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Table 1 Parameter estimates for the GPR50, mel1 a, b, c under Model A and the effects of codon usage bias on LRTs (n = 29)

From: GPR50 is the mammalian ortholog of Mel1c: Evidence of rapid evolution in mammals

Model

p

l

Parameters estimates

Positively selected sites

M0: one-ratio

103

-15666. 37

ω = 0.0655

 

M1a (neutral)

104

-15620.766436

p0 = 0.967, p1 = 0.032

 

Branch-site model:

    

GPR50:

Model A

106

-15608.39

p0 = 0.714, p1 = 0.026

(p2 + p3) = 0.258

ω2 = 1

 

mel1a:

Model A

106

-15613.74

p0 = 0.883, p1 = 0.031

(p2 + p3) = 0.085

ω2 = 999

Site for foreground lineage:

183V

mel1b:

Model A

106

-15611.52

p0 = 0.833, p1 = 0.031

(p2 + p3) = 0.135

ω2 = 999

98K102Q 147I 227D

mel1c:

Model A

106

-15617.63

p0 = 0.955, p1 = 0.032

(p2 + p3) = 0.011

ω2 = 555.04

278A

  1. Note: p is the number of free parameters for the ω ratios. Parameters indicating positive selection are written in bold. Tests comparing sites-specific model M1a and branch-site model A are significant at 1%, df = 2. Sites potentially under positive selection were identified using GPR50 from O. aries according to the Bayes empirical Bayes analyses for Model A (at P > 0.95). These sites are shown in Fig. 3.