Figure 2. Species phylogeny based on partially reconstructed mitogenomes.

Aligned sequences had all gap sites removed with Gblocks, except the sheep light coat (OCL2). Asterisks on branch labels of trees (A) and (C) correspond to clade/haplogroup names where inter-subspecies mono-phylogeny occur. Outgroups used to root trees have been removed (Supplementary Table 1). Black circles on nodes indicate that there was more than 90% bootstrap support in neighbour joining, maximum parsimony and maximum likelihood topologies. Coloured boxes highlight associated haplogroups of samples. Animal illustrations provided by Matthew Collins (pers coms).