Table 3.

Summary of results for Evac3a branch analysis, site and branchsite analysis for mammalian clades

Evac3a	LRTs for Branch Analysis		LRTs for BS analysis		Prop. of sites in ω classes (BS):					Interpretation
Foreground branches	2Δ(M0-MC)	2Δ(MCfixed-MC)	2Δ(BSfixed-BS)	ω	0	1	2a	2b	PSS (BEB p < 0.05)	Selection over whole sequence	Selection on sites
Cricetulus griseus	−1.83	−0.38	−0.09	0.53	0.44	0.53	0.01	0.01	–	relaxed	no
Marmota marmota	−7.18(0.04)	−7.18	−8.07(0.03)	0.00	0.45	0.52	0.02	0.02	35 E, 161 Y	relaxed	positive
Mesocricetus auratus	−0.44	−4.51	0.00	0.53	0.46	0.54	0.00	0.00	–	conserved	no
Microtus ochrogaster	−7.05(0.04)	0.00	−7.29(0.03)	1.00	0.43	0.45	0.06	0.06	49 S, 225 K	relaxed	positive
Mus musculus	−0.12	−2.02	−1.67	0.53	0.45	0.54	0.00	0.01	–	relaxed	no
Nannospalax galili	−0.07	−3.69	−7.30(0.03)	0.53	0.43	0.53	0.02	0.02	(8 L)	relaxed	positive
Peromyscus maniculatus	0.00	−2.41	−5.03	0.53	0.45	0.54	0.01	0.01	187 S	relaxed	no
Rattus norvegicus	−0.05	−2.07	0.00	0.53	0.45	0.53	0.01	0.01	–	relaxed	no
	LRTs for Site Analysis				prop of sites in ω classes (M2a):
Over all branches	2Δ(M7-M8)	2Δ(M1a-M2a)			0	1	2		PSS (BEB p < 0.05, both LRTs)		Selection on sites
Rodentia	−7.54(0.01)	−5.45			0.50	0.25	0.25		64 G, 73 T		positive (trend)

Significant LRTs indicated in bold with p-value in superscript (FDR-corrected for branch analysis and BS analysis), ω = clade omega as caculated by branch analysis, if LRT of M0 versus MC significant MC ω is reported if LRT non significant M0 ω is reported. ω site classes: 0: 0 < ω < 1 for foreground and background branches, 1: ω = 1 for foreground and background branches, 2a: 0 < ω < 1 for background and ω > 1 for foreground, 2b: ω =1 for background and ω > 1 for foreground. Applied models are explained in material and methods (MC = Clade model, BS = Branch-site model). PSS Positively selected sites, BEB Bayes empirical Bayes