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Table 3 Functional groups enrichment with clusters under different evolution modes

From: Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions

Functional group Total clusters in group All positively selected clusters on the Pyrococcus tree branches (as in Figure 2) † Unique positively selected clusters on the Pyrococcus tree branches (as in Figure 2) † Clusters not under positive selection †
   a b c d a b c d  
Translation; ribosomal structure and biogenesis 168 32 45 48 **** 37 13 16 26 **** 19 55****
Transcription 62 13 25 *** 13 15 3 10 5 5 20**
Replication; recombination and repair 51 10 10 4* 6 6 6 3 5 26
Cell cycle control; cell division; chromosome partitioning 13 4 1* 1 1 2 0 0 1 8
Defense mechanisms 12 2 3 2 3 0 1 0 1 7
Signal transduction mechanisms 10 0 3 1 1 0 3 1 1 5
Cell wall/membrane/envelope biogenesis 19 2 1** 1* 2 2 1 1 2 13 *
Cell motility 11 3 2 3 2 1 2 1 1 4
Intracellular trafficking; secretion; vesicular transport 11 2 3 1 5 * 1 1 0 3 3*
Posttranslational modification; protein turnover; chaperones 32 6 8 2* 6 2 4 1 4 16
Energy production and conversion 78 13 14 10 12 5 9 8 5 40
Carbohydrate transport and metabolism 49 4* 10 6 8 2 6 2 6 28
Amino acid transport and metabolism 61 13 18 2*** 10 7 9 2* 4 29
Nucleotide transport and metabolism 38 4 10 8 13 * 2 6 3 10 ** 10**
Coenzyme transport and metabolism 58 12 17 8 11 5 9 4 5 23
Lipid transport and metabolism 15 1 2 0 3 0 2 0 2 10
Inorganic ion transport and metabolism 46 9 4** 4 4* 8 * 3 4 4 26
Secondary metabolites biosynthesis; transport and catabolism 7 2 1 0 2 2 0 0 1 3
Function unknown 170 22* 31* 17* 27 14 15 7* 17 96 **
Total 911 154 208 131 168 75 103 68 96 422
  1. - Bold denotes cases with excess of clusters (*0.01 <p ≤ 0.05; **0.001 <p ≤ 0.01;; ***1 × 10-4 <p ≤ 0.001; ****p ≤ 1 × 10-4), italics denote cases with lack of clusters (*0.01 <p ≤ 0.05; **0.001 <p ≤ 0.01; ***1 × 10-4 <p ≤ 0.001; ****p ≤ 1 × 10-4).