Ancestral character estimation (ACE) analysis.

Results from ACE analysis in subtrees of Archaea and Bacteria comparing the evolution of Pfam and Enzyme Commission (EC) number counts to the evolution of the CBB-positive trait (see Materials and methods). The columns contain rank based on sum of absolute ’r’ weighted by ’q_Correlation’ and ’q_Wilcox’ across subtrees (’Rank’), feature type (’Feature_Type’; DeepEC or Pfam), feature ID (’Feature’), feature name (’Name’), organism domain (’Domain’; Archaea or Bacteria), subtree number (’Subtree’; Archaea has only one subtree numbered ’0’), ancestral feature count versus ancestral CBB-positive likelihood Spearman correlation r (’r’), significance (’Significant’; 1 if both q-values < 0.001, otherwise 0), p-value for the Spearman correlation (’p_Correlation’), Benjamini-Hochberg adjusted correlation p-value (’q_Correlation’), p-value for Wilcoxon rank sum test comparing feature count in CBB-positive, i.e. likelihood > 0.5, and CBB-negative ancestral nodes (’p_Wilcox’), Benjamini-Hochberg adjusted Wilcoxon rank sum test p-value (’q_Wilcox’), feature description (’Description’; the DESC line from the Pfam HMM database, or the full list of enzyme names from KEGG for DeepEC), and the KEGG EC of the entry (’KEGG_EC’). Note that some DeepEC ECs were transferred to one or more new ECs in KEGG, as indicated by a discrepancy between ’Feature’ (if ’Feature_Type’ is DeepEC) and ’KEGG_EC’. A single feature can therefore be listed more than once. (XLSX)