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Table 2 Results obtained from tests of selection on the mitochondrial genome of the Atlantic salmon

From: Patterns of natural selection acting on the mitochondrial genome of a locally adapted fish species

Locus

Position

Type of selection

MEME

FUBAR

TreeSAAP (Category)

   

ω+

P

dN-dS

Post. P

 

ND1

3878:C/T

-

  

−9.924

0.997

 
 

3926:C/T

-

  

−5.068

0.920

 
 

3989:A/G

-

  

−8.576

0.995

 
 

4424:C/T

-

  

−4.683

0.913

 
 

4517:G/A

-

  

−4.613

0.993

 
 

4568:C/T

-

  

−4.683

0.918

 
 

4578:G/A

+

>100

0.175

3.793

0.918

Alpha-helical tendencies (6)

 

4718:C/T

-

  

−5.153

0.902

 

ND2

5161:A/G

-

  

−5.017

0.923

 
 

5290:A/G

-

  

−4.086

0.914

 
 

5341:T/C

+

>100

0.564

−0.328

0.569

Alpha-helical tendencies (6)

 

5365:C/T

-

  

−7.495

0.991

 
 

5416:A/G

-

  

−6.931

0.987

 
 

5768:G/A

+

>100

0.216

0.855

0.805

Alpha-helical tendencies (6)

 

5812:C/A

-

  

−3.339

0.902

 

COX1

6970:C/T

-

  

−6.446

0.987

 
 

7021:A/G

-

  

−4.431

0.906

 
 

7039:A/G

-

  

−4.428

0.905

 
 

7483:G/A

-

  

−7.016

0.997

 
 

7684:T/C

-

  

−6.419

0.983

 

COX2

8492:T/C

-

  

−4.749

0.888

 

ATP6

9281:A/G

-

  

−3.654

0.902

 
 

9314:T/C

-

  

−2.981

0.891

 
 

9356:C/T

-

  

−2.984

0.893

 
 

9551:A/G

-

  

−1.253

0.928

 

ND3

10963:C/A

+

>100

0.423

2.706

0.901

Equil const ion COOH (8)

 

10879:T/C

-

  

−6.959

0.996

 

ND4

11489:A/G

-

  

−3.031

0.979

 
 

11693:C/T

-

  

−9.421

0.989

 
 

11762:T/C

-

  

−8.488

0.994

 
 

11891:G/A

-

  

−1.439

0.915

 
 

11906:C/T

-

  

−4.551

0.912

 
 

11937:A/G

+

>100

0.006

7.564

0.972

Power to be at C-terminal (6)

 

12167:A/G

-

  

−6.616

0.982

 

ND5

14405:T/C

-

  

−4.071

0.900

 
 

14570:C/T

-

  

−4.718

0.923

 

CYTB

16178:A/G

-

  

−9.805

0.996

 
 

16361:G/A

-

  

−2.654

0.950

 
  1. Type of selection: positive (+) or negative (−). Sites in bold correspond to those identified by the three different methods as being under selection, those in italics are sites identified by two different methods. Thresholds for each method: MEME P < 0.1, FUBAR p > 0.9 & amino acid change categories 6–8