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Table 2 Site-by-site signals of positive and negative selection acting on movement protein (mp), coat protein (cp) and replication associated protein (rep) gene codons during the SSRV evolution experiment

From: Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts

Gene Codon Methoda Selectionb Motif/domain (site underlined where relevant)
mp 21 R +  
  63 R + C-terminal boundary of hydrophobic domain
cp 3 R - DNA Binding domain
  67 R - DNA Binding domain
  69 R - DNA Binding domain
  85 FR - DNA Binding domain
  105 FR - DNA Binding domain
  122 FR -  
  136 R -  
  157 FRS -  
  180 R -  
  201 R -  
  217 R -  
  219 R -  
rep b 7 FR -  
  28 FR - RCR motif I (FLTYPHC)
  30 FR +  
  133 FR -  
  147 FR -  
  155 FR -  
  158 FR -  
  185 FRS - Rep-Rep oligomerisation domain (ASKLFPD TVEEY)
  321 FR -  
  326 FR -  
  356 FRS -  
  1. aF = Fixed effects likelihood method; R = Relative effects likelihood method; S = Single likelihood ancestor counting method.
  2. b+ = evidence of positive selection (p-value < 0.1); - = evidence of negative selection (p-value < 0.1).
  3. cExcludes codons 217–282 that are expressed in different frames in rep and repA.