Table 4

Parameter estimates and likelihood scores for branch- site models for 5 species

Species

Model

l (1)

Estimates of parameters (2)

l (3)

Positively selected sites (BEB)


Marmoset

Null

-5660.37202

ρ0 = 0.18, (ρ1 = 0.39), ω0 = 0.23, (ω1 = 1)

18.47 ***

Not allowed



Alternative

-5651.1375

ρ0 = 0.30, ρ1 = 0.63, (ρ2 = 0.07), ω0 = 0.23, (ω1 = 1), ω2 = 60.38

2 sites p > 95%: 159R, 161F


Dog

Null

-5660.55998

ρ0 = 0.25, (ρ1 = 0.52), ω0 = 0.24, (ω1 = 1)

6.78 **

Not allowed



Alternative

-5657.16845

ρ0 = 0.28, ρ1 = 0.58, (ρ2 = s0.14), ω0 = 0.23, (ω1 = 1), ω2 = 11.15

2 sites p > 95%: 14H, 144Y


Guinea pig

Null

-5660.94116

ρ0 = 0.32, (ρ1 = 0.67), ω0 = 0.24, (ω1 = 1)

13.68 ***

Not allowed



Alternative

-5654.10045

ρ0 = 0.27, ρ1 = 0.51, (ρ2 = 0.22), ω0 = 0.25, (ω1 = 1), ω2 = 3.94

3 sites p > 95%: 11S,

    75C
, 104V


Horse

Null

-5660.94121

ρ0 = 0.32, (ρ1 = 0.67), ω0 = 0.24, (ω1 = 1 )

27.22 ***

Not allowed



Alternative

-5647.32999

ρ0 = 0.30, ρ1 = 0.61, (ρ2 = 0.09), ω0 = 0.24, (ω1 = 1), ω2 = 7.57

2 sites p > 99%:

    75C
,
    119L
; 1 site p > 95%: 144Y


Mouse

Null

-5658.60187

ρ0 = 0.24, (ρ1 = 0.55), ω0 = 0.19, (ω1 = 1 )

10.75 **

Not allowed



Alternative

-5653.22783

ρ0 = 0.25, ρ1 = 0.58, (ρ2 = 0.17), ω0 = 0.19, (ω1 = 1), ω2 = 3.25

1 site p > 95%: 162Q


(1) Log- likelihood values.

(2) ρ0, ρ1, and ρ2 are the proportions of codons subject to purifying selection, neutral evolution, and positive selection, respectively. ω0, ω1 and ω2 represented dN/dS for each class (purifying, neutral and positive selection, respectively).

(3) ** significant at p < 0.01

*** significant at p < 0.001.

(4) Underlined: amino acids involved in androstenol and androstenone binding.

Site numbers and amino acids refer to the pig SAL1 reference sequence PDB: 1GM6, except for the amino acid in bold, which is not part of the structure but comes from the dog genome sequence XP_855342.1.

Meslin et al. BMC Evolutionary Biology 2011 11:148   doi:10.1186/1471-2148-11-148

Open Data