Summary of Genome Quartet Analyses

The # column refers to the unique number assigned to each genome quartet analyzed. Columns "((1,2),3,4)", "((1,3),2,4)" and "((1,4),2,3)" refer to the three possible tree topologies (abbreviated in New Hampshire format). Numbers in columns "Total", "90%" and "99%" give the number of orthologues that support the indicated tree topology with a posterior probability higher than the other two posterior probabilities, or with 90% or 99% probability, respectively. "ML Map" columns provide links to ML maps in PostScript and PDF formats.

Cases discussed in the paper are marked in red.

Complete genomes were downloaded from NCBI's FTP site, except for genomes marked with *. The latter ones are not complete and preliminary versions were downloaded from JGI Microbial Genomes and TIGR pages.

#	Genome1	Genome2	Genome3	Genome4	((1,2),3,4)			((1,3),2,4)			((1,4),2,3)			ML map (PS)	ML map (PDF)
#	Genome1	Genome2	Genome3	Genome4	Total	90%	99%	Total	90%	99%	Total	90%	99%	ML map (PS)	ML map (PDF)
1	Pyrococcus horikoshii	Methanobacterium thermoautotrophicum	Halobacterium sp.	Thermoplasma acidophilum	127	102	86	97	79	63	45	34	24
2	Methanococcus jannacshii	Archaeoglobus fulgidus	Halobacterium sp.	Thermoplasma acidophilum	102	87	66	65	42	35	122	97	80
3	Treponema pallidum	Mycobacterium tuberculosis	Bacillus subtilis	Mycoplasma pneumoniae	66	57	49	20	15	12	53	37	32
4	Haemophilus influenzae	Vibrio cholerae	Pseudomonas aeruginosa	Neisseria meningitidis	498	481	464	23	18	13	112	100	86
5	Escherichia coli	Haemophilus influenzae	Vibrio cholerae	Pseudomonas aeruginosa	387	330	294	246	204	157	158	128	98
6	Vibrio cholerae	Pseudomonas aeruginosa	Neisseria meningitidis	Helicobacter pylori	262	234	217	53	39	31	87	64	55
7	Escherichia coli	Buchnera sp.	Vibrio cholerae	Haemophilus influenzae	269	239	202	102	82	58	42	26	18
8	Escherichia coli	Deinococcus radiodurans	Bacillus subtilis	Treponema pallidum	71	53	42	80	63	46	71	56	47
9	Synechocystis sp.	P. aeruginosa	D. radiodurans	B.subtilis	94	76	63	101	73	57	186	158	126
10	Synechocystis sp.	P. aeruginosa	T. pallidum	B.subtilis	69	54	50	51	33	28	102	80	67
11	Synechocystis sp.	T.maritima	A. aeolicus	Halobacterium sp.	29	20	12	45	34	27	86	69	56
12	Synechocystis sp.	A. aeolicus	P. aeruginosa	Halobacterium sp.	59	46	37	53	38	23	55	41	32
13	Synechocystis sp.	T.maritima	A. aeolicus	A.fulgidus	47	36	30	63	51	44	50	34	25
14	Synechocystis sp.	R.sphaeroides*	B.subtilis	E.coli	65	53	44	286	263	248	28	25	17
15	Synechocystis sp.	R.sphaeroides*	B.subtilis	D.radiodurans	95	72	60	201	173	149	73	60	47
16	Synechocystis sp.	D. radiodurans	B.subtilis	T. pallidum	63	50	40	94	74	63	60	46	35
17	Synechocystis sp.	B.subtilis	T. pallidum	E.coli	93	72	66	55	43	34	66	49	39
18	Synechocystis sp.	D. radiodurans	T. pallidum	E.coli	86	68	54	65	49	38	75	54	47
19	Synechocystis sp.	D. radiodurans	B.subtilis	E.coli	129	105	86	156	131	104	98	76	62
20	Synechocystis sp.	D. radiodurans	B.subtilis	Halobacterium sp.	48	38	33	69	58	48	52	41	34
21	Synechocystis sp.	D. radiodurans	T. pallidum	Halobacterium sp.	26	20	17	40	32	24	19	14	11
22	Synechocystis sp.	D. radiodurans	E.coli	Halobacterium sp.	60	44	34	62	51	46	57	45	40
23	Synechocystis sp.	B.subtilis	T. pallidum	Halobacterium sp.	30	27	19	28	22	18	25	15	11
24	Synechocystis sp.	B.subtilis	E.coli	Halobacterium sp.	58	47	34	62	48	37	52	40	32
25	Synechocystis sp.	T. pallidum	E.coli	Halobacterium sp.	27	17	10	31	25	20	24	17	11
26	D. radiodurans	T. pallidum	E.coli	Halobacterium sp.	19	12	6	28	17	13	41	33	27
