with a shared haplotype recovered provide evidence that this data was reliable.