Table 3.
Distribution of amino-acid (aa) changes on the 13 protein coding genes (PCGs) of Macoma balthica
| Lineage comparison level | PCG | Gene length (aa) | Number of aa change (% of total length) | Extramembraneous compartment | Intermembraneous compartment | Intramembraneous compartment | Nucleotide divergence 1 | πA/πS 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 | |
1global divergence: min - max range (mean ± standard-error) calculated using the TN93 model of nucleotide substitutions, as for Figure 1.
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.