Uncovering rate variation of lateral gene transfer during bacterial genome evolution

BMC Genomics

Table 3 Insertion/deletion rates among different phylogenetic groups estimated in rate variation model. Estimation was based on the common-genes trees.

Group	Taxa	Genome Size	Branch Length	Rate Variation			Constant Rate		ΔLnL
				α value	MLE	LnL	MLE	LnL
Bacillus	13	4.9	0.147413	0.39	3.89	-40017	0.44	-40278	261*
Brucella	4	2.1	0.000275	0.035	382.06	-1264	44.50	-1387	123*
Burkholderia	7	3.8	0.044985	0.18	181.93	-17467	2.14	-18391	924*
Candidatus	4	1.3	0.433912	∞	0.49	-4722	0.49	-4722	0
Chlamydophila	7	1.2	0.096709	0.39	0.30	-1439	0.19	-1466	27*
Clostridium	5	3.3	0.151053	0.52	8.49	-9529	7.23	-9756	227*
Corynebacterium	5	3.0	0.223104	1.19	2.48	-8492	0.49	-8509	17*
Ehrlichia	5	1.5	0.063546	∞	0.24	-831	0.24	-831	0
Escherichia	7	5.0	0.006966	0.31	13.43	-10654	4.82	-11006	352*
Helicobacter	5	1.7	0.189516	0.52	1.75	-3961	1.05	-4109	148*
Lactobacillus	6	2.2	0.331530	∞	0.33	-9241	0.33	-9241	0
Mycobacterium	6	4.2	0.087643	0.23	191.03	-14660	1.63	-14718	25*
Mycoplasma	12	0.9	0.244815	∞	0.22	-8214	0.22	-8214	0
Prochlorococcus	5	1.9	0.319829	2.56	0.19	-4413	0.17	-4419	6*
Pseudomonas	8	6.3	0.083078	1.91	1.06	-26994	0.91	-27130	136*
Rhodopseudomonas	4	5.3	0.109002	0.52	1.75	-9352	0.77	-9459	107*
Rickettsia	5	1.3	0.054524	0.35	3.49	-3181	1.36	-3310	129*
Salmonella	5	4.8	0.003016	0.080	96.48	-5214	7.97	-5351	137*
Shigella	6	4.6	0.004433	0.17	131.93	-9784	11.39	-10327	543*
Staphylococcus	13	2.8	0.047252	0.085	279.41	-11390	14.76	-14581	3191*
Streptococcus	19	2.0	0.053313	0.29	18.71	-24327	13.19	-26553	2226*
Synechococcus	5	2.6	0.310236	∞	0.33	-7531	0.33	-7531	0
Vibrio	5	3.2	0.196671	0.17	10.02	-8642	0.37	-8939	260*
Xanthomonas	6	5.1	0.026682	0.59	6.33	-9385	2.73	-9541	156*
Yersinia	6	4.6	0.000355	0.060	221.14	-3172	31.15	-3467	295*

ISSN: 1471-2164