Fig. 3

Maximum parsimony phylogeny based on 119 cat mitogenome sequences compared to the CR variant network. a Maximum parsimony tree rooted to a sand cat mitogenome outgroup (Felis margarita; NC_028308) with the addition of a wildcat mitogenome and the F. catus reference sequence (NC_001700; [10]). Clades are labelled with the original (A-L, and variants thereof) haplogroup names based on control region variant sites. Note the long (here, truncated) terminal branch leading to the NC_001700 reference sequence, which reflects likely sequencing errors. Figure S2 shows the same tree including sample names. b Median-joining network based on variants within the control region in the 119 cat mitogenomes, plus the wildcat and NC_001700 reference sequence [10]. Circles represent haplotypes, with area proportional to sample size, and lines between haplotypes represent mutational steps as shown in the key