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Table 1 Divergence between mouse and rat at sites of divergence between human and dog

From: Extensive parallelism in protein evolution

 

Synonymous

Nonsynonymous

 

Overall1

Parallel2

Overall3

Coincident

    

Parallel4

Divergent5

     

Same site

Different site

Pairs of nucleotides

      

   AC

0.028

0.047

0.0028 (10.1%)

0.024 (122, 51.4%)

0.013 (280, 27.0%)

0.010 (306, 21.1%)

   AG

0.089

0.109

0.0102 (11.5%)

0.069 (1570, 62.9%)

0.040 (448, 36.2%)

0.037 (923, 33.9%)

   AT

0.021

0.024

0.0017 (8.4%)

0.028 (80, 117.4%)

0.008 (118, 32.6%)

0.006 (148, 23.5%)

   CG

0.029

0.036

0.0033 (11.5%)

0.021 (156, 57.3%)

0.014 (302, 38.1%)

0.011 (332, 29.5%)

   CT

0.076

0.090

0.0060 (7.9%)

0.051 (492, 56.5%)

0.027 (239, 30.3%)

0.020 (685, 22.6%)

   GT

0.027

0.040

0.0019 (7.0%)

0.023 (69, 56.6%)

0.010 (175, 25.7%)

0.006 (168, 15.8%)

   Average

0.045

0.058

0.0043 (9.6%)

0.036 (2489, 62.1%)

0.019 (1562, 32.2%)

0.015 (2562, 26.0%)

Genes6

      

   Low d N

0.043

0.059

0.0019 (4.3%)

0.028 (315, 47.1%)

0.012 (145, 21.1%)

0.009 (195, 14.8%)

   Intermediate d N

0.046

0.058

0.0045 (9.9%)

0.036 (895, 61.7%)

0.017 (526, 29.6%)

0.013 (785, 21.8%)

   High d N

0.047

0.057

0.0086 (18.5%)

0.038 (1279, 67.6%)

0.021 (891, 37.6%)

0.019 (1582, 32.7%)

Chemical distance between amino acids7

      

   1

0.045

0.058

0.0043 (9.6%)

0.038 (516, 65.0%)

0.012 (344, 20.1%)

0.016 (662, 27.3%)

   1.5 or 2

0.045

0.058

0.0043 (9.6%)

0.033 (1537, 57.8%)

0.025 (834, 42.5%)

0.014 (1268, 24.7%)

   2.5 or 3

0.045

0.058

0.0043 (9.6%)

0.031 (436, 53.7%)

0.023 (384, 40.4%)

0.018 (632, 31.0%)

  1. 1Mouse-rat divergence at all 4-fold synonymous nucleotide sites.
  2. 2Mouse-rat divergence only at those 4-fold synonymous sites where human and dog also underwent divergence in the same unordered pair of nucleotides.
  3. 3Mouse-rat divergence at all nondegenerate nonsynonymous sites. The magnitude of this divergence relative to overall synonymous mouse-rat divergence is presented in parentheses.
  4. 4Mouse-rat divergence at nondegenerate nonsynonymous sites where human and dog also underwent divergence in the same unordered pair of nucleotides and of amino acids. The number of sites of such mouse-rat divergence and the magnitude of this divergence relative to parallel synonymous mouse-rat divergence are presented in parentheses.
  5. 5Mouse-rat divergence at nondegenerate nonsynonymous nucleotide sites which belong to amino acid sites where human and dog also underwent nonsynonymous divergence, either at the same or at a different nucleotide site, but in a different unordered pair of nucleotides and of amino acids. The number of sites of such mouse-rat divergence and the magnitude of this divergence relative to parallel synonymous mouse-rat divergence are presented in parentheses.
  6. 6Genes were subdivided into three bins of equal sizes, according to their rates of nonsynonymous evolution along the path between mouse and rat.
  7. 7Rank of the Miyata distance between the human and dog amino acids among the distances between all pairs of amino acids that can arise due to a substitution at the same nucleotide site.
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