Table 1.

Results of a heuristic search for the minimum number of horizontal transmissions necessary to reconcile the host and intron trees

No. horizontal transfers	Ln likelihood*	Significantly worse than intron tree†	No. trees‡
0 (Host tree)	−458.8	Yes (P < 0.0001)	NA
1	−429.3	Yes (P < 0.0001)	4
2	−405.5	Yes (P = 0.04)	3
3	−397.6	No (P = 0.22)	18
4	−391.9	No (P = 0.83)	16
5 (Intron tree)	−390.8	No (P = 1)	170

Results of an algorithm to find the minimum number of rearrangements necessary to change the host phylogeny (Fig. 3C) into one of the three most likely intron phylogenies. The latter are given by the three possible resolutions of the following consensus tree: ((((((((S. paradoxus, Brazil), Japan), ((S. cerevisiae, T. delbrueckii), T. globosa)), K. thermotolerans, (S. exiguus, S. castellii)), T. pretoriensis), Z. bisporus), Z. rouxii), (K. dobzhanskii, K. lactis)). Likelihoods were calculated by using the HKY model with the transition-to-transversion ratio and proportion of invariant sites estimated from the data. 

*Ln likelihood of the most likely tree. 

^†By the Kishino–Hasegawa test (see ref. 30). 

^‡ Including most likely tree and all others not significantly worse (at P = 0.5); used as starting trees in the next iteration. NA, not applicable.