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Table 3 Distribution of amino-acid (aa) changes on the 13 protein coding genes (PCGs) of Macoma balthica

From: Mitochondrial genomes of the Baltic clam Macoma balthica(Bivalvia: Tellinidae): setting the stage for studying mito-nuclear incompatibilities

Lineage comparison level

PCG

Gene length (aa)

Number of aa change (% of total length)

Extramembraneous compartment

Intermembraneous compartment

Intramembraneous compartment

Nucleotide divergence 1

Ï€A/Ï€S ratio

Length (aa)

Number of aa change

Length (aa)

Number of aa change

Length (aa)

Number of aa change

Among M. balthica (n = 6)

atp8

42

8 (19.1)

5

0

26

5

11

3

0 - 8.74 (3.35 ± 1.64)

0.03

 

nad6

177

51 (28.8)

37

10

109

32

31

9

0 - 13.76 (5.28 ± 2.25)

0.027

 

atp6

236

38 (16.1)

27

3

120

21

89

14

0 - 7.33 (2.98 ± 1.24)

0.031

 

cox3

270

54 (20)

87

23

141

24

42

7

0.12 - 9.21 (3.97 ± 1.58)

0.017

 

nad2

336

66 (19.6)

34

12

248

46

54

8

0.2 - 10.09 (3.96 ± 1.71)

0.065

 

cox1

556

83 (14.9)

108

14

286

43

162

26

0.06 - 6.71 (2.89 ± 1.13)

0.004

 

nad4

446

75 (16.8)

125

15

268

53

53

7

0 - 8.03 (3.21 ± 1.33)

0.039

 

nad3

120

18 (15)

8

2

72

9

40

7

0 - 7.26 (2.6 ± 1.15)

0.027

 

nad4l

96

18 (18.8)

34

7

56

10

6

1

0 - 8.38 (3.29 ± 1.43)

0.033

 

nad1

307

43 (14)

46

8

203

29

58

6

0 - 6.24 (2.52 ± 1.09)

0.035

 

nad5

597

78 (13.1)

114

16

361

52

122

10

0.06 - 7.32 (3.31 ± 1.2)

0.073

 

cob

412

45 (10.9)

72

8

182

20

158

17

0 - 4.83 (1.99 ± 0.81)

0.008

 

cox2

284

32 (11.3)

19

1

48

7

217

24

0 - 4.56 (1.86 ± 0.8)

0.043

Among M. balthica rubra (n = 5)

atp8

42

2 (4.8)

5

0

26

1

11

1

0 - 1.63 (0.65 ± 0.34)

0

 

nad6

177

17 (9.6)

37

2

109

12

31

3

0 - 2.9 (1.58 ± 0.5)

0.017

 

atp6

236

15 (6.4)

27

1

120

13

89

1

0 - 2.04 (0.95 ± 0.29)

0.02

 

cox3

270

24 (8.9)

87

7

141

13

42

4

0.12 - 3.07 (1.42 ± 0.53)

0.011

 

nad2

336

27 (8)

34

2

248

21

54

4

0.2 - 2.37 (1.14 ± 0.4)

0.084

 

cox1

556

38 (6.8)

108

4

286

25

162

9

0.06 - 1.97 (1.05 ± 0.3)

0

 

nad4

446

29 (6.5)

125

7

268

18

53

4

0 - 1.75 (1.02 ± 0.25)

0.064

 

nad3

120

6 (5)

8

0

72

5

40

1

0 - 1.7 (0.73 ± 0.29)

0.073

 

nad4l

96

6 (6.3)

34

3

56

3

6

0

0 - 1.4 (0.91 ± 0.2)

0

 

nad1

307

15 (4.9)

46

1

203

10

58

4

0 - 1.43 (0.72 ± 0.26)

0.057

 

nad5

597

50 (8.4)

114

11

361

30

122

9

0.06 - 2.64 (1.4 ± 0.45)

0.118

 

cob

412

17 (4.1)

72

4

182

10

158

3

0 - 1.39 (0.67 ± 0.22)

0

 

cox2

284

11 (3.9)

19

4

48

1

217

6

0 - 1.07 (0.54 ± 0.17)

0

  1. 1global divergence: min - max range (mean ± standard-error) calculated using the TN93 model of nucleotide substitutions, as for Figure 1.
  2. The number of aa changes (i.e. synonymous and non-synonymous mutations) is given for each gene overall and for the extra-, inter- and intra-membranous organellar compartments, as delimited in Protter (Additional file 6). The distribution of aa changes across different organellar compartments provides a preliminary roadmap for searching for MNIs. The positions of aa sites bearing synonymous and non-synonymous mutations are mapped on the inferred protein secondary structures presented in Additional file 6.
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BMC Ecology and Evolution

ISSN: 2730-7182

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