Table 2 Comparison of the estimates of selective pattern among codons in PAML

From: Evolutionary conservation and functional divergence of the LFK gene family play important roles in the photoperiodic flowering pathway of land plants

Gene

Numbera

Seqb

ω

2ΔlnLc

Positive selection sitesd

LFK family

151

2577

0.058

0

None

ZTL subfamily

79

2352

0.055

0

None

FKF1 subfamily

60

2376

0.07

8.34*

I 90 (0.544)

LKP2 subfamily

12

1935

0.095

7.34*

S1 (0.833), S8 (0.716), F57 (0.729),

     

A64 (0.678), E79 (0.506), Y106 (0.878),

     

R115 (0.529), Y371 (0.959)

ZmFKF1a m

87

1827

0.033

16.24***

P33 (0.701), I189 (0.645), V504 (0.990)

ZmFKF1b m

87

1863

0.316

1191.4***

T40 (1.000), D58 (1.000), Q122 (1.000),

     

I184 (1.000), M207 (1.000), D616 (1.000), R617 (1.000), Y618 (1.000)

ZmFKF1b t

33

1878

0.400

77.58***

V30 (0.982), H122 (0.985), I184 (0.843),

     

L601 (0.899), D615 (0.655), T616 (1.000)

ZmFKF1b m and t

120

1878

0.328

290.68***

T49 (1.000), H122 (1.000), S184 (1.000),

     

I207 (0.848), A615 (1.000), T616 (1.000)

  1. m maize, t teosinte, ω d N /d S values of the class of codons in M0
  2. aThe CDS number performed for each analysis
  3. bCodon site number based on the multiple sequence alignment of each dataset
  4. cTwice the difference in the natural logs of the likelihoods (2ΔlnL) of the two models (M7–M8) being compared *P < 0.05, ***P < 0.001, under the χ2 test
  5. dCodons assigned to the class evolving under positive selection in M8 with a posterior probability in following parentheses; codons underlined have the posterior probability of > 0.90 by Bayes Empirical Bayes estimates
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