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Table 2 Positively selected sites in corresponding genes of Chlamydomonas sp. ICE-L, Dunaliella salina and Chlorella sp. ArM0029B

From: The Antarctic sea ice alga Chlamydomonas sp. ICE-L provides insights into adaptive patterns of chloroplast evolution

Gene

Branch-site model

-lnL

2δ(lnL)

Q Value

ω Values

Positively selected sites

atpA

Branch (Dunaliella salina)

   

Null

9513.725

  

ω0 = 0.026, ω1 = 1, ω2 = 1

 

Alternative

9503.900

19.650

4.28E-04

ω0 = 0.026, ω1 = 1, ω2 = 49.199

259–0.994, 269–0.951, 373–0.977, 382–0.996, 426–0.969, 429–0.978, 432–0.992, 434–0.998, 450–0.952, 455–0.978

atpB

Branch (Chlamydomonas sp. ICE-L)

   

Null

8590.140

  

ω0 = 0.023, ω1 = 1, ω2 = 1

 

Alternative

8567.141

45.998

5.43E-10

ω0 = 0.022, ω1 = 1, ω2 = 999

24–1.000, 107–0.978, 109–0.999, 375–0.998,

Branch (Dunaliella salina)

   

Null

8566.141

  

ω0 = 0.021, ω1 = 1, ω2 = 1

 

Alternative

8558.602

15.079

2.37E-03

ω0 = 0.021, ω1 = 1, ω2 = 57.824

112–0.975, 297–0.970, 305–0.970, 331–0.966, 371–0.977

atpE

Branch (Chlorella sp. ArM0029B)

   

Null

2572.548

  

ω0 = 0.030, ω1 = 1, ω2 = 1

 

Alternative

2568.079

8.936

4.29E-02

ω0 = 0.030, ω1 = 1, ω2 = 694.685

100–0.987

petA

Branch (Chlorella sp. ArM0029B)

   

Null

5724.705

  

ω0 = 0.042, ω1 = 1, ω2 = 1

 

Alternative

5720.106

9.198

4.29E-02

ω0 = 0.042, ω1 = 1, ω2 = 999

216–0.984, 243–0.986

psaB

Branch (Chlamydomonas sp. ICE-L)

   

Null

12,670.404

  

ω0 = 0.015, ω1 = 1, ω2 = 1

 

Alternative

12,665.032

10.746

1.60E-02

ω0 = 0.016, ω1 = 1, ω2 = 998.999

220–0.972, 356–0.985, 646–0.990

psbC

Branch (Dunaliella salina)

   

Null

7158.342

  

ω0 = 0.019, ω1 = 1, ω2 = 1

 

Alternative

7151.779

13.126

4.47E-03

ω0 = 0.019, ω1 = 1, ω2 = 999

207–0.958, 355–0.988, 360–0.980, 410–0.992

rbcL

Branch (Chlamydomonas sp. ICE-L)

   

Null

6852.947

  

ω0 = 0.016, ω1 = 1, ω2 = 1

 

Alternative

6843.536

18.822

3.31E-04

ω0 = 0.017, ω1 = 1, ω2 = 365.261

372–0.969, 450–0.999, 457–0.994

  1. The number for amino acid residues identified by Bayes empirical bayes (BEB) analyses corresponds to their alignment positions. Number behind hyphen is the posterior probability (PP) under BEB analysis