Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses

Table 2 Summary of the genome quartets that include Synechocystis sp., Bacillus subtilis, and two bacterial genomes from other phyla.

#	Genome 1	Genome 2	Genome 3	Genome 4	((1,2),3,4)			((1,3),2,4)			((1,4),2,3)
					Tot	0.9	0.99	Tot	0.9	0.99	Tot	0.9	0.99
9	Synechocystis	P. aeruginosa	D. radiodurans	B. subtilis	94	76	63	101	73	57	186	158	126
10	Synechocystis	P. aeruginosa	T. pallidum	B. subtilis	69	54	50	51	33	28	102	80	67
14	Synechocystis	R. sphaeroides	B. subtilis	E. coli	65	53	44	286	263	248	28	25	17
15	Synechocystis	R. sphaeroides	B. subtilis	D. radiodurans	95	72	60	201	173	149	73	60	47
16	Synechocystis	D. radiodurans	B. subtilis	T. pallidum	63	50	40	94	74	63	60	46	35
17	Synechocystis	B. subtilis	T. pallidum	E. coli	93	72	66	55	43	34	66	49	39
18	Synechocystis	D. radiodurans	T. pallidum	E. coli	86	68	54	65	49	38	75	54	47
19	Synechocystis	D. radiodurans	B. subtilis	E. coli	129	105	86	156	131	104	98	76	62
50	Synechocystis	B. subtilis	E. coli	M. loti	276	255	228	44	31	21	54	43	38
53	Synechocystis	B. subtilis	E. coli	M. leprae	125	104	82	101	84	65	119	19	66
54	Synechocystis	B. subtilis	E. coli	M. tuberculosis	141	114	97	101	82	69	128	101	89
55	Synechocystis	B. subtilis	M. loti	M. tuberculosis	189	164	139	92	74	59	80	58	44
64	Synechocystis	C. trachomatis	B. subtilis	T. pallidum	47	31	24	108	96	86	36	25	18
67	Synechocystis	C. trachomatis	B. subtilis	M. loti	64	48	32	116	104	84	72	51	44
68	Synechocystis	C. trachomatis	B. subtilis	M. tuberculosis	77	55	45	94	80	62	68	52	38
51	Synechocystis	B. subtilis	E. coli	S. aureus	33	19	15	361	349	333	15	7	5
52	Synechocystis	B. subtilis	E. coli	S. pyogenes	34	22	18	259	249	227	24	17	9

The # column refers to the unique number assigned to the genome quartets analyzed. Columns "((1,2),3,4)", "((1,3),2,4)" and "((1,4),2,3)" refer to the three possible tree topologies. Numbers in columns "Tot", ".90" and ".99" give the number of QuartOPs that support the indicated tree topology with a posterior probability higher than the other two posterior probabilities, or with 90% or 99% probability, respectively. The numbers in bold indicate the number of orthologs supporting the grouping of Synechocystis sp. and Bacillus subtilis in the absence of another low GC gram-positive in the genome quartets. Note that those numbers are the largest of the three numbers, a finding that supports the recent analyses by [43]. In the presence of another low GC Gram-positive in addition to Bacillus subtilis, the largest number of QuartOPs support grouping of low GC Gram-positives with each other (underlined). Other groupings that involve putative sister groups to the cyanobacteria (Deinococaceae and spirochetes) that had been suggested by others (e.g., [40,41]) are indicated in italics.

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