TABLE 3.

Maximum log-likelihood comparison of different evolutionary models considering only gene presence/absence (p/a)

			Bacillaceae			Clostridium			Escherichia			Pseudomonas
Scenario	Model	Parameter	B1	B2	B3	C1	C2	C3	E1	E2	E3	P1	P2	P3
f → a	M00a	μ	1.886	0.463	0.388	5.459	1.061	0.441	12.125	8.250	1.723	1.450	1.038	0.870
		ln L	−13,682	−15,268	−21,207	−6,491	−19,623	−23,554	−10,428	−10,080	−12,546	−14,607	−24,708	−26,670
	M0a	μ	2.474	0.483	0.381	7.611	1.041	0.444	17.150	11.306	2.495	1.736	1.084	0.884
		ln L	−13,970	−15,487	−20,743	−6,444	−19,359	−22,168	−10,457	−10,195	−12,766	−14,961	−25,029	−26,803
	M0 + π	μ	1.842	0.185	0.173	7.514	0.440	0.093	16.075	9.785	1.570	1.138	0.577	0.542
		πa	0.510	0.816	0.831	0.286	0.807	0.933	0.345	0.407	0.534	0.616	0.745	0.725
		ln L	−13,681	−14,866	−20,017	−6,404	−18,705	−21,012	−10,362	−10,062	−12,543	−14,572	−24,253	−26,154
		Δ ln Lb	289	621	726	40	654	1156	95	133	223	389	776	649
f → p	M00	μ	1.490	0.393	0.356	4.593	0.912	0.416	8.072	6.969	1.405	1.289	0.894	0.741
		ln L	−12,470	−14,472	−20,761	−5,902	−19,171	−23,250	−8,578	−9,293	−11,857	−13,785	−23,565	−25,408
	M0	μ	2.045	0.419	0.337	6.747	0.873	0.377	12.813	10.198	2.116	1.605	0.956	0.762
		ln Lb	−12,579	−14,613	−20,443	−5,794	−18,990	−22,318	−8,425	−9,296	−11,944	−13,989	−23,749	−25,478
	M0 + π	μ	1.681	0.209	0.191	6.686	0.471	0.156	12.765	9.263	1.555	1.207	0.639	0.567
		πa	0.442	0.745	0.774	0.242	0.753	0.857	0.238	0.341	0.460	0.534	0.657	0.639
		ln L	−12,460	−14,274	−20,070	−5,784	−18,635	−21,804	−8,425	−9,249	−11,853	−13,782	−23,402	−25,243
		Δ ln Lb	119	339	373	10	355	514	0	47	91	207	347	235

In the two extreme scenarios, all truncated genes were entirely classified as absent (f → a) or present (f → p).

^aAs described in methods, model M₀₀ is the special case of M₀ + π when π_a = π_p = 0.5, while M₀ is the special case of M₀ + π when π_a and π_p are the frequencies of each character in the data.

^bΔ ln L's are shown as (M₀ + π) vs. M₀. Since 2Δ ln L ≈ χ², Δ ln L's > 1.97 (d.f. = 1) are considered significant.