Table 1.

Summary of results for EVAC1 branch analysis and branchsite analysis for mammalian clades

EVAC1	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
Primates	−1.12	−36.43(< 0.01)	−9.03(0.04)	0.48	0.44	0.53	0.01	0.01	222 I, 235 I	conserved	positive
Rodentia	−20.69(< 0.01)	− 152.48(< 0.01)	0.00	0.35	0.44	0.53	0.01	0.01	–	conserved	no
Carnivora	−2.87	−41.55(< 0.01)	−5.97	0.48	0.45	0.55	0.00	0.01	–	conserved	no
Cetartiodactyla	−20.90(< 0.01)	−98.98(< 0.01)	0.01	0.29	0.45	0.55	0.00	0.00	–	conserved	no

Significant LRTs indicated in bold with FDR-corrected p-value in superscript, ω = clade omega as calculated 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