Table 1.

Numbers and Ratio of Events Reported on Different HGT Penalties

HGT penalty^a	Loss events^b	HGT events^b	Families in HGT^c
16S rRNA tree
1	9,342	10,468	5,274
2	14,847	7,374	4,286
3	21,304	4,702	3,263
4	26,307	3,191	2,504
5	29,365	2,474	2,071
Gene content tree
1	7,055	10,864	5,282
2	12,413	7,670	4,426
3	17,557	5,556	3,640
4	24,004	3,633	2,743
5	28,144	2,638	2,203
Shuffled tree
1	10,176	35,942	12,364
2	17,065	31,664	12,121
3	29,590	25,966	11,844
4	50,955	19,104	10,653
5	62,408	15,842	10,079

↵a HGT penalty corresponds to the threshold value used
↵b Loss and HGT events correspond to the number of events observed in the three trees
↵c Families in HGT corresponds to the number of families predicted to be involved in HGT

The Balance of Driving Forces During Genome Evolution in Prokaryotes