Table 1.

Paired-sites analyses with maximum-likelihood/parsimony of alternative tree topologies with each of the four earliest-branching sequences constrained as the most-basal branch

Tree tested	δ 1nL/steps	SD-ML/SD-MP	P
Most basal RPB1 branch
Giardia	best/15	—/25	—/0.54
Trichomonas	18.4/best	26.1/—	0.48/—
Trypanosoma	44.5/31	24.7/18.3	0.07/0.09
Mastigamoeba	9.1/28	13.5/24.3	0.50/0.25
M.i. + CTD taxa	97.3/102	36.9/26.8	0.008/0.0002

Also tested is the placement of Mastigamoeba(M.i.) with the CTD-containing taxa. δ/nL, change in natural logarithm of likelihood; SD, standard deviation; ML, maximum likelihood; MP, Maximum parsimony.