Parrot data
As reported by McElroy et al. (2018), the parrot data set contained
considerable amounts of adapter sequences, ranging from 4 to 41% of the
data, which we excluded in order to generate more accurate abundance
estimates. Our de novo assembly of the parrot mitochondrial
genome, generated from sample SRR6214434, was 19,278 bp in length. The
per-sample mapping rates varied over two orders of magnitude, from 0.02
to 1.9%. A PCA run on individual mitochondrial alleles separated the
samples into two groups corresponding to the phylogroups inferred by
McElroy et al. (2018). The intercept estimate of the nuclear proportion
of mitochondrial inserts was 0.0043% (95% CI: 0.0026%-0.070%) The
mapping depth estimate was 0.017%. As with the grasshopper data, we
analysed the minor allele frequencies at each site that showed fixed
mitochondrial difference between the populations (Figure 4). This
resulted in a diverged sites estimate of 0.0033% (SE 0.00016%).