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Table 3 Site models and tests of selection

From: The mate recognition protein gene mediates reproductive isolation and speciation in the Brachionus plicatiliscryptic species complex

Model

Parameter estimates

ĸ

lnL

p

M0

ω = 0.070

1.01

−1961.39

<<0.001

M3

p0 = 0.585 p1 = 0.383, p2 = 0.032

0.98

−1922.15

 
 

ω0 = 0.001, ω1 = 0.151, ω2 = 0.615

   

M1

p0 = 0.952, p1 = 0.048,

1.13

−1946.80

--

 

ω0 = 0.057 ω1 = 1.000

   

M2

p0 = 0.952, p1 = 0.048, p2 = 0.000,

1.13

−1946.80

 
 

ω0 = 0.057, ω1 = 1.000, ω2 = 42.1

   

M7

p = 0.260, q = 2.948

0.94

−1924.53

--

M8

p0 = 1.000, p = 0.260

0.94

−1924.53

 
 

q = 2.95, (p1 = 0.000), ω = 2.51

   
  1. Model refers to the Nsites value in codeml (e.g. M0 is nSites = 0); other parameter values for all tests were: codon frequency =3, model =0, omega = 0; ω is dN/dS and pn is the proportion of codons with ration ωn; κ is the transition:transversion ratio; LnL is the log likelihood, p is the result of χ2 test, which was not performed when the likelihoods were identical.