Table 3.

Results of clade model C (CmC) analyses on mammalian TRCs.

Gene	Partitiona	Model	np	lnL	Parametersb			LRT	df	p
					ω0	ω1	ω2/ωd
TRAC	n/a	M2a_rel	71	5419.92	0.05 (34.5%)	11 (35.6%)	0.39 (29.9%)
	Habitat	CmC	75	5378.62	0.12 (41.9%)	1 (39.3%)	3.41 (18.8%)	82.60	4	0
							Aquat 4.50
							Aeria 2.92
							SemAq 1.84
							Terre 2.79
	Diet	CmC	76	5378.42	0.12 (41.9%)	1 (39.6%)	2.79 (18.4%)	82.99	5	< 0.01
							Carni 3.19
							Frugi 2.34
							Herbv 3.77
							Insec 3.21
							Omniv 2.07
	Sociality	CmC	73	5376.82	0.12 (41.8%)	1 (39.3%)	1.83 (18.9%)	86.20	2	0
							Socia 2.87
							Solit 10.76
TRDC	n/a	M2a_rel	71	5622.82	0.36 (21.1%)	1 (53.1%)	0.04 (25.8%)
	Habitat	CmC	75	5554.56	0.09 (30.9%)	1 (48.3%)	0.32 (20.8%)	136.52	4	0
							Aquat 0.22
							Aeria 0.34
							SemAq 4.50
							Terre 4.48
	Diet	CmC	76	5585.73	0.09 (30.7%)	1 (47.6%)	0.43 (21.7%)	74.18	5	< 0.01
							Carni 2.09
							Frugi 8.14
							Herbv 2.23
							Insec 0.53
							Omniv 3.51
	Sociality	CmC	73	5595.05	0.08 (29.8%)	1 (44.1%)	4.67 (26.1%)	55.55	2	< 0.01
							Socia 2.21
							Solit 0.28

np, number of parameters; lnL, ln likelihood; df, degrees of freedom; n/a, not applicable; Aquat, Aquatic; SemAq, SemiAquatic; Terre, Terrestrial; Carni, Carnivore; Frugi, Frugivore; Herbv, Herbivore; Insec, Insectivore; Omniv, Omnivore; Socia, Sociality; Solit, Solitary.

^aPartitions listed are explained in Figure S1.

^bω values for each site class (ω₀–ω₂) are shown with the proportion of each in parentheses. ω_d refers to the divergent site class in the CmC models, which has a separate value for each partition: the first value is for the background, followed by the foreground partition(s).