Mitochondrial DNA reconstruction
Data from only the pooled run contained the two cytochrome b PCR
replicates. Raw data was uploaded to Geneious Prime (Biomatters Inc.)
where a published reference (GenBank Accession # AF030390, Demboski,
Jacobsen, & Cook, 1998) was used to map reads. Mapping was done in
Geneious via the bowtie2 plugin v 2.3.0 (Langmead & Salzberg, 2012),
and consensus sequences were extracted. All sequences were aligned with
MAFFT v1.4.0 (Katoh & Standley, 2013) via the Geneious plugin, and
primers were trimmed off. Data were combined from 147 total individuals
(Yuan, 2020, data not shown) to reconstruct haplotypes using PopArt
(http://popart.otago.ac.nz) and
a median spanning network (Bandelt, Forster, & Röhl, 1999).