Table 2.

Likelihood analyses based on phylogenetic hypotheses (H) and the observed DNA sequence data (R)

Phylogenetic hypothesis, H	Sequence, R	Likelihood model	LnLi value	SD
ML clam	Clam	L(HC|RC)	−3344.15	—
ML bacteria	Bacteria	L(HB|RB)	−2808.31	—
Ho: clam and bacterial tree topologies were not different
Bacterial tree topology	Clam	L(HMB|RC)	−3346.68	7.31
Clam tree topology	Bacteria	L(HMC|RB)	−2809.78	2.17
Ho: Phylogenies do not differ from expectations of a constant molecular clock
Clock-like clam phylogeny	Clam	L(HMKC|RC)	−3349.69	3.16
Clock-like bacterial phylogeny	Bacteria	L(HMKB|RB)	−2816.83	3.86*

The model L(H|R) is read as the likelihood of hypothesis H given sequence data R, with the following subscripts: (C) clam; (B) bacteria; (M) maximum likelihood topology; and (MK) clock-like maximum likelihood phylogeny. The estimated standard deviation (S.D.) was obtained by the Kishino-Hasegawa method (32). 

^*Significantly different from the appropriate ML comparison (α = 0.05).