TABLE 2.

Maximum log-likelihood comparison of different evolutionary models

		Bacillaceae			Clostridium			Escherichia			Pseudomonas
		B1	B2	B3	C1	C2	C3	E1	E2	E3	P1	P2	P3
Model	Parameter	(5,453)c	(5,614)	(6,813)	(3,546)	(6,526)	(7,645)	(4,681)	(5,063)	(5,307)	(6,505)	(8,761)	(9,140)
M0	μ	2.705	0.515	0.404	8.315	1.041	0.478	20.143	12.774	2.683	1.847	1.162	0.947
	β	0.577	1.281	1.700	0.326	2.430	1.851	0.372	0.285	0.439	0.587	1.117	1.466
	γ	1.311	2.096	2.725	0.590	3.498	3.050	0.686	0.495	0.817	0.831	1.703	2.209
	ln L	−16,551	−18,432	−24,799	−7,424	−22,783	−27,618	−13,019	−12,016	−15,071	−17,175	−29,926	−32,327
M0 + π	μ	2.102	0.214	0.197	8.385	0.482	0.149	19.805	11.699	1.837	1.332	0.695	0.619
	β	0.440	0.845	1.314	0.315	1.578	1.191	0.335	0.259	0.353	0.535	0.892	1.364
	γ	1.900	3.862	4.489	0.728	4.397	4.742	0.860	0.704	1.109	1.210	2.638	3.254
	πa	0.487	0.788	0.797	0.255	0.774	0.883	0.274	0.377	0.511	0.574	0.691	0.662
	πf	0.041	0.036	0.035	0.029	0.036	0.037	0.074	0.040	0.044	0.041	0.047	0.055
	ln L	−16,243	−17,799	−24,069	−7,385	−22,112	−26,491	−12,924	−11,876	−14,822	−16,787	−29,169	−31,715
	Δ AICa	−612	−1,262	−1,456	−74	−1,338	−2,250	−186	−276	−494	−772	−1,510	−1,220
M0 + Γ + π	μ	3.811	0.264	0.285	8.446	1.623	0.193	22.112	14.150	8.257	4.123	0.948	0.809
	αΓb	0.330	0.736	0.811	1.839	0.334	1.263	0.850	0.487	0.150	0.139	0.575	0.751
	ln L	−15,861	−17,553	−23,738	−7,370	−21,312	−26,253	−12,830	−11,728	−13,951	−16,334	−28,674	−31,325
	Δ AICa	−762	−490	−660	−28	−1598	−474	−190	−294	−1740	−904	−988	−778

^aAkaike's information criteria (Δ AICs) are shown as (M₀ + π) vs. M₀ and (M₀ + Γ + π) vs. (M₀ + π). By definition, AIC = 2(−ln L + K), where K is the number of parameters that are estimated from the data; thereafter, Δ AIC = 2(−Δ ln L + ΔK). The model that best approximates the data is the one with smallest AIC.

^bThis is the shape parameter in a Γ-distribution, which is traditionally described as α. The use of α_Γ is to distinguish it from the symbol α used in the instantaneous rate matrix.

^cThe number of gene families for each clade is shown in parentheses underneath the clade name.