Table 2.

Summary of results for EVAC2 branch analysis and branchsite analysis for mammalian clades

EVAC2	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	−1.59	−63.97(< 0.01)	0.02	0.33	0.61	0.39	0.00	0.00	–	conserved	no
Rodentia	−0.15	−148.19(< 0.01)	0.00	0.33	0.58	0.35	0.05	0.03	–	conserved	no
Chiroptera	−13.57(< 0.01)	−5.47(0.05)	0.00	0.63	0.61	0.39	0.00	0.00	–	conserved	no
Cetartiodactyla	−4.82	− 113.47(< 0.01)	1.27	0.33	0.61	0.39	0.00	0.00	–	conserved	no

Significant LRTs indicated in bold with FDR-corrected p-value in superscript, 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