Table 2.
Statistical tests of alternative phylogenetic hypotheses constraining red algae and plants to be closely related
| Hypothesis | Different steps/ln L | Standard error | P |
|---|---|---|---|
| Parsimony | |||
| (Pl,(R,(A,(F,(Ac,P))))) | Best | ||
| (Pl,((R,P),(A,(F,Ac)))) | 39 | 12.05 | <0.001 |
| (Pl,((A,F),(Ac,(P,R)))) | 25 | 13.5 | 0.06 |
| Likelihood | |||
| (Pl,(R,((Ac,P),(F,A)))) | Best | ||
| (Pl,(((R,P),Ac),(F,A))) | −37.4 | 17.3 | 0.03 |
| (Pl,((R,(P,Ac)),(F,A))) | −32.0 | 11.8 | 0.006 |
Tests were performed by supplying user trees in parsimony (protpars-phylip) and likelihood; (protml-molphy) analyses. All taxa were included in the analyses, but for clarity, deeper branching sequences are not shown in the hypothetical trees shown. ln L, natural log likelihood. A, animals; Ac, Acanthamoeba, F, fungi; P, plants; Pl, Plasmodium; R, Rhodophytes. The P value given is the confidence limit for rejection of the alternative tree topology.