Table 3.

The number of evolutionary event detected by co-phylogeny analyses with the programs Jane and statistical analysis of global-fit PACo^a.

Parameter	Janea,b							PACoc
	S	C	CS	D	DS	L	F	${\text{M}}_{\text{XY}}^2$
Concatenated	7,117	32	11	3	12	5	0	0.28
Capsid	2,974	33	11	3	12	6	0	0.31
Portal	5,434	34	10	3	13	5	0	0.28
Tape	4,077	29	13	3	10	6	0	0.27
Terminase	1,845	33	8	3	15	0	0	0.27

^aJane analyses the combination of co-speciation, duplication, duplication with host switching, loss and failure-to-diverge events in organism-organism co-evolution events, while PACo evaluates the congruence of prophage phylogeny with the host tree and the contribution of each host-prophage link to the congruence (see section Materials and Methods for details).

^bS, solution; C, cost; CS, co-speciation; D, duplication; DS, duplication and host switch; L, loss; F, failure-to-diverge; $M_{XY}^2,$ global-fit value, a measure of the fit of the parasite phylogeny with the host phylogeny.

^cStatistical analyses of global fit were done using 100,000 permutations (P < 0.0001) at α = 0.05.