Fig. 2

Level of sequence difference (D) per protein-coding gene of each possible pairwise combination of four mitochondrial genomes (Chinese reference, Peru–Huancayo, Peru–Puno, and Mexico). D values were computed by performing all possible pairwise alignments and applying the formula D = 1 − (M/L), where L is the difference between the alignment length and the number of ambiguous codons, and M is the number of invariant sites in the alignment. Different D values for each combination were stacked and presented per protein-coding gene in a bar plot. Thus, the height of a particular bar of a gene corresponds to the sum of D values for the different pairwise combinations. In other words, the bar height is a cumulative D value