Sequence alignment and secondary structure prediction of the ND5 gene in O. princeps haplotypes. The first two rows in the sequence alignment are from O. princeps sampled at high and low elevations in BC, respectively. The second two rows are the homologous sections from the published mitochondrial genomes of O. princeps [GenBank: NC005358] and Oryctolagus cuniculus [GenBank: NC001913]. Amino acids in white bold and black background indicate non-synonymous substitutions fixed at low and high elevation pikas in BC. Predicted transmembrane domains are shaded in gray. For the BC samples, residues 16–266 and 405–551 are the result of Sanger sequencing four individuals per elevation; the remaining residues are inferred from transcriptome read data of three individuals per elevation.