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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 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
  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.