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Table 4 Log-likelihood values and parameter estimates under random-site models for two groups DAB1 and DAB3 in gynogenetic triploids and sexually reproducing diploids of Carassius gibelio

From: MHC genes and parasitism in Carassius gibelio, a diploid-triploid fish species with dual reproduction strategies

Fish - DAB-like gene

Model code

Log-likelihood

Estimates of parameters

Number of PSS

Triploids - DAB1-like

M0: one ratio (1)

−1707.7

ω = 2.17

 
 

M3: discrete (5)

−1570.8

p0 = 0.48, p1 = 0.43, (p2 = 0.09),

not analyzed

   

ω0 = 0.31, ω1 = 4.80, ω2 = 35.44

 
 

M1a: nearly neutral (1)

−1660.59

p0 = 0.48, (p1 = 0.52), (ω0 = 0.07), (ω1 = 1)

not allowed

 

M2a: positive selection (3)

−1587.79

p0 = 0.30, p1 = 0.57, (p2 = 0.13)

8*, 3**

   

ω0 = 0, (ω1 = 1), ω2 = 10.50

 
 

M7: beta (2)

−1662.59

p = 0.13, q = 0.1

not allowed

 

M8: beta and ω (4)

−1558.13

p0 = 0.87, (p1 = 0.13)

11*, 8**

   

p = 0.03, q = 0.02, ω = 10.22

 

Triploids - DAB3-like

M0: one ratio (1)

−1088.36

ω = 2.99

 
 

M3: discrete (5)

−992.13

p0 = 0.67, p1 = 0.26, (p2 = 0.07),

not analyzed

   

ω0 = 0.45, ω1 = 12.72, ω2 = 66.25

 
 

M1a: nearly neutral (1)

−1056.48

p0 = 0.59, (p1 = 0.41), (ω0 = 0.02), (ω1 = 1)

not allowed

 

M2a: positive selection (3)

−1002.56

p0 = 0.30, p1 = 0.44, (p2 = 0.26)

21*, 16**

   

ω0 = 0, (ω1 = 1), ω2 = 17.36

 
 

M7: beta (2)

−1056.89

p = 0.01, q = 0.02

not allowed

 

M8: beta and ω (4)

−1002.69

p0 = 0.74, (p1 = 0.26)

22*, 21**

   

p = 0.01, q = 0.005, ω = 19.60

 

Diploids - DAB1-like

M0: one ratio (1)

−995.79

ω = 2.30

 
 

M3: discrete (5)

−968.41

p0 = 0.14, p1 = 0.57, (p2 = 0.29),

not analyzed

   

ω0 = 0, ω1 = 1, ω2 = 8.71

 
 

M1a: nearly neutral (1)

−989.53

p0 = 0.39, (p1 = 0.61), (ω0 = 0.03), (ω1 = 1)

not allowed

 

M2a: positive selection (3)

−968.41

p0 = 0.14, p1 = 0.57, (p2 = 0.29)

13*, 8**

   

ω0 = 0, (ω = 1), ω2 = 8.71

 
 

M7: beta (2)

−989.58

p = 0.03, q = 0.02

not allowed

 

M8: beta and ω (4)

−968.41

p0 = 0.71, (p1 = 0.29)

15*, 11**

   

p = 0.02, q = 0.01, ω = 8.66

 

Diploids - DAB3-like

M0: one ratio (1)

−1343.98

ω = 2.96

 
 

M3: discrete (5)

−1193.40

p0 = 0.65, p1 = 0.27, (p2 = 0.08),

not analyzed

   

ω0 = 0.31, ω1 = 8.47, ω2 = 56.35

 
 

M1a: nearly neutral (1)

−1285.98

p0 = 0.60, (p1 = 0.39), (ω0 = 0.03), (ω1 = 1)

not allowed

 

M2a: positive selection (3)

−1207.25

p0 = 0.43, p1 = 0.41, (p2 = 0.16)

13*, 11**

   

ω0 = 0, (ω = 1), ω2 = 13.52

 
 

M7: beta (2)

−1286.2

p = 0.02, q = 0.02

not allowed

 

M8: beta and ω (4)

−1207.26

p0 = 0.84, (p1 = 0.16)

14*, 11**

   

p = 0.005, q = 0.005, ω = 13.64

 
  1. The number following the model code given in parentheses represents the number of free parameters for the ω ratios. Parameters indicating positive selection are presented in bold type. Parameters in parentheses are presented for clarity only but are not free parameters; for example, under M8 p1 = 1-p0; PSS are the positive selected sites identified using the BEB method at *: P > 95%; **: P > 99%; ω is the selection parameter; pn is the proportion of sites that fall into the ωn site classes; p and q are the shape parameters of the β function (for M7 and M8 models).
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BMC Ecology and Evolution

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