Pairwise divergence among the three passenger pigeon mitogenomes.

We divided the mitogenome into regions encoding 22 transfer RNA genes (Phenylalanine [tRNA-Phe], Valine [tRNA-Val], Leucine [tRNA-Leu], Isoleucine [tRNA-Ile], Glutamine [tRNA-Gln], Methionine [tRNA-Met], Tryptophan [tRNA-Trp], Alanine [tRNA-Ala], Asparagine [tRNA-Asn], Cysteine [tRNA-Cys], Tyrosine [tRNA-Tyr], Serine [tRNA-Ser], Asparate [tRNA-Asp], Lysine [tRNA-Lys], Glycine [tRNA-Gly], Arginine [tRNA-Arg], Histidine [tRNA-His], Serine [tRNA-Ser], Leucine [tRNA-Leu], Threonine [tRNA-Thr], Proline [tRNA-Pro], Glutamate [tRNA-Glu]), 13 protein-coding genes (NADH dehydrogenase subunit 1 [ND1], NADH dehydrogenase subunit 2 [ND2], cytochrome c oxidase subunit I [COX1], cytochrome c oxidase subunit II [COX2], ATP synthase F0 subunit 8 [ATP8], ATP synthase F0 subunit 6 [ATP6], cytochrome c oxidase subunit III [COX3], NADH dehydrogenase subunit 3 [ND3], NADH dehydrogenase subunit 4L [ND4L], NADH dehydrogenase subunit 4 [ND4], NADH dehydrogenase subunit 5 [ND5], cytochrome b [CYTB], NADH dehydrogenase subunit 6 [ND6]), two ribosomal RNA genes (12 s rRNA and16 s rRNA) and a control region. Alignment length (bp), and number of segregating sites/number of nonsynonymous substitutions/number of gaps/number of ambiguous sites are shown for each of these regions. Numbers that are exceptionally high were bolded.