27	D. radiodurans	B.subtilis	T. pallidum	Halobacterium sp.	29	20	17	18	14	12	38	26	22
28	D. radiodurans	B.subtilis	E.coli	Halobacterium sp.	54	43	33	52	40	33	74	55	47
29	B.subtilis	T. pallidum	E.coli	Halobacterium sp.	21	13	9	40	32	24	29	21	18
30	Synechocystis sp.	D. radiodurans	B.subtilis	A. aeolicus	134	109	89	133	108	91	100	82	67
31	Synechocystis sp.	D. radiodurans	T. pallidum	A. aeolicus	85	66	53	52	39	29	72	58	48
32	Synechocystis sp.	D. radiodurans	E.coli	A. aeolicus	143	120	98	96	68	50	124	104	89
33	Synechocystis sp.	D. radiodurans	Halobacterium sp.	A. aeolicus	57	44	36	43	33	25	70	61	52
34	Synechocystis sp.	B.subtilis	T. pallidum	A. aeolicus	103	82	64	53	39	32	53	40	31
35	Synechocystis sp.	B.subtilis	E.coli	A. aeolicus	162	130	111	112	86	71	97	73	62
36	Synechocystis sp.	B.subtilis	Halobacterium sp.	A. aeolicus	69	49	35	55	42	30	56	40	35
37	Synechocystis sp.	T. pallidum	E.coli	A. aeolicus	60	48	41	81	56	42	65	53	41
38	Synechocystis sp.	T. pallidum	Halobacterium sp.	A. aeolicus	32	26	19	17	12	8	34	22	18
39	Synechocystis sp.	E.coli	Halobacterium sp.	A. aeolicus	52	45	34	54	42	36	63	53	41
40	D. radiodurans	B.subtilis	T. pallidum	A. aeolicus	84	67	57	77	62	51	48	34	24
41	D. radiodurans	B.subtilis	E.coli	A. aeolicus	119	94	82	141	106	90	100	86	61
42	D. radiodurans	B.subtilis	Halobacterium sp.	A. aeolicus	48	40	27	73	58	52	44	28	24
43	D. radiodurans	T. pallidum	E.coli	A. aeolicus	74	54	42	74	61	48	56	48	43
44	D. radiodurans	T. pallidum	Halobacterium sp.	A. aeolicus	27	17	10	34	24	18	21	15	11
45	D. radiodurans	E.coli	Halobacterium sp.	A. aeolicus	61	54	45	65	59	45	39	31	24
46	B.subtilis	T. pallidum	E.coli	A. aeolicus	71	53	43	86	61	45	68	60	50
47	B.subtilis	T. pallidum	Halobacterium sp.	A. aeolicus	28	19	15	28	17	16	30	21	15
48	B.subtilis	E.coli	Halobacterium sp.	A. aeolicus	54	43	31	59	47	40	57	45	38
49	T. pallidum	E.coli	Halobacterium sp.	A. aeolicus	31	19	15	33	20	15	19	14	8
50	Synechocystis sp.	B.subtilis	E.coli	M.loti	276	255	228	44	31	21	54	43	38
51	Synechocystis sp.	B.subtilis	E.coli	S.aureus	33	19	15	361	349	333	15	7	5
52	Synechocystis sp.	B.subtilis	E.coli	S.pyogenes	34	22	18	259	249	227	24	17	9
53	Synechocystis sp.	B.subtilis	E.coli	M.leprae	125	104	82	101	84	65	119	19	66
54	Synechocystis sp.	B.subtilis	E.coli	M.tuberculosis	141	114	97	101	82	69	128	101	89
55	Synechocystis sp.	B.subtilis	M.loti	M.tuberculosis	189	164	139	92	74	59	80	58	44
56	D.radiodurans	T.maritima	B.subtilis	A.aeolicus	53	45	31	206	182	159	68	48	39
57	Synechocystis sp.	C.tepidum*	C.aurantiacus*	R.sphaeroides*	64	47	36	131	114	96	71	59	49
58	Synechocystis sp.	C.tepidum*	C.aurantiacus*	R.palustris*	82	69	55	118	102	87	80	59	48
59	Synechocystis sp.	C.tepidum*	R.palustris*	R.capsulatis*	330	322	315	10	7	6	13	9	8
60	Synechocystis sp.	C.tepidum*	P.marinus*	R.capsulatis*	15	13	11	296	289	283	14	9	5
61	B.subtilis	T.maritima	A.aeolicus	Halobacterium sp.	44	32	27	27	19	11	83	62	53
62	B.subtilis	T.maritima	A.aeolicus	A.fulgidus	64	50	40	50	35	30	41	27	23
63	A. tumifaciens	S. meliloti	M. loti	C. crescentus	964	918	870	74	52	41	144	105	81
64	Synechocystis sp.	C.trachomatis	B.subtilis	T.pallidum	47	31	24	108	96	86	36	25	18
65	Synechocystis sp.	C.pneumoniae	B.subtilis	T.pallidum	45	29	26	108	93	76	35	24	19
66	Synechocystis sp.	C.muridarum	B.subtilis	T.pallidum	42	22	26	107	93	74	38	32	17
67	Synechocystis sp.	C.trachomatis	B.subtilis	M.loti	64	48	32	116	104	84	72	51	44
68	Synechocystis sp.	C.trachomatis	B.subtilis	M.tuberculosis	77	55	45	94	80	62	68	52	38