Table 5

Parameter estimates, log-likelihood values and predicted sites under selection for codon evolution models

Locus

Model code

P

Parameter estimates

Sites under positive selection

2Δℓ (p-value)


M0 (one ratio)

1

-481.93

ω = 0.353

None


14.34 (p = 0.006)

M3 (discrete)

5

-474.76

ω0 = 0.044, p0 = 0.589,

ω1 = 0.044, p1 = 0.315,

ω2 = 3.40 p2 = 0.096

Not analysed


DRA

M1a (nearly neutral)

1

-476.43

ω0 = 0, p0 = 0.787,

ω1 = 1, p1 = 0.213

Not allowed


3.34 (p = 0.188)

M2a (positive selection)

3

-474.76

ω0 = 0.044, p0 = 0.904,

ω1 = 1, p1 = 0

ω2 = 3.40 p2 = 0.096

14,19, 47, 49


M7 (beta)

2

-476.35

p = 0.005, q = 0.020

Not allowed


3.18 (p = 0.204)

M8 (beta and omega)

4

-474.76

p0 = 0.904, p1 = 0.096,

p = 4.61, q = 99.0, ω = 3.40

14,19, 47, 49


M0 (one ratio)

1

-1612.03

ω = 0.984

None


197.68 (p < 0.001)

M3 (discrete)

5

-1513.2

ω0 = 0.078, p0 = 0.556,

ω1 = 1.68, p1 = 0.364,

ω2 = 6.80, p2 = 0.080

Not analysed


DQA

M1a (nearly neutral)

1

-1545.23

ω0 = 0.043, p0 = 0.556,

ω1 = 1, p1 = 0.444

Not allowed


66.8 (p < 0.001)

M2a (positive selection)

3

-1516.86

ω0 = 0.047, p0 = 0.521,

ω1 = 1, p1 = 0.389,

ω2 = 4.91, p2 = 0.090

2*, 43*, 53*, 57*, 67*


M7 (beta)

2

-1548.22

p = 0.104, q = 0.119

Not allowed


29.65 (p < 0.001)

M8 (beta and omega)

4

-1518.57

p0 = 0.909, p1 = 0.091,

p = 0.02, q = 0.02, ω = 5.15

2*, 43*, 52, 53*, 57*, 64, 67*


P = number of free parameters in the ω distribution; ℓ = log-likelihood; Model parameter estimates include the nonsynonymous to synonymous rate ratio (ω) and proportion of sites (p) under each ω site class. Estimates for ω that are evidence for positive selection are bolded. Sites under selection were predicted using the Bayes Empirical Bayes (BEB) approach: sites inferred to be under positive selection with posterior probabilities >95% are in bold and sites with posterior probabilities of > 99% are indicated by an asterisk (*).

Kamath and Getz BMC Evolutionary Biology 2011 11:128   doi:10.1186/1471-2148-11-128

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