Skip to main content

Table 1 Summary of results for EVAC1 branch analysis and branchsite analysis for mammalian clades

From: Evolutionary analysis of genes coding for Cysteine-RIch Secretory Proteins (CRISPs) in mammals

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

  1. 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