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.