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Table 1.

Lineage-Specific Gene Family Expansions Detected by Analysis of Completely Sequenced Genomes

Domain	Division	Species	Genes	Lineage-specific clusters	Genes in lineage-specific clusters	Percent genome in lineage-specific clusters	Average score density	No. of clusters with no significant BeTs in other genomes	Percent of clusters with no significant BeTs in other genomes
Archaea	Euryarchaeota	A. fulgidus	2407	197	553	23.0	0.75	35	17.8
		M. thermoautotrophicum	1869	97	265	14.2	0.76	19	19.6
		M. jannaschii	1715	96	238	13.9	0.71	12	12.5
		P. horikoshii	2064	129	310	15.0	0.60	8	6.2
	Crenarchaeota	A. pernix	2694	64	138	5.1	0.64	14	21.9
Bacteria	Aquificales	A. aeolicus	1522	80	184	12.1	0.71	9	11.3
	Thermotogales	T. maritima	1846	93	261	14.1	0.72	12	12.9
	Deinococcus group	D. radiodurans	3103	201	525	16.9	0.66	38	18.9
	Spirochaetales	B. burgdorferi	1255	61	220	17.5	0.86	39	63.9
		T. pallidum	1031	24	74	7.2	0.52	9	37.5
	Chlamydia group	C. pneumoniae	1052	35	129	12.3	0.63	14	40.0
	Cyanobacteria	Synechocystis sp.	3169	238	785	24.8	0.72	59	24.8
	Firmicutes	B. subtilis	4100	437	1202	29.3	0.76	83	19.0
		M. pneumoniae	677	46	191	28.2	0.69	7	15.2
		U. urealyticum	611	25	83	13.6	0.70	9	36.0
		M. tuberculosis	3918	350	1309	33.4	0.70	128	36.6
	Proteobacteria	E. coli	4289	383	1031	24.0	0.81	59	15.4
		H. influenzae	1709	44	96	5.6	1.12	2	4.6
		C. jejuni	1634	50	119	7.3	0.68	11	22.0
		H. pylori	1553	65	203	13.1	0.85	22	33.9
		R. prowazekii	834	15	40	4.8	0.65	3	20.0