A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group

Table 1 Alternative topology tests

	Alternative topologies	P-value
Consensus	Unconstrained 47 protein phylogeny	1.000
Topology 1	D. polycarpum is outgroup to branch I	1e-04
Topology 2	D. polycarpum is outgroup to group 1	1e-04
Topology 3	D. polycarpum is outgroup to branch II	6e-74
Topology 4	Root between group 1 and group 2, as in SSU rDNA tree	5e-74
Topology 5	D. polycephalum is outgroup to branch I	3e-68
Topology 6	P. violaceum is outgroup to group 3	2e-43
Topology 7	P. violaceum groups with P. pallidum	4e-29
Topology 8	A. ellipticum groups with other Acytostelids	5e-47
Topology 9	A. ellipticum groups with Polysphondylids, as in SSU rDNA tree	5e-40

The probabilities (p-value) of the alternative tree topologies listed in Fig. 5 were investigated using the approximately unbiased (AU) test in CONSEL v0.20 [25]. Trees with constrained nodes were generated using RaxML and log likelihood values for the consensus tree and alternative trees were used as input for the AU test