Table 4.

The Shimodaira-Hasegawa topological test results comparing the three hypothetical topologies

Tree	lnL	pSH
Best tree (hypothesis 3)	-25126.753	-
Hypothesis 1	-25130.147	0.578
Hypothesis 2	-25154.740	0.023*

The best tree was the tree provided by the maximum likelihood analysis (see Figure 3) and concurred with hypothesis 3. The log-likelihoods of the other two trees, based on hypothesis 1 and 2 (see Figure 2), are compared with the best tree. The hypothesis 2 tree, which has Polychromophilus grouped with Haemoproteus, has a significantly worse fit and can be rejected.

It is less clear where within the Plasmodium clade Polychromophilus belongs. Neither phylogenetic method indicates that Polychromophilus originated from mammalian Plasmodium/Hepatocystis and both instead produced topologies suggesting a sauropsid origin (see Figure 3). However, the actual support for the node separating the mammalian clade from sauropsid Plasmodium/Polychromophilus clade is low. The BI supports the monophyly of sauropsid Plasmodium and Polychromophilus (hypothesis 3) with a posterior probability of 0.92, but the ML support of that same critical node is absent (bootstrap value of 40/100). The topological test comparing the different phylogenetic scenarios did not provide more support for either hypothesis 1 or 3 (see Table 4).