Table 2

Parameter estimates and likelihood scores for branch-site models for paralogs

Genes

Model

l (1)

Estimates of parameters (2)

l (3)

Positively selected sites (BEB)


Cow LOC783399

Null

-5660.941163

ρ0 = 0.32, (ρ1 = 0.68), ω0 = 0.24, (ω1 = 1)

27.10 ***

Not allowed



Alternative

-5647.392083

ρ0 = 0.30, ρ1 = 0.66, (ρ2 = 0.05), ω0 = 0.23, (ω1 = 1), ω2 = ∞

1 site p > 99%: 36Y


Guinea pig ENSCPOG00000023399

Null

-5660.050892

ρ0 = 0.25, (ρ1 = 0.50), ω0 = 0.24, (ω1 = 1)

56.40 ***

Not allowed



Alternative

-5631.851037

ρ0 = 0.27, ρ1 = 0.55, (ρ2 = 0.18), ω0 = 0.23, (ω1 = 1), ω2 = 336.70

7 sites p > 99%: 24R, 27A, 113L, 118Q, 123T, 125T, 128T, 8 sites p > 95%: 31L, 25E, 26T, 85V, 114T, 117T, 122V, 126L


Horse LOC100053653

Null

-5665.171131

ρ0 = 0.22, (ρ1 = 0.47), ω0 = 0.23, (ω1 = 1)

15.86 ***

Not allowed



Alternative

-5657.239232

ρ0 = 0.09, ρ1 = 0.19, (ρ2 = 0.72), ω0 = 0.23, (ω1 = 1), ω2 = 6.44

6 sites p > 95%: 81E, 97A, 123Q, 135K, 166K, 168F


Mouse Mup19

Null

-5660.941163

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

53.87 ***

Not allowed



Alternative

-5634.004112

ρ0 = 0.30, ρ1 = 0.66, (ρ2 = 0.04), ω0 = 0.23, (ω1 = 1), ω2 = ∞

2 sites p > 99%: 174K, 177F


Rat LOC298116

Null

-5660.941163

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

8.69 ***

Not allowed



Alternative

-5656.597218

ρ0 = 0.32, ρ1 = 0.66, (ρ2 = 0.02), ω0 = 0.24, (ω1 = 1), ω2 = ∞

1 site p > 99%: 135A


(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 < 0.001.

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

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