Fig. 5. Maximum Likelihood (ML) phylogenetic reconstruction of the mitochondrial Cytochrome C oxidase Subunit I (cox1) gene tree of the Sarcocystis spp. under investigation. Where possible, sequences of the same species were used as shown in the 18S rRNA gene tree, including the outgroup. The newly sequenced Sarcocystis spp. are marked with black symbols. A total of 25 nucleotide sequences and 603 sites of the barcode area (all codon positions included) was analyzed with 1000 bootstrap replicates. Branch support from three replicate analyses is shown. The evolutionary history was inferred by using ML based on the HKY model. The tree with the highest log likelihood (– 6438.6551) is shown. A discrete Gamma distribution was used to model evolutionary rate differences among sites (four categories [+G, parameter = 0.9037]). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 17.4959% sites). All positions with less than 98% site coverage were eliminated. Branch lengths are measured in the number of substitutions per site. Note the long branch lengths of ruminant Sarcocytis spp. in comparison to other members of the Sarcocystidae as well as eimeriid coccidia from phylogenetically diverse hosts.