Figures

Figure 1. A schematic showing the proportions of reads in four different categories. In samples 1, 2 and 3, the first two categories of read cannot be distinguished by mapping because (organellar) mitochondrial reads and NUMT reads carry the same SNP allele (as an example, the A allele). Only the n reads carrying an alternative allele (T, G or C) can be classified as of NUMT origin. Sample 4 had another (T, green) allele in its organellar mitochondrial genome; hence, in this case, the k orange reads carrying the alternative alleles (A, G or C) can be classified as NUMTs. We wish to estimate the proportion of the nuclear DNA which consists of NUMTs,v/N , but this ratio cannot be observed directly in any one of these samples. Fraction m denotes all reads with sequence similarity to the mitochondrial genome.
Figure 2. Change in frequency of NUMT alleles with the mitochondrial mapping ratio (un-mapped / mapped). The raw data are plotted as circles. The vertical stacks of points represent frequencies of different loci from the same sample, each locus being given a different colour (from red to violet according to the global average allele frequency). The lines with the corresponding colour show the best fit to equation [1]. Both axes are logarithmic. The intercept on the log scale will correspond to x=1 (half the reads mapping to the mitochondrial genome, log(1) = 0). The two solid lines correspond to the minimum proportion of reads mapping to the mitochondrial genome across all samples (vertical) and to the intercept of the SNPs with the highest fitted allele frequency (horizontal). The dashed line shows the fitted relationship for the locus with the highest estimated allele frequency. The values of the horizontal solid and dashed lines at x=1 are both estimates of the proportion of the genome composed of NUMTs (intercept estimate).
(full width) Figure 3. Sequence relationships and spatial distribution of grasshopper mitotypes. (a) A dendrogram based on (true) mitochondrial sequence polymorphism between samples of the grasshopperP. pedestris . The scale bar indicates the number of substitutions per mitochondrial genome. The symbols match the legend in (b). (b) The locations of the sampling sites and the distribution of two diverged mitotypes
Figure 4. Insert quantification in diverged populations.Within-individual allele frequencies are shown for sites with fixed mitochondrial differences between two populations of the grasshopperP. pedestris (top, 111 sites) and the parrot P. varius(bottom, 178 sites). Both histograms share the same x axis. Fat vertical lines indicate the means, dashed lines the associated standard errors.